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Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024; 56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Many drug formulations containing small active molecules are used for the treatment of coronary artery disease, which affects a significant part of the world's population. However, the inadequate profile of these molecules in terms of therapeutic efficacy has led to the therapeutic use of protein and peptide-based biomolecules with superior properties, such as target-specific affinity and low immunogenicity, in critical diseases. Protein‒protein interactions, as a consequence of advances in molecular techniques with strategies involving the combined use of in silico methods, have enabled the design of therapeutic peptides to reach an advanced dimension. In particular, with the advantages provided by protein/peptide structural modeling, molecular docking for the study of their interactions, molecular dynamics simulations for their interactions under physiological conditions and machine learning techniques that can work in combination with all these, significant progress has been made in approaches to developing therapeutic peptides that can modulate the development and progression of coronary artery diseases. In this scope, this review discusses in silico methods for the development of peptide therapeutics for the treatment of coronary artery disease and strategies for identifying the molecular mechanisms that can be modulated by these designs and provides a comprehensive perspective for future studies.
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Affiliation(s)
- Ayca Aslan
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey
| | - Selcen Ari Yuka
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey.
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Zhang Y, Wang G, Zhang Q, Wang Q, Luo J, Ling C. The value of lung function assessment and Testin expression detection in clinicopathological features and prognosis of NSCLC patients. J Cardiothorac Surg 2024; 19:223. [PMID: 38627776 PMCID: PMC11020752 DOI: 10.1186/s13019-024-02720-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 03/29/2024] [Indexed: 04/19/2024] Open
Abstract
OBJECTIVE The aim of this study is to investigate the clinical value and potential prognostic significance of lung function assessment and Testin expression in non-small cell lung cancer (NSCLC) patients. METHODS The NSCLC patients were classified into three groups according to lung function: group of normal lung function, group of PRISm (preserved ratio impaired spirometry) (FEV1, forced expiratory volume during the first second < 80% predicted and FEV1/FVC (forced vital capacity) ≥ 70%) and group of COPD (chronic obstructive pulmonary disease) (FEV1/FVC < 70%). The pre-operational clinicopathological characteristics of these patients were recorded and the markers of systemic inflammatory response, including neutrophil to lymphocyte ratio (NLR), lymphocyte to monocyte ratio (LMR), platelet to lymphocyte ratio (PLR) and eosinophils (EOS), were compared between three groups. The expression of Testin in NSCLC samples was detected by IHC and we further explored the correlation between Testin expression and clinicopathological characteristics and prognosis of NSCLC patients. Finally, Cox regression analysis was conducted to study the prognostic factors of NSCLC patients. RESULTS Of the 158 NSCLC patients, percentages of normal lung function, PRISm and COPD were 41.4%, 22.8% and 36.1%, respectively. Patients with tumor in the left lung were more likely to have pulmonary dysfunction (PRISm and COPD) than the right lung. The markers of systemic inflammatory response showed differences to various degree in the three groups and NSCLC patients with PRISm or COPD presented more unfavorable prognosis than patients with normal function. The expression of Testin correlated with lymph node metastasis, TNM stage and tumor invasion of NSCLC patients. Moreover, patients with low Testin expression exhibited poorer disease-free survival and overall survival than those with high Testin expression. In Cox regression analysis, we found that PRISm, COPD and Testin expression served as prognostic factors in NSCLC patients. CONCLUSIONS The presence of COPD or PRISm influenced systemic inflammatory response and prognosis of NSCLC patients. Testin expression correlated with clinicopathological features and could be potentially used as a prognostic marker in NSCLC.
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Affiliation(s)
- Yanmin Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, P.R. China
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, P.R. China
| | - Gaoming Wang
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, 221006, Jiangsu, P.R. China
| | - Qian Zhang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, P.R. China
| | - Qian Wang
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, Jiangsu, P.R. China
| | - Jing Luo
- Department of Cardiothoracic Surgery, Jinling Hospital, Medical School of Nanjing University, 210000, Nanjing, Jiangsu, P.R. China.
| | - Chunhua Ling
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, P.R. China.
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Kugathas I, Johansson HKL, Chan Sock Peng E, Toupin M, Evrard B, Darde TA, Boberg J, Draskau MK, Rolland AD, Mazaud-Guittot S, Chalmel F, Svingen T. Transcriptional profiling of the developing rat ovary following intrauterine exposure to the endocrine disruptors diethylstilbestrol and ketoconazole. Arch Toxicol 2023; 97:849-863. [PMID: 36653537 PMCID: PMC9968686 DOI: 10.1007/s00204-023-03442-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023]
Abstract
Exposure to endocrine-disrupting chemicals (EDCs) during development may cause reproductive disorders in women. Although female reproductive endpoints are assessed in rodent toxicity studies, a concern is that typical endpoints are not sensitive enough to detect chemicals of concern to human health. If so, measured endpoints must be improved or new biomarkers of effects included. Herein, we have characterized the dynamic transcriptional landscape of developing rat ovaries exposed to two well-known EDCs, diethylstilbestrol (DES) and ketoconazole (KTZ), by 3' RNA sequencing. Rats were orally exposed from day 7 of gestation until birth, and from postnatal day 1 until days 6, 14 or 22. Three exposure doses for each chemical were used: 3, 6 and 12 µg/kg bw/day of DES; 3, 6, 12 mg/kg bw/day of KTZ. The transcriptome changed dynamically during perinatal development in control ovaries, with 1137 differentially expressed genes (DEGs) partitioned into 3 broad expression patterns. A cross-species deconvolution strategy based on a mouse ovary developmental cell atlas was used to map any changes to ovarian cellularity across the perinatal period to allow for characterization of actual changes to gene transcript levels. A total of 184 DEGs were observed across dose groups and developmental stages in DES-exposed ovaries, and 111 DEGs in KTZ-exposed ovaries across dose groups and developmental stages. Based on our analyses, we have identified new candidate biomarkers for female reproductive toxicity induced by EDC, including Kcne2, Calb2 and Insl3.
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Affiliation(s)
- Indusha Kugathas
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Hanna K. L. Johansson
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kongens Lyngby, Denmark
| | - Edith Chan Sock Peng
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Maryne Toupin
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Bertrand Evrard
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | | | - Julie Boberg
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kongens Lyngby, Denmark
| | - Monica K. Draskau
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kongens Lyngby, Denmark
| | - Antoine D. Rolland
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Séverine Mazaud-Guittot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000 Rennes, France
| | - Frédéric Chalmel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, 9 avenue du Professeur Léon Bernard, 35000, Rennes, France.
| | - Terje Svingen
- National Food Institute, Technical University of Denmark, Kemitorvet, Building 202, 2800, Kongens Lyngby, Denmark.
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Abbott GW. Kv Channel Ancillary Subunits: Where Do We Go from Here? Physiology (Bethesda) 2022; 37:0. [PMID: 35797055 PMCID: PMC9394777 DOI: 10.1152/physiol.00005.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/10/2023] Open
Abstract
Voltage-gated potassium (Kv) channels each comprise four pore-forming α-subunits that orchestrate essential duties such as voltage sensing and K+ selectivity and conductance. In vivo, however, Kv channels also incorporate regulatory subunits-some Kv channel specific, others more general modifiers of protein folding, trafficking, and function. Understanding all the above is essential for a complete picture of the role of Kv channels in physiology and disease.
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Affiliation(s)
- Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California
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Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry. Sci Rep 2021; 11:10719. [PMID: 34021177 PMCID: PMC8140153 DOI: 10.1038/s41598-021-90002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 11/08/2022] Open
Abstract
Voltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.
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