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Rathore AS, Choudhury S, Arora A, Tijare P, Raghava GPS. ToxinPred 3.0: An improved method for predicting the toxicity of peptides. Comput Biol Med 2024; 179:108926. [PMID: 39038391 DOI: 10.1016/j.compbiomed.2024.108926] [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: 08/24/2023] [Revised: 05/17/2024] [Accepted: 07/17/2024] [Indexed: 07/24/2024]
Abstract
Toxicity emerges as a prominent challenge in the design of therapeutic peptides, causing the failure of numerous peptides during clinical trials. In 2013, our group developed ToxinPred, a computational method that has been extensively adopted by the scientific community for predicting peptide toxicity. In this paper, we propose a refined variant of ToxinPred that showcases improved reliability and accuracy in predicting peptide toxicity. Initially, we utilized a similarity/alignment-based approach employing BLAST to predict toxic peptides, which yielded satisfactory accuracy; however, the method suffered from inadequate coverage. Subsequently, we employed a motif-based approach using MERCI software to uncover specific patterns or motifs that are exclusively observed in toxic peptides. The search for these motifs in peptides allowed us to predict toxic peptides with a high level of specificity with poor sensitivity. To overcome the coverage limitations, we developed alignment-free methods using machine/deep learning techniques to balance sensitivity and specificity of prediction. Deep learning model (ANN - LSTM with fixed sequence length) developed using one-hot encoding achieved a maximum AUROC of 0.93 with MCC of 0.71 on an independent dataset. Machine learning model (extra tree) developed using compositional features of peptides achieved a maximum AUROC of 0.95 with MCC of 0.78. We also developed large language models and achieved maximum AUC of 0.93 using ESM2-t33. Finally, we developed hybrid or ensemble methods combining two or more methods to enhance performance. Our specific hybrid method, which combines a motif-based approach with a machine learning-based model, achieved a maximum AUROC of 0.98 with MCC 0.81 on an independent dataset. In this study, all models were trained and tested on 80 % of data using five-fold cross-validation and evaluated on the remaining 20 % of data called independent dataset. The evaluation of all methods on an independent dataset revealed that the method proposed in this study exhibited better performance than existing methods. To cater to the needs of the scientific community, we have developed a standalone software, pip package and web-based server ToxinPred3 (https://github.com/raghavagps/toxinpred3 and https://webs.iiitd.edu.in/raghava/toxinpred3/).
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Affiliation(s)
- Anand Singh Rathore
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Shubham Choudhury
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Akanksha Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Purva Tijare
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, 110020, India.
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2
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Panchalingam S, Kasivelu G. A Computational Approach to Identifying Peptide Inhibitors against White Spot Syndrome Virus: Targeting the Virus Envelope Protein. Microb Pathog 2024; 195:106849. [PMID: 39147215 DOI: 10.1016/j.micpath.2024.106849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 08/12/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024]
Abstract
The white spot syndrome virus (WSSV), a rapidly replicating and highly lethal pathogen that targets Penaeid shrimp, has emerged as one of the most widespread viruses globally due to its high virulence. With effective chemotherapeutics still unavailable, the pursuit of novel and viable strategies against WSSV remains a crucial focus in the field of shrimp farming. The envelope proteins of WSSV are essential for virus entry, serving as excellent targets for the development of antiviral therapeutics. Novel strategies in the design of inhibitory peptides, especially those targeting envelope protein (VP28) located on the surface of the virus particle, play a critical role as a significant virulence factor during the early stages of inherent WSSV infection in shrimp. In this direction, the current computational study focused on identifying self-inhibitory peptides from the hydrophobic membrane regions of the VP28 protein, employing peptide docking and molecular dynamics simulation (MDS) approaches. Such inhibitory peptides could be useful building blocks for the rational engineering of inhibitory therapeutics since they imitate the mechanism of binding to homologous partners used by their origin domain to interact with other molecules. The N-terminal sequence of VP28 has been reported as the potential site for membrane interactions during the virus entry. Moreover, drug delivery systems mediated by chitosan and gold nanoparticles are being developed to enhance the therapeutic efficacy of anti-viral peptides. These systems can increase the solubility, stability, and selectivity of peptides, possessing better qualities than conventional delivery methods. This computational study on self-inhibitory peptides could be a valuable resource for further in vitro and in vivo studies on anti-viral therapeutics in the aquaculture industry.
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Affiliation(s)
- Santhiya Panchalingam
- Centre for Ocean Research, Sathyabama Institute of Science and Technology, Chennai - 600 119, India
| | - Govindaraju Kasivelu
- Centre for Ocean Research, Sathyabama Institute of Science and Technology, Chennai - 600 119, India.
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3
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Wang Q, Liang M, Xiao Y, Li Z, Chen X, Cheng P, Qi B, Yu Y, Lei T, Huang Z. In silico and in vivo discovery of antioxidant sea cucumber peptides with antineurodegenerative properties. Food Funct 2024; 15:5972-5986. [PMID: 38739010 DOI: 10.1039/d4fo01542h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Since oxidative stress is often associated with neurodegenerative diseases, antioxidants are likely to confer protection against neurodegeneration. Despite an increasing number of food-derived peptides being identified as antioxidants, their antineurodegenerative potentials remain largely unexplored. Here, a sea cucumber peptide preparation - the peptide-rich fraction of <3 kDa (UF<3K) obtained by ultrafiltration from Apostichopus japonicus protein hydrolyzate - was found to protect PC12 cells and Caenorhabditis elegans from neurodegeneration by reducing oxidative stress and apoptosis, demonstrating its in vitro and in vivo neuroprotective effects. As many food-originated peptides are cryptides (cryptic peptides - short amino acid sequences encrypted in parent proteins) released in quantities by protein hydrolysis, UF<3K was subjected to sequencing analysis. As expected, a large repertoire of peptides were identified in UF<3K, establishing a sea cucumber cryptome (1238 peptides in total). Then 134 peptides were randomly selected from the cryptome (>10%) and analyzed for their antioxidant activities using a number of in silico bioinformatic programs as well as in vivo experimental assays in C. elegans. From these results, a novel antioxidant peptide - HoloPep#362 (FETLMPLWGNK) - was shown to not only inhibit aggregation of neurodegeneration-associated polygluatmine proteins but also ameliorate behavioral deficits in proteotoxicity nematodes. Proteomic analysis revealed an increased expression of several lysosomal proteases by HoloPep#362, suggesting proteostasis maintenance as a mechanism for its antineurodegenerative action. These findings provide an insight into the health-promoting potential of sea cucumber peptides as neuroprotective nutraceuticals and also into the importance of training in silico peptide bioactivity prediction programs with in vivo experimental data.
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Affiliation(s)
- Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Ming Liang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
- Research and Development Center, Infinitus (China) Company Ltd, Guangzhou 510405, China
| | - Yue Xiao
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
| | - Zhenhua Li
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xiaohe Chen
- Rehabilitation Department, Wuhan Children's Hospital, Wuhan Maternal and Child Healthcare Center, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
| | - Peng Cheng
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Bing Qi
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yi Yu
- Research and Development Center, Infinitus (China) Company Ltd, Guangzhou 510405, China
| | - Tao Lei
- Rehabilitation Department, Wuhan Children's Hospital, Wuhan Maternal and Child Healthcare Center, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China.
- School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
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4
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Gatto MS, Johnson MP, Najahi-Missaoui W. Targeted Liposomal Drug Delivery: Overview of the Current Applications and Challenges. Life (Basel) 2024; 14:672. [PMID: 38929656 PMCID: PMC11204409 DOI: 10.3390/life14060672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/14/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
In drug development, it is not uncommon that an active substance exhibits efficacy in vitro but lacks the ability to specifically reach its target in vivo. As a result, targeted drug delivery has become a primary focus in the pharmaceutical sciences. Since the approval of Doxil® in 1995, liposomes have emerged as a leading nanoparticle in targeted drug delivery. Their low immunogenicity, high versatility, and well-documented efficacy have led to their clinical use against a wide variety of diseases. That being said, every disease is accompanied by a unique set of physiological conditions, and each liposomal product must be formulated with this consideration. There are a multitude of different targeting techniques for liposomes that can be employed depending on the application. Passive techniques such as PEGylation or the enhanced permeation and retention effect can improve general pharmacokinetics, while active techniques such as conjugating targeting molecules to the liposome surface may bring even further specificity. This review aims to summarize the current strategies for targeted liposomes in the treatment of diseases.
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Affiliation(s)
| | | | - Wided Najahi-Missaoui
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (M.S.G.); (M.P.J.)
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Goles M, Daza A, Cabas-Mora G, Sarmiento-Varón L, Sepúlveda-Yañez J, Anvari-Kazemabad H, Davari MD, Uribe-Paredes R, Olivera-Nappa Á, Navarrete MA, Medina-Ortiz D. Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides. Brief Bioinform 2024; 25:bbae275. [PMID: 38856172 PMCID: PMC11163380 DOI: 10.1093/bib/bbae275] [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: 02/08/2024] [Revised: 04/23/2024] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
With their diverse biological activities, peptides are promising candidates for therapeutic applications, showing antimicrobial, antitumour and hormonal signalling capabilities. Despite their advantages, therapeutic peptides face challenges such as short half-life, limited oral bioavailability and susceptibility to plasma degradation. The rise of computational tools and artificial intelligence (AI) in peptide research has spurred the development of advanced methodologies and databases that are pivotal in the exploration of these complex macromolecules. This perspective delves into integrating AI in peptide development, encompassing classifier methods, predictive systems and the avant-garde design facilitated by deep-generative models like generative adversarial networks and variational autoencoders. There are still challenges, such as the need for processing optimization and careful validation of predictive models. This work outlines traditional strategies for machine learning model construction and training techniques and proposes a comprehensive AI-assisted peptide design and validation pipeline. The evolving landscape of peptide design using AI is emphasized, showcasing the practicality of these methods in expediting the development and discovery of novel peptides within the context of peptide-based drug discovery.
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Affiliation(s)
- Montserrat Goles
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
- Departamento de Ingeniería Química, Biotecnología y Materiales, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Anamaría Daza
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Gabriel Cabas-Mora
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Lindybeth Sarmiento-Varón
- Centro Asistencial de Docencia e Investigación, CADI, Universidad de Magallanes, Av. Los Flamencos 01364, 6210005, Punta Arenas, Chile
| | - Julieta Sepúlveda-Yañez
- Facultad de Ciencias de la Salud, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Hoda Anvari-Kazemabad
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Mehdi D Davari
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Roberto Uribe-Paredes
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - Álvaro Olivera-Nappa
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
| | - Marcelo A Navarrete
- Centro Asistencial de Docencia e Investigación, CADI, Universidad de Magallanes, Av. Los Flamencos 01364, 6210005, Punta Arenas, Chile
- Escuela de Medicina, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
| | - David Medina-Ortiz
- Departamento de Ingeniería en Computación, Universidad de Magallanes, Av. Pdte. Manuel Bulnes 01855, 6210427, Punta Arenas, Chile
- Centre for Biotechnology and Bioengineering, CeBiB, Universidad de Chile, Beauchef 851, 8370456, Santiago, Chile
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Deigin V, Linkova N, Vinogradova J, Vinogradov D, Polyakova V, Medvedev D, Krasichkov A, Volpina O. The First Reciprocal Activities of Chiral Peptide Pharmaceuticals: Thymogen and Thymodepressin, as Examples. Int J Mol Sci 2024; 25:5042. [PMID: 38732260 PMCID: PMC11084461 DOI: 10.3390/ijms25095042] [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: 03/15/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
Peptides show high promise in the targeting and intracellular delivery of next-generation biotherapeutics. The main limitation is peptides' susceptibility to proteolysis in biological systems. Numerous strategies have been developed to overcome this challenge by chemically enhancing the resistance to proteolysis. In nature, amino acids, except glycine, are found in L- and D-enantiomers. The change from one form to the other will change the primary structure of polypeptides and proteins and may affect their function and biological activity. Given the inherent chiral nature of biological systems and their high enantiomeric selectivity, there is rising interest in manipulating the chirality of polypeptides to enhance their biomolecular interactions. In this review, we discuss the first examples of up-and-down homeostasis regulation by two enantiomeric drugs: immunostimulant Thymogen (L-Glu-L-Trp) and immunosuppressor Thymodepressin (D-Glu(D-Trp)). This study shows the perspective of exploring chirality to remove the chiral wall between L- and D-biomolecules. The selected clinical result will be discussed.
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Affiliation(s)
- Vladislav Deigin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia; (V.D.); (O.V.)
| | - Natalia Linkova
- St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
| | - Julia Vinogradova
- The Department of Hospital Therapy No. 2, I.M. Sechenov First Moscow State Medical University, 8 Trubetskaya Str., Building 2, Moscow 119991, Russia; (J.V.); (D.V.)
| | - Dmitrii Vinogradov
- The Department of Hospital Therapy No. 2, I.M. Sechenov First Moscow State Medical University, 8 Trubetskaya Str., Building 2, Moscow 119991, Russia; (J.V.); (D.V.)
| | - Victoria Polyakova
- St. Petersburg Research Institute of Phthisiopulmonology, Ligovskii Prospect, 2-4, St. Petersburg 191036, Russia;
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
| | - Dmitrii Medvedev
- St. Petersburg Institute of Bioregulation and Gerontology, 3 Dynamo Ave., St. Petersburg 197110, Russia
- The Department of Social Rehabilitation and Occupational Therapy of the St. Petersburg Medical and Social Institute, Kondratievsky St., 72A, St. Petersburg 195271, Russia
| | - Alexander Krasichkov
- Department of Radio Engineering Systems, Saint Petersburg Electrotechnical University ‘LETI’, St. Petersburg 197376, Russia
| | - Olga Volpina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St., 16/10, Moscow 117997, Russia; (V.D.); (O.V.)
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7
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Marinova P, Tamahkyarova K. Synthesis and Biological Activities of Some Metal Complexes of Peptides: A Review. BIOTECH 2024; 13:9. [PMID: 38651489 PMCID: PMC11036290 DOI: 10.3390/biotech13020009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted using various database platforms such as MetalPDB. The rising prominence of therapeutic peptides encompasses anticancer, antiviral, antimicrobial, and anti-neurodegenerative properties. The metals Na, K, Mg, Ca, Fe, Mn, Co, Cu, Zn, and Mo are ten of the twenty elements that are considered essential for life. Crucial for understanding the biological role of metals is the exploration of metal-bound proteins and peptides. Aside from essential metals, there are other non-essential metals that also interact biologically, exhibiting either therapeutic or toxic effects. Irregularities in metal binding contribute to diseases like Alzheimer's, neurodegenerative disorders, Wilson's, and Menkes disease. Certain metal complexes have potential applications as radiopharmaceuticals. The examination of these complexes was achieved by preforming UV-Vis, IR, EPR, NMR spectroscopy, and X-ray analysis. This summary, although unable to cover all of the studies in the field, offers a review of the ongoing experimentation and is a basis for new ideas, as well as strategies to explore and gain knowledge from the extensive realm of peptide-chelated metals and biotechnologies.
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Affiliation(s)
- Petja Marinova
- Department of General and Inorganic Chemistry with Methodology of Chemistry Education, Faculty of Chemistry, University of Plovdiv, “Tzar Assen” Str. 24, 4000 Plovdiv, Bulgaria;
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Zhang Y, Li Y, Quan Z, Xiao P, Duan JA. New Insights into Antioxidant Peptides: An Overview of Efficient Screening, Evaluation Models, Molecular Mechanisms, and Applications. Antioxidants (Basel) 2024; 13:203. [PMID: 38397801 PMCID: PMC10886007 DOI: 10.3390/antiox13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Antioxidant peptides are currently a hotspot in food science, pharmaceuticals, and cosmetics. In different fields, the screening, activity evaluation, mechanisms, and applications of antioxidant peptides are the pivotal areas of research. Among these topics, the efficient screening of antioxidant peptides stands at the forefront of cutting-edge research. To this end, efficient screening with novel technologies has significantly accelerated the research process, gradually replacing the traditional approach. After the novel antioxidant peptides are screened and identified, a time-consuming activity evaluation is another indispensable procedure, especially in in vivo models. Cellular and rodent models have been widely used for activity evaluation, whilst non-rodent models provide an efficient solution, even with the potential for high-throughput screening. Meanwhile, further research of molecular mechanisms can elucidate the essence underlying the activity, which is related to several signaling pathways, including Keap1-Nrf2/ARE, mitochondria-dependent apoptosis, TGF-β/SMAD, AMPK/SIRT1/PGC-1α, PI3K/Akt/mTOR, and NF-κB. Last but not least, antioxidant peptides have broad applications in food manufacture, therapy, and the cosmetics industry, which requires a systematic review. This review introduces novel technologies for the efficient screening of antioxidant peptides, categorized with a new vision. A wide range of activity evaluation assays, encompassing cellular models, as well as rodent and non-rodent models, are provided in a comprehensive manner. In addition, recent advances in molecular mechanisms are analyzed with specific cases. Finally, the applications of antioxidant peptides in food production, therapy, and cosmetics are systematically reviewed.
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Affiliation(s)
| | | | | | - Ping Xiao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China; (Y.Z.); (Y.L.); (Z.Q.)
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China; (Y.Z.); (Y.L.); (Z.Q.)
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Stefanik O, Majerova P, Kovac A, Mikus P, Piestansky J. Capillary electrophoresis in the analysis of therapeutic peptides-A review. Electrophoresis 2024; 45:120-164. [PMID: 37705480 DOI: 10.1002/elps.202300141] [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: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
Therapeutic peptides are a growing class of innovative drugs with high efficiency and a low risk of adverse effects. These biomolecules fall within the molecular mass range between that of small molecules and proteins. However, their inherent instability and potential for degradation underscore the importance of reliable and effective analytical methods for pharmaceutical quality control, therapeutic drug monitoring, and compliance testing. Liquid chromatography-mass spectrometry (LC-MS) has long time been the "gold standard" conventional method for peptide analysis, but capillary electrophoresis (CE) is increasingly being recognized as a complementary and, in some cases, superior, highly efficient, green, and cost-effective alternative technique. CE can separate peptides composed of different amino acids owing to differences in their net charge and size, determining their migration behavior in an electric field. This review provides a comprehensive overview of therapeutic peptides that have been used in the clinical environment for the last 25 years. It describes the properties, classification, current trends in development, and clinical use of therapeutic peptides. From the analytical point of view, it discusses the challenges associated with the analysis of therapeutic peptides in pharmaceutical and biological matrices, as well as the evaluation of CE as a whole and the comparison with LC methods. The article also highlights the use of microchip electrophoresis, nonaqueous CE, and nonconventional hydrodynamically closed CE systems and their applications. Overall, the article emphasizes the importance of developing new CE-based analytical methods to ensure the high quality, safety, and efficacy of therapeutic peptides in clinical practice.
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Affiliation(s)
- Ondrej Stefanik
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Mikus
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
| | - Juraj Piestansky
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Bratislava, Slovak Republic
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Patharapankal EJ, Ajiboye AL, Mattern C, Trivedi V. Nose-to-Brain (N2B) Delivery: An Alternative Route for the Delivery of Biologics in the Management and Treatment of Central Nervous System Disorders. Pharmaceutics 2023; 16:66. [PMID: 38258077 PMCID: PMC10818989 DOI: 10.3390/pharmaceutics16010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
In recent years, there have been a growing number of small and large molecules that could be used to treat diseases of the central nervous system (CNS). Nose-to-brain delivery can be a potential option for the direct transport of molecules from the nasal cavity to different brain areas. This review aims to provide a compilation of current approaches regarding drug delivery to the CNS via the nose, with a focus on biologics. The review also includes a discussion on the key benefits of nasal delivery as a promising alternative route for drug administration and the involved pathways or mechanisms. This article reviews how the application of various auxiliary agents, such as permeation enhancers, mucolytics, in situ gelling/mucoadhesive agents, enzyme inhibitors, and polymeric and lipid-based systems, can promote the delivery of large molecules in the CNS. The article also includes a discussion on the current state of intranasal formulation development and summarizes the biologics currently in clinical trials. It was noted that significant progress has been made in this field, and these are currently being applied to successfully transport large molecules to the CNS via the nose. However, a deep mechanistic understanding of this route, along with the intimate knowledge of various excipients and their interactions with the drug and nasal physiology, is still necessary to bring us one step closer to developing effective formulations for nasal-brain drug delivery.
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Affiliation(s)
- Elizabeth J. Patharapankal
- Medway School of Pharmacy, University of Kent, Central Avenue, Chatham Maritime, Canterbury ME4 4TB, UK; (E.J.P.); (A.L.A.)
| | - Adejumoke Lara Ajiboye
- Medway School of Pharmacy, University of Kent, Central Avenue, Chatham Maritime, Canterbury ME4 4TB, UK; (E.J.P.); (A.L.A.)
| | | | - Vivek Trivedi
- Medway School of Pharmacy, University of Kent, Central Avenue, Chatham Maritime, Canterbury ME4 4TB, UK; (E.J.P.); (A.L.A.)
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11
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Karachaliou CE, Livaniou E. Neuroprotective Action of Humanin and Humanin Analogues: Research Findings and Perspectives. BIOLOGY 2023; 12:1534. [PMID: 38132360 PMCID: PMC10740898 DOI: 10.3390/biology12121534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Humanin is a 24-mer peptide first reported in the early 2000s as a new neuroprotective/cytoprotective factor rescuing neuronal cells from death induced by various Alzheimer's disease-associated insults. Nowadays it is known that humanin belongs to the novel class of the so-called mitochondrial-derived peptides (which are encoded by mitochondrial DNA) and has been shown to exert beneficial cytoprotective effects in a series of in vitro and/or in vivo experimental models of human diseases, including not only neurodegenerative disorders but other human diseases as well (e.g., age-related macular degeneration, cardiovascular diseases, or diabetes mellitus). This review article is focused on the presentation of recent in vitro and in vivo research results associated with the neuroprotective action of humanin as well as of various, mainly synthetic, analogues of the peptide; moreover, the main mode(s)/mechanism(s) through which humanin and humanin analogues may exert in vitro and in vivo regarding neuroprotection have been reported. The prospects of humanin and humanin analogues to be further investigated in the frame of future research endeavors against neurodegenerative/neural diseases have also been briefly discussed.
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Affiliation(s)
| | - Evangelia Livaniou
- Immunopeptide Chemistry Lab., Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, National Centre for Scientific Research “Demokritos”, P.O. Box 60037, 153 10 Agia Paraskevi, Greece;
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12
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Shen L, Monasson O, Peroni E, Le Bideau F, Messaoudi S. Electrochemical Nickel-Catalyzed Selective Inter- and Intramolecular Arylations of Cysteine-Containing Peptides. Angew Chem Int Ed Engl 2023; 62:e202315748. [PMID: 37906608 DOI: 10.1002/anie.202315748] [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: 10/18/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
Here we report a simple electrochemical route towards the synthesis of S-arylated peptides by a site selective coupling of peptides with aryl halides under base free conditions. This approach demonstrates the power of electrochemistry to access both highly complex peptide conjugates and cyclic peptides.
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Affiliation(s)
- Linhua Shen
- Université Paris-Saclay, CNRS, BioCIS, 92290, Orsay, France
| | - Olivier Monasson
- Université Paris-Saclay, CNRS, BioCIS, 92290, Orsay, France
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
| | - Elisa Peroni
- Université Paris-Saclay, CNRS, BioCIS, 92290, Orsay, France
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
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13
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Shin MK, Hwang IW, Jang BY, Bu KB, Han DH, Lee SH, Oh JW, Yoo JS, Sung JS. The Identification of a Novel Spider Toxin Peptide, Lycotoxin-Pa2a, with Antibacterial and Anti-Inflammatory Activities. Antibiotics (Basel) 2023; 12:1708. [PMID: 38136742 PMCID: PMC10740532 DOI: 10.3390/antibiotics12121708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
With the increasing challenge of controlling infectious diseases due to the emergence of antibiotic-resistant strains, the importance of discovering new antimicrobial agents is rapidly increasing. Animal venoms contain a variety of functional peptides, making them a promising platform for pharmaceutical development. In this study, a novel toxin peptide with antibacterial and anti-inflammatory activities was discovered from the spider venom gland transcriptome by implementing computational approaches. Lycotoxin-Pa2a (Lytx-Pa2a) showed homology to known-spider toxin, where functional prediction indicated the potential of both antibacterial and anti-inflammatory peptides without hemolytic activity. The colony-forming assay and minimum inhibitory concentration test showed that Lytx-Pa2a exhibited comparable or stronger antibacterial activity against pathogenic strains than melittin. Following mechanistic studies revealed that Lytx-Pa2a disrupts both cytoplasmic and outer membranes of bacteria while simultaneously inducing the accumulation of reactive oxygen species. The peptide exerted no significant toxicity when treated to human primary cells, murine macrophages, and bovine red blood cells. Moreover, Lytx-Pa2a alleviated lipopolysaccharide-induced inflammation in mouse macrophages by suppressing the expression of inflammatory mediators. These findings not only suggested that Lytx-Pa2a with dual activity can be utilized as a new antimicrobial agent for infectious diseases but also demonstrated the implementation of in silico methods for discovering a novel functional peptide, which may enhance the future utilization of biological resources.
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Affiliation(s)
- Min Kyoung Shin
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - In-Wook Hwang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - Bo-Young Jang
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - Kyung-Bin Bu
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - Dong-Hee Han
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - Seung-Ho Lee
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - Jin Wook Oh
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
| | - Jung Sun Yoo
- Species Diversity Research Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea;
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea; (M.K.S.); (I.-W.H.); (B.-Y.J.); (K.-B.B.); (D.-H.H.); (S.-H.L.); (J.W.O.)
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14
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Ma C, Wolfinger R. A prediction model for blood-brain barrier penetrating peptides based on masked peptide transformers with dynamic routing. Brief Bioinform 2023; 24:bbad399. [PMID: 37985456 DOI: 10.1093/bib/bbad399] [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: 07/20/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
Blood-brain barrier penetrating peptides (BBBPs) are short peptide sequences that possess the ability to traverse the selective blood-brain interface, making them valuable drug candidates or carriers for various payloads. However, the in vivo or in vitro validation of BBBPs is resource-intensive and time-consuming, driving the need for accurate in silico prediction methods. Unfortunately, the scarcity of experimentally validated BBBPs hinders the efficacy of current machine-learning approaches in generating reliable predictions. In this paper, we present DeepB3P3, a novel framework for BBBPs prediction. Our contribution encompasses four key aspects. Firstly, we propose a novel deep learning model consisting of a transformer encoder layer, a convolutional network backbone, and a capsule network classification head. This integrated architecture effectively learns representative features from peptide sequences. Secondly, we introduce masked peptides as a powerful data augmentation technique to compensate for small training set sizes in BBBP prediction. Thirdly, we develop a novel threshold-tuning method to handle imbalanced data by approximating the optimal decision threshold using the training set. Lastly, DeepB3P3 provides an accurate estimation of the uncertainty level associated with each prediction. Through extensive experiments, we demonstrate that DeepB3P3 achieves state-of-the-art accuracy of up to 98.31% on a benchmarking dataset, solidifying its potential as a promising computational tool for the prediction and discovery of BBBPs.
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Affiliation(s)
- Chunwei Ma
- JMP Statistical Discovery, LLC, Cary, 27513, NC, USA
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, 14260, NY, USA
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15
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Chandrasekhar G, Pengyong H, Pravallika G, Hailei L, Caixia X, Rajasekaran R. Defensin-based therapeutic peptide design in attenuating V30M TTR-induced Familial Amyloid Polyneuropathy. 3 Biotech 2023; 13:227. [PMID: 37304406 PMCID: PMC10250285 DOI: 10.1007/s13205-023-03646-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
In the present study, we aimed to formulate an effective therapeutic candidate against V30M mutant transthyretin (TTR) protein to hinder its pathogenic misfolding. Nicotiana alata Defensin 1 (NaD1) Antimicrobial Peptide (AMP) was availed due to its tendency to aggregate, which may compete for aggregation-prone regions of pathogenic TTR protein. Based on NaD1's potential to bind to V30M TTR, we proposed NaD1-derived tetra peptides: CKTE and SKIL to be initial therapeutic candidates. Based on their association with mutant TTR protein, CKTE tetra peptide showed considerable interaction and curative potential as compared to SKIL tetra peptide. Further analyses from discrete molecular dynamics simulation corroborate CKTE tetra peptide's effectiveness as a 'beta-sheet breaker' against V30M TTR. Various post-simulation trajectory analyses suggested that CKTE tetra peptide alters the structural dynamics of pathogenic V30M TTR protein, thereby potentially attenuating its beta-sheets and impeding its aggregation. Normal mode analysis simulation corroborated that V30M TTR conformation is altered upon its interaction with CKTE peptide. Moreover, simulated thermal denaturation findings suggested that CKTE-V30M TTR complex is more susceptible to simulated denaturation, relative to pathogenic V30M TTR; further substantiating CKTE peptide's potential to alter V30M TTR's pathogenic conformation. Moreover, the residual frustration analysis augmented CKTE tetra peptide's proclivity in reorienting the conformation of V30M TTR. Therefore, we predicted that the tetra peptide, CKTE could be a promising therapeutic candidate in mitigating the amyloidogenic detrimental effects of V30M TTR-mediated familial amyloid polyneuropathy (FAP). Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03646-4.
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Affiliation(s)
- G. Chandrasekhar
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
| | - H. Pengyong
- Changzhi Medical College, Changzhi, 046000 China
| | - G. Pravallika
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
| | - L. Hailei
- Changzhi Medical College, Changzhi, 046000 China
| | - X. Caixia
- Changzhi Medical College, Changzhi, 046000 China
| | - R. Rajasekaran
- Quantitative Biology Lab, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology (VIT, Deemed to Be University), Vellore, Tamil Nadu 632014 India
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16
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Tong Z, Chu G, Wan C, Wang Q, Yang J, Meng Z, Du L, Yang J, Ma H. Multiple Metabolites Derived from Mushrooms and Their Beneficial Effect on Alzheimer's Diseases. Nutrients 2023; 15:2758. [PMID: 37375662 DOI: 10.3390/nu15122758] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Mushrooms with edible and medicinal potential have received widespread attention because of their diverse biological functions, nutritional value, and delicious taste, which are closely related to their rich active components. To date, many bioactive substances have been identified and purified from mushrooms, including proteins, carbohydrates, phenols, and vitamins. More importantly, molecules derived from mushrooms show great potential to alleviate the pathological manifestations of Alzheimer's disease (AD), which seriously affects the health of elderly people. Compared with current therapeutic strategies aimed at symptomatic improvement, it is particularly important to identify natural products from resource-rich mushrooms that can modify the progression of AD. This review summarizes recent investigations of multiple constituents (carbohydrates, peptides, phenols, etc.) isolated from mushrooms to combat AD. In addition, the underlying molecular mechanisms of mushroom metabolites against AD are discussed. The various mechanisms involved in the antiAD activities of mushroom metabolites include antioxidant and anti-neuroinflammatory effects, apoptosis inhibition, and stimulation of neurite outgrowth, etc. This information will facilitate the application of mushroom-derived products in the treatment of AD. However, isolation of new metabolites from multiple types of mushrooms and further in vivo exploration of the molecular mechanisms underlying their antiAD effect are still required.
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Affiliation(s)
- Zijian Tong
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Guodong Chu
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Chenmeng Wan
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Qiaoyu Wang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Jialing Yang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Zhaoli Meng
- Laboratory of Tumor Immunolgy, The First Hospital of Jilin University, Changchun 130061, China
| | - Linna Du
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Jing Yang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
| | - Hongxia Ma
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, Changchun 130118, China
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17
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Barman P, Joshi S, Sharma S, Preet S, Sharma S, Saini A. Strategic Approaches to Improvise Peptide Drugs as Next Generation Therapeutics. Int J Pept Res Ther 2023; 29:61. [PMID: 37251528 PMCID: PMC10206374 DOI: 10.1007/s10989-023-10524-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2023] [Indexed: 05/31/2023]
Abstract
In recent years, the occurrence of a wide variety of drug-resistant diseases has led to an increase in interest in alternate therapies. Peptide-based drugs as an alternate therapy hold researchers' attention in various therapeutic fields such as neurology, dermatology, oncology, metabolic diseases, etc. Previously, they had been overlooked by pharmaceutical companies due to certain limitations such as proteolytic degradation, poor membrane permeability, low oral bioavailability, shorter half-life, and poor target specificity. Over the last two decades, these limitations have been countered by introducing various modification strategies such as backbone and side-chain modifications, amino acid substitution, etc. which improve their functionality. This has led to a substantial interest of researchers and pharmaceutical companies, moving the next generation of these therapeutics from fundamental research to the market. Various chemical and computational approaches are aiding the production of more stable and long-lasting peptides guiding the formulation of novel and advanced therapeutic agents. However, there is not a single article that talks about various peptide design approaches i.e., in-silico and in-vitro along with their applications and strategies to improve their efficacy. In this review, we try to bring different aspects of peptide-based therapeutics under one article with a clear focus to cover the missing links in the literature. This review draws emphasis on various in-silico approaches and modification-based peptide design strategies. It also highlights the recent progress made in peptide delivery methods important for their enhanced clinical efficacy. The article would provide a bird's-eye view to researchers aiming to develop peptides with therapeutic applications. Graphical Abstract
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Affiliation(s)
- Panchali Barman
- Institute of Forensic Science and Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014 India
| | - Shubhi Joshi
- Energy Research Centre, Panjab University, Sector 14, Chandigarh, 160014 India
| | - Sheetal Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
| | - Simran Preet
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
| | - Shweta Sharma
- Institute of Forensic Science and Criminology (UIEAST), Panjab University, Sector 14, Chandigarh, 160014 India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh, U.T 160014 India
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18
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Kuo YC, De S. Development of carbon dots to manage Alzheimer's disease and Parkinson's disease. J Taiwan Inst Chem Eng 2023. [DOI: 10.1016/j.jtice.2023.104799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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19
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Bernardes CP, Santos NAG, Costa TR, Menaldo DL, Sisti FM, Amstalden MK, Ribeiro DL, Antunes LMG, Sampaio SV, Santos AC. Effects of C-Terminal-Ethyl-Esterification in a Snake-Venom-Based Peptide Against the Neurotoxicity of Acrolein in PC12 Cells. Int J Pept Res Ther 2023. [DOI: 10.1007/s10989-023-10517-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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20
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Porosk L, Härk HH, Bicev RN, Gaidutšik I, Nebogatova J, Armolik EJ, Arukuusk P, da Silva ER, Langel Ü. Aggregation Limiting Cell-Penetrating Peptides Derived from Protein Signal Sequences. Int J Mol Sci 2023; 24:ijms24054277. [PMID: 36901707 PMCID: PMC10002422 DOI: 10.3390/ijms24054277] [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: 01/23/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease (ND) and the leading cause of dementia. It is characterized by non-linear, genetic-driven pathophysiological dynamics with high heterogeneity in the biological alterations and the causes of the disease. One of the hallmarks of the AD is the progression of plaques of aggregated amyloid-β (Aβ) or neurofibrillary tangles of Tau. Currently there is no efficient treatment for the AD. Nevertheless, several breakthroughs in revealing the mechanisms behind progression of the AD have led to the discovery of possible therapeutic targets. Some of these include the reduction in inflammation in the brain, and, although highly debated, limiting of the aggregation of the Aβ. In this work we show that similarly to the Neural cell adhesion molecule 1 (NCAM1) signal sequence, other Aβ interacting protein sequences, especially derived from Transthyretin, can be used successfully to reduce or target the amyloid aggregation/aggregates in vitro. The modified signal peptides with cell-penetrating properties reduce the Aβ aggregation and are predicted to have anti-inflammatory properties. Furthermore, we show that by expressing the Aβ-EGFP fusion protein, we can efficiently assess the potential for reduction in aggregation, and the CPP properties of peptides in mammalian cells.
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Affiliation(s)
- Ly Porosk
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
- Correspondence:
| | - Heleri Heike Härk
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Renata Naporano Bicev
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Ilja Gaidutšik
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | | | - Eger-Jasper Armolik
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Piret Arukuusk
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | | | - Ülo Langel
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
- Department Biochemistry and Biophysics, Stockholm University, S.Arrheniusv. 16B, Room C472, 106 91 Stockholm, Sweden
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21
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Biswas S, Basak S, Samui S, Pasadi S, Muniyappa K, Naskar J. Co‐Assembly of Peptide with G‐Quadruplex DNA: A Strategic Approach to Develop Anticancer Therapeutics. ChemistrySelect 2023. [DOI: 10.1002/slct.202203563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Affiliation(s)
- Soumi Biswas
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Shubhanwita Basak
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Satyabrata Samui
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
| | - Sanjeev Pasadi
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - K. Muniyappa
- Department of Biochemistry Indian Institute of Science Bangalore Karnataka 560 012 India
| | - Jishu Naskar
- Department of Biochemistry and Biophysics University of Kalyani Nadia WB 741235 India
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22
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Guadagno AH, Medina SH. The manifold role of octapeptide repeats in prion protein assembly. Pept Sci (Hoboken) 2023; 115. [PMID: 37153755 PMCID: PMC10162500 DOI: 10.1002/pep2.24303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Prion protein misfolding is associated with fatal neurodegenerative disorders such as kuru, Creutzfeldt-Jakob disease, and several animal encephalopathies. While the C-terminal 106-126 peptide has been well studied for its role in prion replication and toxicity, the octapeptide repeat (OPR) sequence found within the N-terminal domain has been relatively under explored. Recent findings that the OPR has both local and long-range effects on prion protein folding and assembly, as well as its ability to bind and regulate transition metal homeostasis, highlights the important role this understudied region may have in prion pathologies. This review attempts to collate this knowledge to advance a deeper understanding on the varied physiologic and pathologic roles the prion OPR plays, and connect these findings to potential therapeutic modalities focused on OPR-metal binding. Continued study of the OPR will not only elucidate a more complete mechanistic model of prion pathology, but may enhance knowledge on other neurodegenerative processes underlying Alzheimer's, Parkinson's, and Huntington's diseases.
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Affiliation(s)
- Amy H. Guadagno
- Nanomedicine, Intercollegiate Degree Program Pennsylvania State University University Park Pennsylvania USA
| | - Scott H. Medina
- Department of Biomedical Engineering Pennsylvania State University University Park Pennsylvania USA
- Huck Institutes of the Life Sciences Pennsylvania State University University Park Pennsylvania USA
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23
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Trisciuzzi D, Siragusa L, Baroni M, Cruciani G, Nicolotti O. An Integrated Machine Learning Model To Spot Peptide Binding Pockets in 3D Protein Screening. J Chem Inf Model 2022; 62:6812-6824. [PMID: 36320100 DOI: 10.1021/acs.jcim.2c00583] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The prediction of peptide-protein binding sites is of utmost importance to tackle the onset of severe neurodegenerative diseases and cancer. In this work, we detail a novel machine learning model based on Linear Discriminant Analysis (LDA) demonstrating to be highly predictive in detecting the putative protein binding regions of small peptides. Starting from 439 high-quality pockets derived from peptide-protein crystallographic complexes, three sets of well-established peptide-binding regions were first selected through a Partitioning Around Medoids (PAM) clustering algorithm based on morphological and energetic 3D GRID-MIF molecular descriptors. Next, the best combination between all the putative interacting peptide pockets and related GRID-MIF scores was automatically explored by using the LDA-based protocol implemented in BioGPS. This approach proved successful to recognize the actual interacting peptide regions (that is, AUC = 0.86 and partial ROC enrichment at 5% of 0.48) from all the other pockets of the protein. Validated on two external collections sets, including 445 and 347 crystallographic peptide-protein complexes, our LDA-based model could be effective to further run peptide-protein virtual screening campaigns.
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Affiliation(s)
- Daniela Trisciuzzi
- Department of Pharmacy-Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125Bari, Italy.,Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, HertfordshireWD6 4PJ, United Kingdom
| | - Lydia Siragusa
- Molecular Horizon s.r.l., Via Montelino, 30, 06084Bettona (PG), Italy.,Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, HertfordshireWD6 4PJ, United Kingdom
| | - Massimo Baroni
- Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, HertfordshireWD6 4PJ, United Kingdom
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, via Elce di Sotto, 8, 06123Perugia (PG), Italy
| | - Orazio Nicolotti
- Department of Pharmacy-Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125Bari, Italy
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24
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Studying Peptide-Metal Ion Complex Structures by Solution-State NMR. Int J Mol Sci 2022; 23:ijms232415957. [PMID: 36555599 PMCID: PMC9782655 DOI: 10.3390/ijms232415957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Metal chelation can provide structural stability and form reactive centers in metalloproteins. Approximately one third of known protein structures are metalloproteins, and metal binding, or the lack thereof, is often implicated in disease, making it necessary to be able to study these systems in detail. Peptide-metal complexes are both present in nature and can provide a means to focus on the binding region of a protein and control experimental variables to a high degree. Structural studies of peptide complexes with metal ions by nuclear magnetic resonance (NMR) were surveyed for all the essential metal complexes and many non-essential metal complexes. The various methods used to study each metal ion are presented together with examples of recent research. Many of these metal systems have been individually reviewed and this current overview of NMR studies of metallopeptide complexes aims to provide a basis for inspiration from structural studies and methodology applied in the field.
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25
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Chamoli T, Khera A, Sharma A, Gupta A, Garg S, Mamgain K, Bansal A, Verma S, Gupta A, Alajangi HK, Singh G, Barnwal RP. Peptide Utility (PU) search server: A new tool for peptide sequence search from multiple databases. Heliyon 2022; 8:e12283. [PMID: 36590540 PMCID: PMC9800339 DOI: 10.1016/j.heliyon.2022.e12283] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Proteins are essential building blocks in humans that have garnered huge attention from researchers worldwide due to their numerous therapeutic applications. To date, different computational tools have been developed to extract pre-existing information on these biological molecules, but most of these tools suffer from limitations such as non-user friendly interface, redundancy of data, etc. To overcome these limitations, a user-friendly interface, the Peptide Utility (PU) webserver (https://chain-searching.herokuapp.com/) has been developed for searching and analyzing homologous and identical protein/peptide sequences that can be searched from approximately 0.4 million sequences (structural and sequence information) in both online and offline modes. The PU web server can also be used to study different types of interactions in PDBSum, identifying the most dominating interface residues, the most prevalent interactions, and the interaction preferences of different residues. The webserver would also pave way for the design of novel therapeutic peptides and folds by identifying conserved residues in the three-dimensional structure space of proteins.
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Affiliation(s)
- Tanishq Chamoli
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Alisha Khera
- Department of Biophysics, Panjab University, Chandigarh 160014, India,National Centre for Cell Science, NCCS Complex, S. P. Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India,University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Anshul Gupta
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Sonam Garg
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Kanishk Mamgain
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Aayushi Bansal
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Shriya Verma
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Ankit Gupta
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India
| | - Hema K. Alajangi
- Department of Biophysics, Panjab University, Chandigarh 160014, India,University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India,Corresponding author.
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India,Corresponding author.
| | - Ravi P. Barnwal
- Department of Computer Science and Engineering, Chandigarh College of Engineering and Technology, Chandigarh, India,Corresponding author.
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26
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Vivekanandan S, Vetrivel U, Hanna LE. Design of human immunodeficiency virus-1 neutralizing peptides targeting CD4-binding site: An integrative computational biologics approach. Front Med (Lausanne) 2022; 9:1036874. [DOI: 10.3389/fmed.2022.1036874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022] Open
Abstract
Peptide therapeutics have recently gained momentum in antiviral therapy due to their increased potency and cost-effectiveness. Interaction of the HIV-1 envelope gp120 with the host CD4 receptor is a critical step for viral entry, and therefore the CD4-binding site (CD4bs) of gp120 is a potential hotspot for blocking HIV-1 infection. The present study aimed to design short peptides from well-characterized CD4bs targeting broadly neutralizing antibodies (bNAbs), which could be utilized as bNAb mimetics for viral neutralization. Co-crystallized structures of HIV-1 gp120 in complex with CD4bs-directed bNAbs were used to derive hexameric peptides using the Rosetta Peptiderive protocol. Based on empirical insights into co-crystallized structures, peptides derived from the heavy chain alone were considered. The peptides were docked with both HIV-1 subtype B and C gp120, and the stability of the peptide–antigen complexes was validated using extensive Molecular Dynamics (MD) simulations. Two peptides identified in the study demonstrated stable intermolecular interactions with SER365, GLY366, and GLY367 of the PHE43 cavity in the CD4 binding pocket, and with ASP368 of HIV-1 gp120, thereby mimicking the natural interaction between ASP368gp120 and ARG59CD4–RECEPTOR. Furthermore, the peptides featured favorable physico-chemical properties for virus neutralization suggesting that these peptides may be highly promising bNAb mimetic candidates that may be taken up for experimental validation.
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27
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Mlakar L, Garrett SM, Watanabe T, Sanderson M, Nishimoto T, Heywood J, Helke KL, Pilewski JM, Herzog EL, Feghali-Bostwick C. Ameliorating Fibrosis in Murine and Human Tissues with END55, an Endostatin-Derived Fusion Protein Made in Plants. Biomedicines 2022; 10:2861. [PMID: 36359382 PMCID: PMC9687961 DOI: 10.3390/biomedicines10112861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022] Open
Abstract
Organ fibrosis, particularly of the lungs, causes significant morbidity and mortality. Effective treatments are needed to reduce the health burden. A fragment of the carboxyl-terminal end of collagen XVIII/endostatin reduces skin and lung fibrosis. This fragment was modified to facilitate its production in plants, which resulted in the recombinant fusion protein, END55. We found that expression of END55 had significant anti-fibrotic effects on the treatment and prevention of skin and lung fibrosis in a bleomycin mouse model. We validated these effects in a second mouse model of pulmonary fibrosis involving inducible, lung-targeted expression of transforming growth factor β1. END55 also exerted anti-fibrotic effects in human lung and skin tissues maintained in organ culture in which fibrosis was experimentally induced. The anti-fibrotic effect of END55 was mediated by a decrease in the expression of extracellular matrix genes and an increase in the levels of matrix-degrading enzymes. Finally, END55 reduced fibrosis in the lungs of patients with systemic sclerosis (SSc) and idiopathic pulmonary fibrosis (IPF) who underwent lung transplantation due to the severity of their lung disease, displaying efficacy in human tissues directly relevant to human disease. These findings demonstrate that END55 is an effective anti-fibrotic therapy in different organs.
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Affiliation(s)
- Logan Mlakar
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sara M. Garrett
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tomoya Watanabe
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Matthew Sanderson
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Tetsuya Nishimoto
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Jonathan Heywood
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kristi L. Helke
- Department of Comparative Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joseph M. Pilewski
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Erica L. Herzog
- Yale ILD Center of Excellence, Department of Medicine, Yale School of Medicine, New Haven, CT 06519, USA
| | - Carol Feghali-Bostwick
- Division of Rheumatology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
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28
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Rational designing of peptide-ligand conjugates-based immunotherapy for the treatment of complicated malaria. Life Sci 2022; 311:121121. [DOI: 10.1016/j.lfs.2022.121121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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29
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Nogueira FC, Costa AS, de Carvalho Oliveira Campos D, Silva RGG, Franco ÁX, Soares PMG, de Oliveira Rocha R, Damasceno ROS, de Alencar NMN, de Souza MHLP, de Oliveira HD. Peptide Isolated from Noni Seeds Confers Gastroprotective Effect by Improving Inflammation and Oxidative Stress in Mice. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10440-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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30
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Kim H, Son B, Seo EU, Kwon M, Ahn JH, Shin H, Song GY, Park EJ, Na DH, Cho S, Kim HN, Park HH, Lee W. Cleavage-Responsive Biofactory T Cells Suppress Infectious Diseases-Associated Hypercytokinemia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201883. [PMID: 35751470 PMCID: PMC9475519 DOI: 10.1002/advs.202201883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Severe infectious diseases, such as coronavirus disease 2019 (COVID-19), can induce hypercytokinemia and multiple organ failure. In spite of the growing demand for peptide therapeutics against infectious diseases, current small molecule-based strategies still require frequent administration due to limited half-life and enzymatic digestion in blood. To overcome this challenge, a strategy to continuously express multi-level therapeutic peptide drugs on the surface of immune cells, is established. Here, chimeric T cells stably expressing therapeutic peptides are presented for treatment of severe infectious diseases. Using lentiviral system, T cells are engineered to express multi-level therapeutic peptides with matrix metallopeptidases- (MMP-) and tumor necrosis factor alpha converting enzyme- (TACE-) responsive cleavage sites on the surface. The enzymatic cleavage releases γ-carboxyglutamic acid of protein C (PC-Gla) domain and thrombin receptor agonist peptide (TRAP), which activate endothelial protein C receptor (EPCR) and protease-activated receptor-1 (PAR-1), respectively. These chimeric T cells prevent vascular damage in tissue-engineered blood vessel and suppress hypercytokinemia and lung tissue damages in vivo, demonstrating promise for use of engineered T cells against sepsis and other infectious-related diseases.
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Affiliation(s)
- Hyelim Kim
- Brain Science InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
- Department of BiotechnologyYonsei UniversitySeoul03722Republic of Korea
| | - Boram Son
- Department of BioengineeringHanyang UniversitySeoul04763Republic of Korea
| | - Eun U Seo
- Brain Science InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
- Division of Bio‐Medical Science and Technology (KIST School)Korea University of Science and Technology (UST)Seoul02792Republic of Korea
| | - Miji Kwon
- Department of Smart Health Science and TechnologyKangwon National UniversityChuncheon24341Republic of Korea
| | - June Hong Ahn
- Division of Pulmonology and AllergyDepartment of Internal MedicineCollege of MedicineYeungnam University and Regional Center for Respiratory DiseasesYeungnam University Medical CenterDaegu42415Republic of Korea
| | - Heungsoo Shin
- Department of BioengineeringHanyang UniversitySeoul04763Republic of Korea
| | - Gyu Yong Song
- College of PharmacyChungnam National UniversityDaejeon34134Republic of Korea
- AREZ Co. LtdDaejeon34134Republic of Korea
| | - Eun Ji Park
- D&D PharmatechSeongnam13486Republic of Korea
| | - Dong Hee Na
- College of PharmacyChung‐Ang UniversitySeoul06974Republic of Korea
| | - Seung‐Woo Cho
- Department of BiotechnologyYonsei UniversitySeoul03722Republic of Korea
| | - Hong Nam Kim
- Brain Science InstituteKorea Institute of Science and Technology (KIST)Seoul02792Republic of Korea
- Division of Bio‐Medical Science and Technology (KIST School)Korea University of Science and Technology (UST)Seoul02792Republic of Korea
- School of Mechanical EngineeringYonsei UniversitySeoul03722Republic of Korea
- Yonsei‐KIST Convergence Research InstituteYonsei UniversitySeoul03722Republic of Korea
| | - Hee Ho Park
- Department of BioengineeringHanyang UniversitySeoul04763Republic of Korea
- BK21 FOUR Education and Research Group for Biopharmaceutical Innovation LeaderHanyang UniversitySeoul04763Republic of Korea
- Research Institute for Convergence of Basic ScienceHanyang UniversitySeoul04763Republic of Korea
| | - Wonhwa Lee
- Department of ChemistrySungkyunkwan UniversitySuwon16419Republic of Korea
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31
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Ashraf H, Solla P, Sechi LA. Current Advancement of Immunomodulatory Drugs as Potential Pharmacotherapies for Autoimmunity Based Neurological Diseases. Pharmaceuticals (Basel) 2022; 15:ph15091077. [PMID: 36145298 PMCID: PMC9504155 DOI: 10.3390/ph15091077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
Dramatic advancement has been made in recent decades to understand the basis of autoimmunity-mediated neurological diseases. These diseases create a strong influence on the central nervous system (CNS) and the peripheral nervous system (PNS), leading to various clinical manifestations and numerous symptoms. Multiple sclerosis (MS) is the most prevalent autoimmune neurological disease while NMO spectrum disorder (NMOSD) is less common. Furthermore, evidence supports the presence of autoimmune mechanisms contributing to the pathogenesis of amyotrophic lateral sclerosis (ALS), which is a neurodegenerative disorder characterized by the progressive death of motor neurons. Additionally, autoimmunity is believed to be involved in the basis of Alzheimer’s and Parkinson’s diseases. In recent years, the prevalence of autoimmune-based neurological disorders has been elevated and current findings strongly suggest the role of pharmacotherapies in controlling the progression of autoimmune diseases. Therefore, this review focused on the current advancement of immunomodulatory drugs as novel approaches in the management of autoimmune neurological diseases and their future outlook.
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Affiliation(s)
- Hajra Ashraf
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Paolo Solla
- Department of Medicine, Surgery and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Leonardo Atonio Sechi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
- Complex Structure of Microbology and Virology, AOU Sassari, 07100 Sassari, Italy
- Correspondence:
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32
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Lo WL, Wang YH, Chen EHL, Wang SM, Chen LC, Chen RPY. Biodistribution analysis of an intranasal-delivered peptide by the nanoSPECT/CT imaging. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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Khandibharad S, Singh S. Artificial intelligence channelizing protein-peptide interactions pipeline for host-parasite paradigm in IL-10 and IL-12 reciprocity by SHP-1. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166466. [PMID: 35750267 DOI: 10.1016/j.bbadis.2022.166466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/12/2022]
Abstract
Identification of molecular targets in any cellular phenomena is a challenge and a path that one endeavors upon independently. We have identified a phosphatase SHP-1 as a point of intervention of IL-10 and IL-12 reciprocity in leishmaniasis. The therapeutic model that we have developed uniquely targets this protein but the pipeline in general can be used by the researchers for their unique targets. Naturally occurring peptides are well known for their biochemical participation in cellular functions hence we were motivated to use this uniqueness of physico-chemical properties of peptides conferred by amino acids through machine learning to channelize a mode of therapeutic exploration in infectious disease. Using computational approaches, we identified high order sequence conservation and similarity in SHP-1 sequence which was also evolutionarily conserved, complete structure of Mouse SHP-1 was predicted and validated, a unique motif of the same was identified against which library of synthetic peptides were designed and validated followed by screening the library by docking them with MuSHP-1 protein structure. Our findings showed 3 peptides had high binding affinity and in future can be validated using cell based and in vivo assays.
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Affiliation(s)
- Shweta Khandibharad
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, INDIA
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, INDIA.
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34
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Patil PJ, Sutar SS, Usman M, Patil DN, Dhanavade MJ, Shehzad Q, Mehmood A, Shah H, Teng C, Zhang C, Li X. Exploring bioactive peptides as potential therapeutic and biotechnology treasures: A contemporary perspective. Life Sci 2022; 301:120637. [PMID: 35568229 DOI: 10.1016/j.lfs.2022.120637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/02/2022] [Accepted: 05/09/2022] [Indexed: 12/21/2022]
Abstract
In preceding years, bioactive peptides (BAPs) have piqued escalating attention owing to their multitudinous biological features. To date, many potential BAPs exhibiting anti-cancer activities have been documented; yet, obstacles such as their safety profiles and consumer acceptance continue to exist. Moreover, BAPs have been discovered to facilitate the suppression of Coronavirus Disease 2019 (CoVID-19) and maybe ideal for treating the CoVID-19 infection, as stated by published experimental findings, but their widespread knowledge is scarce. Likewise, there is a cornucopia of BAPs possessing neuroprotective effects that mend neurodegenerative diseases (NDs) by regulating gut microbiota, but they remain a subject of research interest. Additionally, a plethora of researchers have attempted next-generation approaches based on BAPs, but they need scientific attention. The text format of this critical review is organized around an overview of BAPs' versatility and diverse bio functionalities with emphasis on recent developments and novelties. The review is alienated into independent sections, which are related to either BAPs based disease management strategies or next-generation BAPs based approaches. BAPs based anti-cancer, anti-CoVID-19, and neuroprotective strategies have been explored, which may offer insights that could help the researchers and industries to find an alternate regimen against the three aforementioned fatal diseases. To the best of our knowledge, this is the first review that has systematically discussed the next-generation approaches in BAP research. Furthermore, it can be concluded that the BAPs may be optimal for the management of cancer, CoVID-19, and NDs; nevertheless, experimental and preclinical studies are crucial to validate their therapeutic benefits.
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Affiliation(s)
- Prasanna J Patil
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China
| | - Shubham S Sutar
- Department of Biotechnology, Shivaji University, Vidyanagar, Kolhapur, Maharashtra 416004, India
| | - Muhammad Usman
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China
| | - Devashree N Patil
- Department of Biotechnology, Shivaji University, Vidyanagar, Kolhapur, Maharashtra 416004, India
| | - Maruti J Dhanavade
- Department of Microbiology, Bharati Vidyapeeth's Dr. Patangrao Kadam Mahavidyalaya, Sangli, Maharashtra 416416, India
| | - Qayyum Shehzad
- National Engineering Laboratory for Agri-Product Quality Traceability, Beijing Technology and Business University, Beijing 100048, China
| | - Arshad Mehmood
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing 100048, China
| | - Haroon Shah
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China
| | - Chao Teng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing 100048, China
| | - Chengnan Zhang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing 100048, China.
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048, China; School of Food and Health, Beijing Technology and Business University, No. 11, Fucheng Road, Beijing 100048, China; Beijing Engineering and Technology Research Center of Food Additives, School of Food and Chemical Technology, Beijing Technology and Business University, Beijing 100048, China.
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35
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Lee EJ, Shaikh S, Baig MH, Park SY, Lim JH, Ahmad SS, Ali S, Ahmad K, Choi I. MIF1 and MIF2 Myostatin Peptide Inhibitors as Potent Muscle Mass Regulators. Int J Mol Sci 2022; 23:ijms23084222. [PMID: 35457038 PMCID: PMC9031736 DOI: 10.3390/ijms23084222] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/08/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023] Open
Abstract
The use of peptides as drugs has progressed over time and continues to evolve as treatment paradigms change and new drugs are developed. Myostatin (MSTN) inhibition therapy has shown great promise for the treatment of muscle wasting diseases. Here, we report the MSTN-derived novel peptides MIF1 (10-mer) and MIF2 (10-mer) not only enhance myogenesis by inhibiting MSTN and inducing myogenic-related markers but also reduce adipogenic proliferation and differentiation by suppressing the expression of adipogenic markers. MIF1 and MIF2 were designed based on in silico interaction studies between MSTN and its receptor, activin type IIB receptor (ACVRIIB), and fibromodulin (FMOD). Of the different modifications of MIF1 and MIF2 examined, Ac-MIF1 and Ac-MIF2-NH2 significantly enhanced cell proliferation and differentiation as compared with non-modified peptides. Mice pretreated with Ac-MIF1 or Ac-MIF2-NH2 prior to cardiotoxin-induced muscle injury showed more muscle regeneration than non-pretreated controls, which was attributed to the induction of myogenic genes and reduced MSTN expression. These findings imply that Ac-MIF1 and Ac-MIF2-NH2 might be valuable therapeutic agents for the treatment of muscle-related diseases.
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Affiliation(s)
- Eun Ju Lee
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Sibhghatulla Shaikh
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Mohammad Hassan Baig
- Department of Family Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06273, Korea;
| | - So-Young Park
- Department of Physiology, College of Medicine, Yeungnam University, Daegu 42415, Korea;
| | - Jeong Ho Lim
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Syed Sayeed Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Shahid Ali
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
| | - Khurshid Ahmad
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence: (K.A.); (I.C.)
| | - Inho Choi
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea; (E.J.L.); (S.S.); (J.H.L.); (S.S.A.); (S.A.)
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence: (K.A.); (I.C.)
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36
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Shin MK, Lee B, Kim ST, Yoo JS, Sung JS. Designing a Novel Functional Peptide With Dual Antimicrobial and Anti-inflammatory Activities via in Silico Methods. Front Immunol 2022; 13:821070. [PMID: 35432369 PMCID: PMC9010562 DOI: 10.3389/fimmu.2022.821070] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/10/2022] [Indexed: 01/31/2023] Open
Abstract
As spider venom is composed of various bioactive substances, it can be utilized as a platform for discovering future therapeutics. Host defense peptides are great candidates for developing novel antimicrobial agents due to their multifunctional properties. In this study, novel functional peptides were rationally designed to have dual antibacterial and anti-inflammatory activities with high cytocompatibility. Based on a template sequence from the transcriptome of spider Agelena koreana, a series of via in silico analysis were conducted, incorporating web-based machine learning tools along with the alteration of amino acid residues. Two peptides, Ak-N’ and Ak-N’m, were designed and were subjected to functional validation. The peptides inhibited gram-negative and gram-positive bacteria by disrupting the outer and bacterial cytoplasmic membrane. Moreover, the peptides down-regulated the expression of pro-inflammatory mediators, tumor necrosis factor-α, interleukin (IL)-1β, and IL6. Along with low cytotoxicity, Ak-N’m was shown to interact with macrophage surface receptors, inhibiting both Myeloid differentiation primary response 88-dependent and TIR-domain-containing adapter-inducing interferon-β-dependent pathways of Toll-like receptor 4 signaling on lipopolysaccharide-stimulated THP-1-derived macrophages. Here, we rationally designed functional peptides based on the suggested in silico strategy, demonstrating new insights for utilizing biological resources as well as developing therapeutic agents with enhanced properties.
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Affiliation(s)
- Min Kyoung Shin
- Department of Life Science, Dongguk University-Seoul, Goyang, South Korea
| | - Byungjo Lee
- Department of Life Science, Dongguk University-Seoul, Goyang, South Korea
| | - Seung Tae Kim
- Life and Environment Research Institute, Konkuk University, Seoul, South Korea
| | - Jung Sun Yoo
- Animal Resources Division, National Institute of Biological Resources, Incheon, South Korea
| | - Jung-Suk Sung
- Department of Life Science, Dongguk University-Seoul, Goyang, South Korea
- *Correspondence: Jung-Suk Sung,
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37
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Borrajo ML, Alonso MJ. Using nanotechnology to deliver biomolecules from nose to brain - peptides, proteins, monoclonal antibodies and RNA. Drug Deliv Transl Res 2022; 12:862-880. [PMID: 34731414 PMCID: PMC8888512 DOI: 10.1007/s13346-021-01086-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 02/06/2023]
Abstract
There is a growing number of biomolecules, including peptides, proteins, monoclonal antibodies and RNA, that could be potentially used for the treatment of central nervous system (CNS) diseases. However, the realization of their potential is being hampered by the extraordinary difficulties these complex biomolecules have to reach the brain in therapeutically meaningful amounts. Nose-to-brain (N-to-B) delivery is now being investigated as a potential option for the direct transport of biomolecules from the nasal cavity to different brain areas. Here, we discuss how different technological approaches enhance this N-to-B transport, with emphasis on those that have shown a potential for clinical translation. We also analyse how the physicochemical properties of nanocarriers and their modification with cell-penetrating peptides (CPPs) and targeting ligands affect their efficacy as N-to-B carriers for biomolecules.
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Affiliation(s)
- Mireya L Borrajo
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Av. Barcelona s/n, Campus Vida, 15782, Santiago de Compostela, Spain
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Av. Barcelona s/n, Campus Vida, 15782, Santiago de Compostela, Spain.
- Department of Pharmacy and Pharmaceutical Technology, School of Pharmacy, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain.
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38
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Deigin VI, Poluektova EA, Beniashvili AG, Kozin SA, Poluektov YM. Development of Peptide Biopharmaceuticals in Russia. Pharmaceutics 2022; 14:pharmaceutics14040716. [PMID: 35456550 PMCID: PMC9030433 DOI: 10.3390/pharmaceutics14040716] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/07/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Peptides are low-molecular-weight substances that participate in numerous important physiological functions, such as human growth and development, stress, regulation of the emotional state, sexual behavior, and immune responses. Their mechanisms of action are based on receptor–ligand interactions, which result in highly selective effects. These properties and low toxicity enable them to be considered potent drugs. Peptide preparations became possible at the beginning of the 20th century after a method was developed for selectively synthesizing peptides; however, after synthesis of the first peptide drugs, several issues related to increasing the stability, bioavailability, half-life, and ability to move across cell membranes remain unresolved. Here, we briefly review the history of peptide production and development in the biochemical industry and outline potential areas of peptide biopharmaceutical applications and modern approaches for creating pharmaceuticals based on synthetic peptides and their analogs. We also focus on original peptide drugs and the approaches used for their development by the Russian Federation.
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Affiliation(s)
- Vladislav I. Deigin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Moscow, Russia;
| | - Elena A. Poluektova
- Department of Propaedeutics of Internal Diseases, Gastroenterology and Hepatology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia;
| | - Allan G. Beniashvili
- Mental Health Research Center, Federal State Budgetary Scientific Institution, Ministry of Health of the Russian Federation, 115522 Moscow, Russia;
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Yuri M. Poluektov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
- Correspondence: ; Tel.: +7-916-407-7570
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39
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de Oliveira ECL, da Costa KS, Taube PS, Lima AH, Junior CDSDS. Biological Membrane-Penetrating Peptides: Computational Prediction and Applications. Front Cell Infect Microbiol 2022; 12:838259. [PMID: 35402305 PMCID: PMC8992797 DOI: 10.3389/fcimb.2022.838259] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
Peptides comprise a versatile class of biomolecules that present a unique chemical space with diverse physicochemical and structural properties. Some classes of peptides are able to naturally cross the biological membranes, such as cell membrane and blood-brain barrier (BBB). Cell-penetrating peptides (CPPs) and blood-brain barrier-penetrating peptides (B3PPs) have been explored by the biotechnological and pharmaceutical industries to develop new therapeutic molecules and carrier systems. The computational prediction of peptides’ penetration into biological membranes has been emerged as an interesting strategy due to their high throughput and low-cost screening of large chemical libraries. Structure- and sequence-based information of peptides, as well as atomistic biophysical models, have been explored in computer-assisted discovery strategies to classify and identify new structures with pharmacokinetic properties related to the translocation through biomembranes. Computational strategies to predict the permeability into biomembranes include cheminformatic filters, molecular dynamics simulations, artificial intelligence algorithms, and statistical models, and the choice of the most adequate method depends on the purposes of the computational investigation. Here, we exhibit and discuss some principles and applications of these computational methods widely used to predict the permeability of peptides into biomembranes, exhibiting some of their pharmaceutical and biotechnological applications.
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Affiliation(s)
- Ewerton Cristhian Lima de Oliveira
- Institute of Technology, Federal University of Pará, Belém, Brazil
- *Correspondence: Kauê Santana da Costa, ; Ewerton Cristhian Lima de Oliveira,
| | - Kauê Santana da Costa
- Laboratory of Computational Simulation, Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
- *Correspondence: Kauê Santana da Costa, ; Ewerton Cristhian Lima de Oliveira,
| | - Paulo Sérgio Taube
- Laboratory of Computational Simulation, Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
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40
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Ahmed S, Pande AH, Sharma SS. Therapeutic potential of ApoE-mimetic peptides in CNS disorders: Current perspective. Exp Neurol 2022; 353:114051. [DOI: 10.1016/j.expneurol.2022.114051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/23/2022] [Accepted: 03/14/2022] [Indexed: 02/07/2023]
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41
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Trisciuzzi D, Siragusa L, Baroni M, Autiero I, Nicolotti O, Cruciani G. Getting Insights into Structural and Energetic Properties of Reciprocal Peptide-Protein Interactions. J Chem Inf Model 2022; 62:1113-1125. [PMID: 35148095 DOI: 10.1021/acs.jcim.1c01343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptide-protein interactions play a key role for many cellular and metabolic processes involved in the onset of largely spread diseases such as cancer and neurodegenerative pathologies. Despite the progress in the structural characterization of peptide-protein interfaces, the in-depth knowledge of the molecular details behind their interactions is still a daunting task. Here, we present the first comprehensive in silico morphological and energetic study of peptide binding sites by focusing on both peptide and protein standpoints. Starting from the PixelDB database, a nonredundant benchmark collection of high-quality 3D crystallographic structures of peptide-protein complexes, a classification analysis of the most representative categories based on the nature of each cocrystallized peptide has been carried out. Several interpretable geometrical and energetic descriptors have been computed both from peptide and target protein sides in the attempt to unveil physicochemical and structural causative correlations. Finally, we investigated the most frequent peptide-protein residue pairs at the binding interface and made extensive energetic analyses, based on GRID MIFs, with the aim to study the peptide affinity-enhancing interactions to be further exploited in rational drug design strategies.
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Affiliation(s)
- Daniela Trisciuzzi
- Department of Pharmacy, Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy.,Molecular Horizon s.r.l., Via Montelino, 30, 06084 Bettona (PG), Italy
| | - Lydia Siragusa
- Molecular Horizon s.r.l., Via Montelino, 30, 06084 Bettona (PG), Italy.,Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Massimo Baroni
- Molecular Discovery Ltd., Kinetic Business Centre, Theobald Street, Elstree, Borehamwood, Hertfordshire WD6 4PJ, United Kingdom
| | - Ida Autiero
- Molecular Horizon s.r.l., Via Montelino, 30, 06084 Bettona (PG), Italy.,National Research Council, Institute of Biostructures and Bioimaging, 80138 Naples, Italy
| | - Orazio Nicolotti
- Department of Pharmacy, Pharmaceutical Sciences, Università degli Studi di Bari "Aldo Moro", 70125 Bari, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, via Elce di Sotto, 8, 06123 Perugia (PG), Italy
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42
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Relevance of AIF/CypA Lethal Pathway in SH-SY5Y Cells Treated with Staurosporine. Int J Mol Sci 2021; 23:ijms23010265. [PMID: 35008690 PMCID: PMC8745523 DOI: 10.3390/ijms23010265] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/18/2022] Open
Abstract
The AIF/CypA complex exerts a lethal activity in several rodent models of acute brain injury. Upon formation, it translocates into the nucleus of cells receiving apoptotic stimuli, inducing chromatin condensation, DNA fragmentation, and cell death by a caspase-independent mechanism. Inhibition of this complex in a model of glutamate-induced cell death in HT-22 neuronal cells by an AIF peptide (AIF(370-394)) mimicking the binding site on CypA, restores cell survival and prevents brain injury in neonatal mice undergoing hypoxia-ischemia without apparent toxicity. Here, we explore the effects of the peptide on SH-SY5Y neuroblastoma cells stimulated with staurosporine (STS), a cellular model widely used to study Parkinson’s disease (PD). This will pave the way to understanding the role of the complex and the potential therapeutic efficacy of inhibitors in PD. We find that AIF(370-394) confers resistance to STS-induced apoptosis in SH-SY5Y cells similar to that observed with CypA silencing and that the peptide works on the AIF/CypA translocation pathway and not on caspases activation. These findings suggest that the AIF/CypA complex is a promising target for developing novel therapeutic strategies against PD.
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43
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Guo Y, Hu Z, Wang Z. Recent Advances in the Application Peptide and Peptoid in Diagnosis Biomarkers of Alzheimer's Disease in Blood. Front Mol Neurosci 2021; 14:778955. [PMID: 35002620 PMCID: PMC8733658 DOI: 10.3389/fnmol.2021.778955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases with irreversible damage of the brain and a continuous pathophysiological process. Early detection and accurate diagnosis are essential for the early intervention of AD. Precise detection of blood biomarkers related to AD could provide a shortcut to identifying early-stage patients before symptoms. In recent years, targeting peptides or peptoids have been chosen as recognition elements in nano-sensors or fluorescence detection to increase the targeting specificity, while peptide-based probes were also developed considering their specific advantages. Peptide-based sensors and probes have been developed according to different strategies, such as natural receptors, high-throughput screening, or artificial design for AD detection. This review will briefly summarize the recent developments and trends of AD diagnosis platforms based on peptide and peptoid as recognition elements and provide insights into the application of peptide and peptoid with different sources and characteristics in the diagnosis of AD biomarkers.
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Affiliation(s)
- Yuxin Guo
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiyuan Hu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, China
| | - Zihua Wang
- Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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44
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Wahiduzzaman, Kumar V, Anjum F, Shafie A, Elasbali AM, Islam A, Ahmad F, Hassan MI. Delineating the Aggregation-Prone Hotspot Regions (Peptides) in the Human Cu/Zn Superoxide Dismutase 1. ACS OMEGA 2021; 6:33985-33994. [PMID: 34926946 PMCID: PMC8675042 DOI: 10.1021/acsomega.1c05321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 11/19/2021] [Indexed: 02/29/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, incurable neurodegenerative disease described by progressive degeneration of motor neurons. The most common familial form of ALS (fALS) has been associated with mutations in the Cu/Zn superoxide dismutase (SOD1) gene. Mutation-induced misfolding and aggregation of SOD1 is often found in ALS patients. In this work, we probe the aggregation properties of peptides derived from the SOD1. To examine the source of SOD1 aggregation, we have employed a computational algorithm to identify four peptides from the SOD1 protein sequence that aggregates into a fibril. Aided by computational algorithms, we identified four peptides likely involved in SOD1 fibrillization. These four aggregation-prone peptides were 14VQGIINFE21, 30KVWGSIKGL38, 101DSVISLS107, and 147GVIGIAQ153. In addition, the formation of fibril propensities from the identified peptides was investigated through different biophysical techniques. The atomic structures of two fibril-forming peptides from the C-terminal SOD1 showed that the steric zippers formed by 101DSVISLS107 and 147GVIGIAQ153 vary in their arrangement. We also discovered that fALS mutations in the peptide 147GVIGIAQ153 increased the fibril-forming propensity and altered the steric zipper's packing. Thus, our results suggested that the C-terminal peptides of SOD1 have a central role in amyloid formation and might be involved in forming the structural core of SOD1 aggregation observed in vivo.
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Affiliation(s)
- Wahiduzzaman
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Vijay Kumar
- Amity
Institute of Neuropsychology & Neurosciences, Amity University, Noida, UP 201303, India
| | - Farah Anjum
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Alaa Shafie
- Department
of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Abdelbaset Mohamed Elasbali
- Clinical
Laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka 72388, Saudi Arabia
| | - Asimul Islam
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Faizan Ahmad
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Md. Imtaiyaz Hassan
- Centre
for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
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45
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Oboh G, Busari GM, Ademosun AO, Oyeleye SI. Effect of dietary inclusion of Fireweed (
Crassocephalum crepidioides
) on behavioural patterns, memory indices, and activities of cholinergic and monoaminergic enzymes in a fruit fly (
Drosophila melanogaster
) model of Alzheimer's disease. FOOD FRONTIERS 2021. [DOI: 10.1002/fft2.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Ganiyu Oboh
- Functional Foods and Nutraceuticals Unit Department of Biochemistry Federal University of Technology Akure Ondo State Nigeria
| | - Gbemisola Margaret Busari
- Functional Foods and Nutraceuticals Unit Department of Biochemistry Federal University of Technology Akure Ondo State Nigeria
| | - Ayokunle Olubode Ademosun
- Functional Foods and Nutraceuticals Unit Department of Biochemistry Federal University of Technology Akure Ondo State Nigeria
| | - Sunday Idowu Oyeleye
- Functional Foods and Nutraceuticals Unit Department of Biochemistry Federal University of Technology Akure Ondo State Nigeria
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46
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Romagnoli A, Di Marino D. The Use of Peptides in the Treatment of Fragile X Syndrome: Challenges and Opportunities. Front Psychiatry 2021; 12:754485. [PMID: 34803767 PMCID: PMC8599826 DOI: 10.3389/fpsyt.2021.754485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 01/17/2023] Open
Abstract
Fragile X Syndrome (FXS) is the most frequent cause of inherited intellectual disabilities and autism spectrum disorders, characterized by cognitive deficits and autistic behaviors. The silencing of the Fmr1 gene and consequent lack of FMRP protein, is the major contribution to FXS pathophysiology. FMRP is an RNA binding protein involved in the maturation and plasticity of synapses and its absence culminates in a range of morphological, synaptic and behavioral phenotypes. Currently, there are no approved medications for the treatment of FXS, with the approaches under study being fairly specific and unsatisfying in human trials. Here we propose peptides/peptidomimetics as candidates in the pharmacotherapy of FXS; in the last years this class of molecules has catalyzed the attention of pharmaceutical research, being highly selective and well-tolerated. Thanks to their ability to target protein-protein interactions (PPIs), they are already being tested for a wide range of diseases, including cancer, diabetes, inflammation, Alzheimer's disease, but this approach has never been applied to FXS. As FXS is at the forefront of efforts to develop new drugs and approaches, we discuss opportunities, challenges and potential issues of peptides/peptidomimetics in FXS drug design and development.
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Affiliation(s)
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Ancona, Italy
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47
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Peptide-Based Vaccines for Neurodegenerative Diseases: Recent Endeavors and Future Perspectives. Vaccines (Basel) 2021; 9:vaccines9111278. [PMID: 34835209 PMCID: PMC8622585 DOI: 10.3390/vaccines9111278] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/25/2021] [Accepted: 10/30/2021] [Indexed: 02/06/2023] Open
Abstract
The development of peptide-based vaccines for treating human neurodegenerative diseases has been the eventual aim of many research endeavors, although no active immunotherapies have been approved for clinical use till now. A typical example of such endeavors is the effort to develop vaccines for Alzheimer’s disease based on the beta-amyloid peptide, which continues to be intensively investigated despite previous setbacks. In this paper, recent developments in peptide-based vaccines which target beta-amyloid as well as tau protein and α-synuclein are presented. Particular focus has been directed toward peptide epitopes and formulation systems selected/developed and employed to enhance vaccine efficacy and safety. Results from both, human clinical trials and animal preclinical studies conducted mainly in transgenic mice have been included. Future perspectives on the topic are also briefly discussed.
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48
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Oyster-Derived Tyr-Ala (YA) Peptide Prevents Lipopolysaccharide/D-Galactosamine-Induced Acute Liver Failure by Suppressing Inflammatory, Apoptotic, Ferroptotic, and Pyroptotic Signals. Mar Drugs 2021; 19:md19110614. [PMID: 34822485 PMCID: PMC8624370 DOI: 10.3390/md19110614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
Models created by the intraperitoneal injection of lipopolysaccharide (LPS) and D-galactosamine (D-GalN) have been widely used to study the pathogenesis of human acute liver failure (ALF) and drug development. Our previous study reported that oyster (Crassostrea gigas) hydrolysate (OH) had a hepatoprotective effect in LPS/D-GalN-injected mice. This study was performed to identify the hepatoprotective effect of the tyrosine-alanine (YA) peptide, the main component of OH, in a LPS/D-GalN-injected ALF mice model. We analyzed the effect of YA on previously known mechanisms of hepatocellular injury in the model. LPS/D-GalN-injected mice showed inflammatory, apoptotic, ferroptotic, and pyroptotic liver injury. The pre-administration of YA (10 mg/kg or 50 mg/kg) significantly reduced the liver damage factors. The hepatoprotective effect of YA was higher in the 50 mg/kg YA pre-administered group than in the 10 mg/kg YA pre-administered group. These results showed that YA had a hepatoprotective effect by reducing inflammation, apoptosis, ferroptosis, and pyroptosis in the LPS/D-GalN-injected ALF mouse model. We suggest that YA can be used as a functional peptide for the prevention of acute liver injury.
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49
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Beutgen VM, Schmelter C, Pfeiffer N, Grus FH. Contribution of the Commensal Microflora to the Immunological Homeostasis and the Importance of Immune-Related Drug Development for Clinical Applications. Int J Mol Sci 2021; 22:8896. [PMID: 34445599 PMCID: PMC8396286 DOI: 10.3390/ijms22168896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/16/2022] Open
Abstract
Not long ago, self-reactive immune activity was considered as pathological trait. A paradigm shift has now led to the recognition of autoimmune processes as part of natural maintenance of molecular homeostasis. The immune system is assigned further roles beneath the defense against pathogenic organisms. Regarding the humoral immune system, the investigation of natural autoantibodies that are frequently found in healthy individuals has led to further hypotheses involving natural autoimmunity in other processes as the clearing of cellular debris or decrease in inflammatory processes. However, their role and origin have not been entirely clarified, but accumulating evidence links their formation to immune reactions against the gut microbiome. Antibodies targeting highly conserved proteins of the commensal microflora are suggested to show self-reactive properties, following the paradigm of the molecular mimicry. Here, we discuss recent findings, which demonstrate potential links of the commensal microflora to the immunological homeostasis and highlight the possible implications for various diseases. Furthermore, specific components of the immune system, especially antibodies, have become a focus of attention for the medical management of various diseases and provide attractive treatment options in the future. Nevertheless, the development and optimization of such macromolecules still represents a very time-consuming task, shifting the need to more medical agents with simple structural properties and low manufacturing costs. Synthesizing only the biologically active sites of antibodies has become of great interest for the pharmaceutical industry and offers a wide range of therapeutic application areas as it will be discussed in the present review article.
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Affiliation(s)
| | | | | | - Franz H. Grus
- Experimental and Translational Ophthalmology, Department of Ophthalmology, University Medical Center, 55131 Mainz, Germany; (V.M.B.); (C.S.); (N.P.)
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50
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B3Pred: A Random-Forest-Based Method for Predicting and Designing Blood-Brain Barrier Penetrating Peptides. Pharmaceutics 2021; 13:pharmaceutics13081237. [PMID: 34452198 PMCID: PMC8399279 DOI: 10.3390/pharmaceutics13081237] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/07/2021] [Accepted: 07/14/2021] [Indexed: 12/14/2022] Open
Abstract
The blood–brain barrier is a major obstacle in treating brain-related disorders, as it does not allow the delivery of drugs into the brain. We developed a method for predicting blood–brain barrier penetrating peptides to facilitate drug delivery into the brain. These blood–brain barrier penetrating peptides (B3PPs) can act as therapeutics, as well as drug delivery agents. We trained, tested, and evaluated our models on blood–brain barrier peptides obtained from the B3Pdb database. First, we computed a wide range of peptide features. Then, we selected relevant peptide features. Finally, we developed numerous machine-learning-based models for predicting blood–brain barrier peptides using the selected features. The random-forest-based model performed the best with respect to the top 80 selected features and achieved a maximal 85.08% accuracy with an AUROC of 0.93. We also developed a webserver, B3pred, that implements our best models. It has three major modules that allow users to predict/design B3PPs and scan B3PPs in a protein sequence.
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