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Bizzotto E, Zampieri G, Treu L, Filannino P, Di Cagno R, Campanaro S. Classification of bioactive peptides: A systematic benchmark of models and encodings. Comput Struct Biotechnol J 2024; 23:2442-2452. [PMID: 38867723 PMCID: PMC11168199 DOI: 10.1016/j.csbj.2024.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
Bioactive peptides are short amino acid chains possessing biological activity and exerting physiological effects relevant to human health. Despite their therapeutic value, their identification remains a major problem, as it mainly relies on time-consuming in vitro tests. While bioinformatic tools for the identification of bioactive peptides are available, they are focused on specific functional classes and have not been systematically tested on realistic settings. To tackle this problem, bioactive peptide sequences and functions were here gathered from a variety of databases to generate a unified collection of bioactive peptides from microbial fermentation. This collection was organized into nine functional classes including some previously studied and some unexplored such as immunomodulatory, opioid and cardiovascular peptides. Upon assessing their sequence properties, four alternative encoding methods were tested in combination with a multitude of machine learning algorithms, from basic classifiers like logistic regression to advanced algorithms like BERT. Tests on a total of 171 models showed that, while some functions are intrinsically easier to detect, no single combination of classifiers and encoders worked universally well for all classes. For this reason, we unified all the best individual models for each class and generated CICERON (Classification of bIoaCtive pEptides fRom micrObial fermeNtation), a classification tool for the functional classification of peptides. State-of-the-art classifiers were found to underperform on our realistic benchmark dataset compared to the models included in CICERON. Altogether, our work provides a tool for real-world peptide classification and can serve as a benchmark for future model development.
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Affiliation(s)
- Edoardo Bizzotto
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
| | - Guido Zampieri
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
| | - Laura Treu
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
| | - Pasquale Filannino
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Via G. Amendola 165/a, Bari 70126, Italy
| | - Raffaella Di Cagno
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bolzano, Piazza Universita, 5, Bolzano 39100, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padua, Via U. Bassi 58/b, Padova 35131, Italy
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Andrianova E, Putilovskiy M. Efficacy and safety of Ergoferon versus oseltamivir: Reply to the Letter to the Editor. Int J Infect Dis 2019; 89:190-192. [PMID: 31626982 DOI: 10.1016/j.ijid.2019.09.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 10/25/2022] Open
Affiliation(s)
- Elena Andrianova
- Research and Development Department, Materia Medica Holding, Moscow, Russian Federation, Russia.
| | - Mikhail Putilovskiy
- Research and Development Department, Materia Medica Holding, Moscow, Russian Federation, Russia
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Fateeva VV. [Pathogenesis of endothelial dysfunction in cerebral atherosclerosis and their correction]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 117:67-70. [PMID: 29376986 DOI: 10.17116/jnevro201711712167-70] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The authors review the studies on oxidative stress in the pathogenesis of cerebrovascular diseases (CVD) and highlight a contribution of endothelial dysfunction to the CVD development. Own experience of using divasa in patients of old and very old age with chronic CVD comorbid to cerebral atherosclerosis is described.
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Affiliation(s)
- V V Fateeva
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow, Russia
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Parfenov VA, Ostroumova OD, Ostroumova TM, Kochetkov AI, Fateeva VV, Khacheva KK, Khakimova GR, Epstein OI. Vascular cognitive impairment: pathophysiological mechanisms, insights into structural basis, and perspectives in specific treatments. Neuropsychiatr Dis Treat 2019; 15:1381-1402. [PMID: 31190841 PMCID: PMC6535085 DOI: 10.2147/ndt.s197032] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 02/14/2019] [Indexed: 01/19/2023] Open
Abstract
Vascular cognitive impairment (VCI) and vascular dementia are the most common forms of cognitive disorder associated with cerebrovascular disease and related to increased morbidity and mortality among the older population. Growing evidence suggests the contribution of blood-pressure variability, cardiac arrhythmia, hyperactivation of the renin-angiotensin-aldosterone system, endothelial dysfunction, vascular remodeling and stiffness, different angiopathies, neural tissue homeostasis, and systemic metabolic disorders to the pathophysiology of VCI. In this review, we focus on factors contributing to cerebrovascular disease, neurovascular unit alterations, and novel approaches to cognitive improvement in patients with cognitive decline. One of the important factors associated with the neuronal causes of VCI is the S100B protein, which can affect the expression of cytokines in the brain, support homeostasis, and regulate processes of differentiation, repair, and apoptosis of the nervous tissue. Since the pathological basis of VCI is complex and diverse, treatment affecting the mechanisms of cognitive disorders should be developed. The prospective role of a novel complex drug consisting of released-active antibodies to S100 and to endothelial NO synthase in VCI treatment is highlighted.
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Affiliation(s)
- Vladimir A Parfenov
- Department of Neurology, Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russian Federation
| | - Olga D Ostroumova
- Laboratory of Clinical Pharmacology and therapy, Federal State Budgetary Educational Institution of Higher Education "N.I. Pirogov Russian National Research Medical University" of the Ministry of Health of the Russian Federation, Russian Clinical and Research Center of Gerontology, Moscow, Russia.,Department of Clinical Pharmacology, Internal Medicine and Propaedeutics I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Tatiana M Ostroumova
- Department of Neurology, Federal State Autonomous Educational Institution of Higher Education, I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russian Federation
| | - Alexey I Kochetkov
- Laboratory of Clinical Pharmacology and therapy, Federal State Budgetary Educational Institution of Higher Education "N.I. Pirogov Russian National Research Medical University" of the Ministry of Health of the Russian Federation, Russian Clinical and Research Center of Gerontology, Moscow, Russia
| | - Victoria V Fateeva
- Medical Information Department, OOO NPF Materia Medica Holding, Moscow, Russian Federation
| | - Kristina K Khacheva
- Medical Information Department, OOO NPF Materia Medica Holding, Moscow, Russian Federation
| | - Gulnara R Khakimova
- Research and Analytical Division of Scientific Research and Development Department, Moscow, Russian Federation
| | - Oleg I Epstein
- Laboratory of Physiologicaly Active Substances, Department of Molecular and Cellular Pathophysiology, Research Institute of General Pathology and Pathophysiology, Moscow, Russian Federation
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Parfenov VA, Zhivolupov SA, Nikulina KV, Poverennova IE, Lapatuhin VG, Zhestikova MG, Zhukova NG, Glazunov AB. [Diagnosis and treatment of cognitive impairment in patients with chronic cerebral ischemia: the results of observational Russian program DIAMANT]. Zh Nevrol Psikhiatr Im S S Korsakova 2018; 118:15-23. [PMID: 30040796 DOI: 10.17116/jnevro20181186115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AIM To investigate the efficacy of divaza in outpatients with cognitive disorders and chronic brain ischemia (CBI). MATERIAL AND METHODS The non-interventional observational program included the data of 2583 outpatients with CBI from 30 cities (8 federal okrugs of the Russian Federation) who were on outpatient neurological treatment and received divaza in a dose of 2 tablets three times a day from Oct 2016 to Jan 2017. Cognitive functions were evaluated using the MoCA scale before and after 3 months of treatment. RESULTS AND CONCLUSION Cognitive disorders were identified in 90.7% of patients (<26 MoCA scores). After treatment, the mean MoCA score increased from 19.58±5.13 to 23.99±4.21 (p<0.0001), the number of patients with normal cognitive functions rate (≥26 scores) increased from 9.3 to 41.3%, the number of patients with marked cognitive impairment decreased. The drug was well-tolerated by old and very old patients, adverse events were observed rarely (0.6% of cases). The majority of doctors (88.4%) noticed the effect of divaza as significant improvement or improvement, and 89.6% of patients valued the effect to be excellent or good. The use of divaza, the drug with endothelioprotective and nootropic effects, is pathogenetically justified and promising in patients with cognitive disorders of vascular etiology.
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Affiliation(s)
- V A Parfenov
- Sechenov First Moscow State Medical University, Ministry of Health of Russia, Moscow, Russia
| | | | - K V Nikulina
- OOO 'NPF "Materia Medica Holding"', Moscow, Russia
| | | | - V G Lapatuhin
- Penza Institute of Improvement of Doctors, Penza, Russia
| | - M G Zhestikova
- Novokuznetsk State Institute of Postgraduate Medicine, Novokuznetsk, Russia
| | - N G Zhukova
- Siberian State Medical University, Tomsk, Russia
| | - A B Glazunov
- Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation, Moscow, Russia
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Fateeva VV, Vorobyova OV. [Nitric oxide: from the mechanism of action to pharmacological effects in cerebrovascular diseases]. Zh Nevrol Psikhiatr Im S S Korsakova 2017; 117:131-135. [PMID: 29171501 DOI: 10.17116/jnevro2017117101131-135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The article presents the data of studies of nitric oxide (NO) in the pathogenesis of cerebrovascular diseases. It is emphasized that endothelial dysfunction contributes to the formation of cerebrovascular diseases. Generalized data on preparations with endothelioprotective effect, as well as own data on the use of the preparation 'Divaza' in patients of middle and advanced age with chronic cerebrovascular disease are given.
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Affiliation(s)
- V V Fateeva
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - O V Vorobyova
- Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation, Moscow, Russia
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