1
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Mudgil P, Gan CY, Yap PG, Redha AA, Alsaadi RHS, Mohteshamuddin K, Aguilar-Toalá JE, Vidal-Limon AM, Liceaga AM, Maqsood S. Exploring the dipeptidyl peptidase IV inhibitory potential of probiotic-fermented milk: An in vitro and in silico comprehensive investigation into peptides from milk of different farm animals. J Dairy Sci 2024:S0022-0302(24)01060-9. [PMID: 39122154 DOI: 10.3168/jds.2024-25108] [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: 04/30/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024]
Abstract
Bioactive peptides produced via enzymatic hydrolysis have been widely investigated for their dipeptidyl peptidase-IV (DPP-IV) inhibitory properties. However, deficit of studies on fermentation as a mean to produce DPP-IV inhibitory peptides prompted us to draw a comparative study on DPP-IV inhibitory peptides generated from cow, camel, goat, and sheep milk using probiotic fermentation. Further, peptide identification, in silico molecular interactions with DPP-IV, and ensemble docking were performed. Results obtained suggested that goat milk consistently exhibited higher hydrolysis than other milk types. Further, Pediococcus pentosaceus (PP-957) emerged as a potent probiotic, with significantly lower DPP-IV-IC50 values 0.17, 0.12, and 0.25 µg/mL protein equivalent in fermented cow, camel, and goat milk, respectively. Overall, peptides (RPPPPVAM, CHNLDELKDTR, and VLSLSQPK) exhibited strong binding affinity with binding energies of -9.31, -9.18 and -8.9 Kcal·mol-1, respectively, suggesting their potential role as DPP-IV inhibitors. Overall, this study, offers valuable information toward antidiabetic benefits of fermented milk products via inhibition of DPP-IV.
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Affiliation(s)
- Priti Mudgil
- Food Science Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates..
| | - Chee-Yuen Gan
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
| | - Pei-Gee Yap
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
| | - Ali Ali Redha
- The Department of Public Health and Sport Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter EX1 2 LU, United Kingdom; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QDPP-IVFI), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Reem H Sultan Alsaadi
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - Khaja Mohteshamuddin
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates
| | - José E Aguilar-Toalá
- Departamento de Ciencias de la Alimentación. División de Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana Unidad Lerma. Av. de las Garzas 10. Col. El Panteón, Lerma de Villada 52005, Estado de México, Mexico
| | - Abraham M Vidal-Limon
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Carretera Antigua a Coatepec 351, El Haya, Xalapa 91073, Veracruz, Mexico
| | - Andrea M Liceaga
- Protein Chemistry and Bioactive Peptides Laboratory. Department of Food Science, Purdue University, 745 Agriculture Mall Dr., West Lafayette, IN 47907, USA
| | - Sajid Maqsood
- Food Science Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain, 15551, United Arab Emirates.; Zayed Centre of Health Science, United Arab Emirates University, Al-Ain 15551, United Arab Emirates.
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2
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Tian J, Zhang L, La X, An Y, Fan X, Li Z. QPH-FR: A Novel Quinoa Peptide Enhances Chemosensitivity by Targeting Leucine-Rich Repeat-Containing G Protein-Coupled Receptor 5 in Colorectal Cancer. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17417-17430. [PMID: 39047262 DOI: 10.1021/acs.jafc.4c03761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Chemoresistance is one of the difficulties in the treatment of colorectal cancer (CRC), and the enhanced stemness of tumor cells is the underlying contributing factor. Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5) is a classical marker of CRC stem cells and can be an important potential target for CRC chemotherapy. Quinoa, a protein-rich plant, offers potential as a source of high-quality active peptides. Novelly, the study obtained quinoa protein hydrolysate (QPH) from whole quinoa grains by simulated digestion. In vivo experiments revealed that the tumor volume in the 5-FU+QPH group decreased from 145.90 ± 13.35 to 94.49 ± 13.05 mm3 in the 5-FU group, suggesting that QPH enhances the chemosensitivity of CRC. Further, the most effective peptide QPH-FR from 631 peptides in QPH was screened by activity prediction, molecular docking, and experimental validation. Mechanistically, QPH-FR competitively suppressed the formation of the LGR5/RSPO1 complex by binding to LGR5, causing RNF43/ZNRF3 to ubiquitinate the FZD receptor, thereby suppressing the Wnt/β-catenin signaling pathway and exerting stemness inhibition. In summary, the study proposes that a novel peptide QPH-FR from quinoa elucidates the mechanism by which QPH-FR targets LGR5 to enhance chemosensitivity, providing theoretical support for the development of chemotherapeutic adjuvant drugs based on plant peptides.
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Affiliation(s)
- Jinmiao Tian
- Key Laboratory of Chemical Biology and Molecular Engineering of the National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Lichao Zhang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Xiaoqin La
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Yuxuan An
- Key Laboratory of Chemical Biology and Molecular Engineering of the National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Xiaxia Fan
- Key Laboratory of Chemical Biology and Molecular Engineering of the National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
| | - Zhuoyu Li
- Key Laboratory of Chemical Biology and Molecular Engineering of the National Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China
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3
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Wang J, Koirala K, Do HN, Miao Y. PepBinding: A Workflow for Predicting Peptide Binding Structures by Combining Peptide Docking and Peptide Gaussian Accelerated Molecular Dynamics Simulations. J Phys Chem B 2024; 128:7332-7340. [PMID: 39041172 DOI: 10.1021/acs.jpcb.4c02047] [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: 07/24/2024]
Abstract
Predicting protein-peptide interactions is crucial for understanding peptide binding processes and designing peptide drugs. However, traditional computational modeling approaches face challenges in accurately predicting peptide-protein binding structures due to the slow dynamics and high flexibility of the peptides. Here, we introduce a new workflow termed "PepBinding" for predicting peptide binding structures, which combines peptide docking, all-atom enhanced sampling simulations using the Peptide Gaussian accelerated Molecular Dynamics (Pep-GaMD) method, and structural clustering. PepBinding has been demonstrated on seven distinct model peptides. In peptide docking using HPEPDOCK, the peptide backbone root-mean-square deviations (RMSDs) of their bound conformations relative to X-ray structures ranged from 3.8 to 16.0 Å, corresponding to the medium to inaccurate quality models according to the Critical Assessment of PRediction of Interactions (CAPRI) criteria. The Pep-GaMD simulations performed for only 200 ns significantly improved the docking models, resulting in five medium and two acceptable quality models. Therefore, PepBinding is an efficient workflow for predicting peptide binding structures and is publicly available at https://github.com/MiaoLab20/PepBinding.
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Affiliation(s)
- Jinan Wang
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kushal Koirala
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Hung N Do
- Computational Biology Program, Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yinglong Miao
- Computational Medicine Program and Department of Pharmacology, University of North Carolina - Chapel Hill, Chapel Hill, North Carolina 27599, United States
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4
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Zhang Y, Ren EF, Wen T, Lyu S, Gai L, Chen S, Li K, Han Z, Niu F, Niu D. Investigation into potential allergenicity of DBD plasma-treated casein digestion products based on immunoglobulin E linear epitopes and the sensitized-cell model. Food Chem 2024; 447:138940. [PMID: 38484545 DOI: 10.1016/j.foodchem.2024.138940] [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: 11/26/2023] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
The study aimed to investigate the allergenicity change in casein treated with dielectric barrier discharge (DBD) plasma during in vitro simulated digestion, focusing on the immunoglobulin E (IgE) linear epitopes and utilizing a sensitized-cell model. Results indicated that prior treatment with DBD plasma treatment (4 min) before simulated digestion led to a 10.5% reduction in the IgE-binding capacity of casein digestion products. Moreover, the release of biologically active substances induced from KU812 cells, including β-HEX release rate, human histamine, IL-4, IL-6, and TNF-α, decreased by 2.1, 28.1, 20.6, 11.6, and 17.3%, respectively. Through a combined analysis of LC-MS/MS and immunoinformatics tools, it was revealed that DBD plasma treatment promoted the degradation of the IgE linear epitopes of casein during digestion, particularly those located in the α-helix region of αs1-CN and αs2-CN. These findings suggest that DBD plasma treatment prior to digestion may alleviate casein allergic reactions.
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Affiliation(s)
- Yongniu Zhang
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Er-Fang Ren
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Wen
- Guangxi Zhuang Autonomous Region Testing Institute of Product Quality, Nanning 530200, China
| | - Shijun Lyu
- Guangxi Zhuang Autonomous Region Testing Institute of Product Quality, Nanning 530200, China
| | - Lili Gai
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Siyu Chen
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Kai Li
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Zhong Han
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China
| | - Fuge Niu
- Food Safety Key Lab of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Debao Niu
- College of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China.
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5
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Li H, Wang J, Zhang B, Guo Y. Preliminary exploration of the anti-ovarian cancer activity of peptides derived from bovine bone collagen hydrolysate and its related mechanisms. Int J Biol Macromol 2024; 277:134198. [PMID: 39084419 DOI: 10.1016/j.ijbiomac.2024.134198] [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: 12/25/2023] [Revised: 07/24/2024] [Accepted: 07/25/2024] [Indexed: 08/02/2024]
Abstract
Ovarian cancer, a malignant tumor that poses a significant threat to women's health, has seen a rise in incidence, prompting the urgent need for more effective treatment. This study primarily aimed to explore the potential of bovine collagen peptides in inhibiting ovarian cancer. The investigation in this study began with the identification of 268 peptide sequences through LC-MS/MS, followed by a screening process using molecular docking techniques to identify potential peptides capable of binding to EGFR. Subsequently, a series of experiments were performed, demonstrating the inhibitory effects of the peptide GPAGADGDRGEAGPAGPAGPAGPR on the proliferation of ovarian cancer cells. Transcriptomic analysis further revealed that this peptide can regulate cholesterol metabolism in ovarian cancer cells. Finally, a combination of time-resolved fluorescence resonance energy transfer, isothermal titration calorimetry, molecular docking, and molecular dynamics simulations were utilized to validate the ability of this peptide to bind to the epidermal growth factor receptor (EGFR) and impede the binding of epidermal growth factor (EGF) and EGFR.
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Affiliation(s)
- Hanfeng Li
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China; School of Chemical Sciences, University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China.
| | - Jianing Wang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Bing Zhang
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yanchuan Guo
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China; School of Chemical Sciences, University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China.
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6
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Rendon-Marin S, Ruíz-Saenz J. Universal peptide-based potential vaccine design against canine distemper virus (CDV) using a vaccinomic approach. Sci Rep 2024; 14:16605. [PMID: 39026076 PMCID: PMC11258135 DOI: 10.1038/s41598-024-67781-5] [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: 12/19/2023] [Accepted: 07/16/2024] [Indexed: 07/20/2024] Open
Abstract
Canine distemper virus (CDV) affects many domestic and wild animals. Variations among CDV genome linages could lead to vaccination failure. To date, there are several vaccine alternatives, such as a modified live virus and a recombinant vaccine; however, most of these alternatives are based on the ancestral strain Onderstepoort, which has not been circulating for years. Vaccine failures and the need to update vaccines have been widely discussed, and the development of new vaccine candidates is necessary to reduce circulation and mortality. Current vaccination alternatives cannot be used in wildlife animals due to the lack of safety data for most of the species, in addition to the insufficient immune response against circulating strains worldwide in domestic species. Computational tools, including peptide-based therapies, have become essential for developing new-generation vaccines for diverse models. In this work, a peptide-based vaccine candidate with a peptide library derived from CDV H and F protein consensus sequences was constructed employing computational tools. The molecular docking and dynamics of the selected peptides with canine MHC-I and MHC-II and with TLR-2 and TLR-4 were evaluated. In silico safety was assayed through determination of antigenicity, allergenicity, toxicity potential, and homologous canine peptides. Additionally, in vitro safety was also evaluated through cytotoxicity in cell lines and canine peripheral blood mononuclear cells (cPBMCs) and through a hemolysis potential assay using canine red blood cells. A multiepitope CDV polypeptide was constructed, synthetized, and evaluated in silico and in vitro by employing the most promising peptides for comparison with single CDV immunogenic peptides. Our findings suggest that predicting immunogenic CDV peptides derived from most antigenic CDV proteins could aid in the development of new vaccine candidates, such as multiple single CDV peptides and multiepitope CDV polypeptides, that are safe in vitro and optimized in silico. In vivo studies are being conducted to validate potential vaccines that may be effective in preventing CDV infection in domestic and wild animals.
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Affiliation(s)
- Santiago Rendon-Marin
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, sede Bucaramanga, Bucaramanga, Colombia
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
| | - Julián Ruíz-Saenz
- Grupo de Investigación en Ciencias Animales - GRICA, Facultad de Medicina Veterinaria y Zootecnia, Universidad Cooperativa de Colombia, sede Bucaramanga, Bucaramanga, Colombia.
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7
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Zhou Y, Cai G, Wang Y, Guo Y, Yang Z, Wang A, Chen Y, Li X, Chen X, Hu Z, Wang Z. Microarray Chip-Based High-Throughput Screening of Neurofilament Light Chain Self-Assembling Peptide for Noninvasive Monitoring of Alzheimer's Disease. ACS NANO 2024; 18:18160-18175. [PMID: 38940834 DOI: 10.1021/acsnano.3c09642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Alzheimer's disease (AD) starts decades before cognitive symptoms develop. Easily accessible and cost-effective biomarkers that accurately reflect AD pathology are essential for both monitoring and therapeutics of AD. Neurofilament light chain (NfL) levels in blood and cerebrospinal fluid are increased in AD more than a decade before the expected onset, thus providing one of the most promising blood biomarkers for monitoring of AD. The clinical practice of employing single-molecule array (Simoa) technology for routine use in patient care is limited by the high costs. Herein, we developed a microarray chip-based high-throughput screening method and screened an attractive self-assembling peptide targeting NfL. Through directly "imprinting" and further analyzing the sequences, morphology, and affinity of the identified self-assembling peptides, the Pep-NfL peptide nanosheet with high binding affinity toward NfL (KD = 1.39 × 10-9 mol/L), high specificity, and low cost was characterized. The superior binding ability of Pep-NfL was confirmed in AD mouse models and cell lines. In the clinical setting, the Pep-NfL peptide nanosheets hold great potential for discriminating between patients with AD (P < 0.001, n = 37), mild cognitive impairment (P < 0.05, n = 26), and control groups (n = 30). This work provides a high-throughput, high-sensitivity, and economical system for noninvasive tracking of AD to monitor neurodegeneration at different stages of disease. The obtained Pep-NfL peptide nanosheet may be useful for assessing dynamic changes in plasma NfL concentrations to evaluate disease-modifying therapies as a surrogate end point of neurodegeneration in clinical trials.
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Affiliation(s)
- Ying Zhou
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Guoen Cai
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou 350001, China
| | - Yuanzhuo Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuxin Guo
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhimin Yang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Anqi Wang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Yongshou Chen
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xuejie Li
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Xiaochun Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou 350001, China
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou 350001, China
| | - Zhiyuan Hu
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- School of Nanoscience and Technology, Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Zihua Wang
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350108, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
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8
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Babu N, Freeman BC. Establishing Order Through Disorder by the Hsp90 Molecular Chaperone. J Mol Biol 2024; 436:168460. [PMID: 38301804 PMCID: PMC11211062 DOI: 10.1016/j.jmb.2024.168460] [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: 11/01/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
The Heat Shock Protein 90 (Hsp90) molecular chaperone is a key driver of protein homeostasis (proteostasis) under physiologically normal and stress conditions. In eukaryotes, Hsp90 is essential and is one of the most abundant proteins in a cell where the chaperone shuttles between the cytoplasm and nucleus to fold, stabilize, and regulate client proteins and protein complexes. Numerous high-throughput screens have mapped the Hsp90 interactome, building a vast network comprising ∼25% of the proteome in budding yeast. How Hsp90 is able to associate with this diverse and large cadre of targets is critical to comprehending how the proteostatic process works. Here, we review recent progress on our understanding of the molecular underpinnings driving Hsp90-client interactions from both the perspective of the targets and Hsp90. In addition to considering the available Hsp90-client structures, we also assessed recently identified Hsp90-client peptide complexes to build a model that justifies how Hsp90 might recognize a wide spectrum of target proteins. In brief, Hsp90 either directly recognizes a site within an intrinsically disordered region (IDR) of a client protein to transiently regulate that client or it associates with an unstructured polypeptide section created by the concerted efforts of multiple chaperones and cochaperones to stably associate with a client. Overall, Hsp90 exploits a common recognition property (i.e., IDR) within diverse clients to support chaperone-actionthereby enabling its central role in proteostasis.
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Affiliation(s)
- Neethu Babu
- University of Illinois, Urbana-Champaign Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA
| | - Brian C Freeman
- University of Illinois, Urbana-Champaign Department of Cell and Developmental Biology, 601 S. Goodwin Avenue, Urbana, IL 61801, USA.
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9
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Pawnikar S, Magenheimer BS, Joshi K, Munoz EN, Haldane A, Maser RL, Miao Y. Activation of Polycystin-1 Signaling by Binding of Stalk-derived Peptide Agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.06.574465. [PMID: 38260358 PMCID: PMC10802338 DOI: 10.1101/2024.01.06.574465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Polycystin-1 (PC1) is the membrane protein product of the PKD1 gene whose mutation is responsible for 85% of the cases of autosomal dominant polycystic kidney disease (ADPKD). ADPKD is primarily characterized by the formation of renal cysts and potential kidney failure. PC1 is an atypical G protein-coupled receptor (GPCR) consisting of 11 transmembrane helices and an autocatalytic GAIN domain that cleaves PC1 into extracellular N-terminal (NTF) and membrane-embedded C-terminal (CTF) fragments. Recently, signaling activation of the PC1 CTF was shown to be regulated by a stalk tethered agonist (TA), a distinct mechanism observed in the adhesion GPCR family. A novel allosteric activation pathway was elucidated for the PC1 CTF through a combination of Gaussian accelerated molecular dynamics (GaMD), mutagenesis and cellular signaling experiments. Here, we show that synthetic, soluble peptides with 7 to 21 residues derived from the stalk TA, in particular, peptides including the first 9 residues (p9), 17 residues (p17) and 21 residues (p21) exhibited the ability to re-activate signaling by a stalkless PC1 CTF mutant in cellular assays. To reveal molecular mechanisms of stalk peptide-mediated signaling activation, we have applied a novel Peptide GaMD (Pep-GaMD) algorithm to elucidate binding conformations of selected stalk peptide agonists p9, p17 and p21 to the stalkless PC1 CTF. The simulations revealed multiple specific binding regions of the stalk peptide agonists to the PC1 protein including an "intermediate" bound yet inactive state. Our Pep-GaMD simulation findings were consistent with the cellular assay experimental data. Binding of peptide agonists to the TOP domain of PC1 induced close TOP-putative pore loop interactions, a characteristic feature of the PC1 CTF signaling activation mechanism. Using sequence covariation analysis of PC1 homologs, we further showed that the peptide binding regions were consistent with covarying residue pairs identified between the TOP domain and the stalk TA. Therefore, structural dynamic insights into the mechanisms of PC1 activation by stalk-derived peptide agonists have enabled an in-depth understanding of PC1 signaling. They will form a foundation for development of PC1 as a therapeutic target for the treatment of ADPKD.
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Affiliation(s)
- Shristi Pawnikar
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66047
| | - Brenda S. Magenheimer
- Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160
| | - Keya Joshi
- Department of Pharmacology and Computational Medicine Program, University of North Carolina – Chapel Hill, Chapel Hill, NC 27599
| | - Ericka Nevarez Munoz
- Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160
| | - Allan Haldane
- Dept of Physics, and Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA 19122
| | - Robin L. Maser
- Departments of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
- Clinical Laboratory Sciences, University of Kansas Medical Center, Kansas City, KS 66160
- The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160
| | - Yinglong Miao
- Department of Pharmacology and Computational Medicine Program, University of North Carolina – Chapel Hill, Chapel Hill, NC 27599
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10
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Park S, Kim MA, Sohn YC. Characterization of myoinhibitory peptide signaling system and its implication in larval metamorphosis and spawning behavior in Pacific abalone. Gen Comp Endocrinol 2024; 353:114521. [PMID: 38621462 DOI: 10.1016/j.ygcen.2024.114521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/15/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Myoinhibitory peptides (MIPs) affect various physiological functions, including juvenile hormone signaling, muscle contraction, larval development, and reproduction in invertebrates. Although MIPs are ligands for MIP and/or sex peptide receptors (MIP/SPRs) in diverse arthropods and model organisms belonging to Lophotrochozoa, the MIP signaling system has not yet been fully investigated in mollusks. In this study, we identified the MIP signaling system in the Pacific abalone Haliotis discus hannai (Hdh). Similar to the invertebrate MIPs, a total of eight paracopies of MIPs (named Hdh-MIP1 to Hdh-MIP8), harboring a WX5-7Wamide motif, except for Hdh-MIP2, were found in the Hdh-MIP precursor. Furthermore, we characterized a functional Hdh-MIPR, which responded to the Hdh-MIPs, except for Hdh-MIP2, possibly linked with the PKC/Ca2+ and PKA/cAMP signaling pathways. Hdh-MIPs delayed larval metamorphosis but increased the spawning behavior. These results suggest that the Hdh-MIP signaling system provides insights into the unique function of MIP in invertebrates.
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Affiliation(s)
- Sungwoo Park
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Mi Ae Kim
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea.
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11
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Samman N, Mohabatkar H, Behbahani M, Ganjlikhani Hakemi M. Bioinformatics design of a peptide vaccine containing sarcoma antigen NY-SAR-35 epitopes against breast cancer and evaluation of its immunological function in BALB/c mouse model. PLoS One 2024; 19:e0306117. [PMID: 38923980 PMCID: PMC11207152 DOI: 10.1371/journal.pone.0306117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
The development of a cancer vaccine has become an essential focus in the field of medical biotechnology and immunology. In our study, the NY-SAR-35 cancer/testis antigen was targeted to design a novel peptide vaccine using bioinformatics tools, and BALB/c mice were used to evaluate the vaccine's immunological function. This evaluation involved assessing peptide-specific IgG levels in the serum via ELISA and measuring the levels of IFN-γ, IL-4, and granzyme B in the supernatant of cultured splenocytes. The final vaccine construct consisted of two T lymphocyte epitopes linked by the AAY linker. This construct displayed high antigenicity, non-allergenicity, non-toxicity, stability, and ability to induce IFN-γ and IL-4. It showed stable dynamics with both human MHC-I and II molecules, as well as mouse MHC-II molecules, and revealed strong Van der Waals and electrostatic energies. Emulsifying our peptide vaccine in incomplete Freund's adjuvant resulted in a remarkable increase in the levels of IgG. The splenocytes of mice that received the combination of peptide and adjuvant displayed a noteworthy increase in IFN-γ, IL-4, and granzyme B secretion. Additionally, their lymphocytes exhibited higher proliferation rates compared to the control group. Our data demonstrated that our vaccine could stimulate a robust immune response, making it a promising candidate for cancer prevention. However, clinical trials are necessary to assess its efficacy in humans.
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Affiliation(s)
- Nour Samman
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mazdak Ganjlikhani Hakemi
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
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12
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Sehgal A, Sharma D, Kaushal N, Gupta Y, Martynova E, Kabwe E, Chandy S, Rizvanov A, Khaiboullina S, Baranwal M. Designing a Conserved Immunogenic Peptide Construct from the Nucleocapsid Protein of Puumala orthohantavirus. Viruses 2024; 16:1030. [PMID: 39066193 PMCID: PMC11281540 DOI: 10.3390/v16071030] [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: 04/14/2024] [Revised: 06/09/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
Puumala orthohantavirus (PUUV) is an emerging zoonotic virus endemic to Europe and Russia that causes nephropathia epidemica, a mild form of hemorrhagic fever with renal syndrome (HFRS). There are limited options for treatment and diagnosis of orthohantavirus infection, making the search for potential immunogenic candidates crucial. In the present work, various bioinformatics tools were employed to design conserved immunogenic peptides containing multiple epitopes of PUUV nucleocapsid protein. Eleven conserved peptides (90% conservancy) of the PUUV nucleocapsid protein were identified. Three conserved peptides containing multiple T and B cell epitopes were selected using a consensus epitope prediction algorithm. Molecular docking using the HPEP dock server demonstrated strong binding interactions between the epitopes and HLA molecules (ten alleles for each class I and II HLA). Moreover, an analysis of population coverage using the IEDB database revealed that the identified peptides have over 90% average population coverage across six continents. Molecular docking and simulation analysis reveal a stable interaction with peptide constructs of chosen immunogenic peptides and Toll-like receptor-4. These computational analyses demonstrate selected peptides' immunogenic potential, which needs to be validated in different experimental systems.
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Affiliation(s)
- Ayushi Sehgal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Diksha Sharma
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Neha Kaushal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Yogita Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
| | - Ekaterina Martynova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Emmanuel Kabwe
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Sara Chandy
- Childs Trust Medical Research Foundation (CTMRF) Kanchi, Chennai 600034, India;
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Svetlana Khaiboullina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan 420008, Russia; (E.M.); (E.K.); (S.K.)
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala 147001, India; (A.S.); (D.S.); (N.K.); (Y.G.)
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13
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Arillotta D, Floresta G, Papanti Pelletier GD, Guirguis A, Corkery JM, Martinotti G, Schifano F. Exploring the Potential Impact of GLP-1 Receptor Agonists on Substance Use, Compulsive Behavior, and Libido: Insights from Social Media Using a Mixed-Methods Approach. Brain Sci 2024; 14:617. [PMID: 38928616 PMCID: PMC11202225 DOI: 10.3390/brainsci14060617] [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: 05/16/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Glucagon-like peptide-1 (GLP-1) is involved in a range of central and peripheral pathways related to appetitive behavior. Hence, this study explored the effects of glucagon-like peptide-1 receptor agonists (GLP-1 RAs) on substance and behavioral addictions, including alcohol, caffeine, nicotine, cannabis, psychostimulants, compulsive shopping, and sex drive/libido. Data were collected from various social platforms. Keywords related to GLP-1 RAs and substance/behavioral addiction were used to extract relevant comments. The study employed a mixed-methods approach to analyze online discussions posted from December 2019 to June 2023 and collected using a specialized web application. Reddit entries were the focus here due to limited data from other platforms, such as TikTok and YouTube. A total of 5859 threads and related comments were extracted from six subreddits, which included threads about GLP-1 RAs drugs and associated brand names. To obtain relevant posts, keywords related to potential substance use and compulsive behavior were selected. Further analysis involved two main steps: (1) manually coding posts based on users' references to the potential impact of GLP-1 RAs on substance use and non-substance habits, excluding irrelevant or unclear comments; (2) performing a thematic analysis on the dataset of keywords, using AI-assisted techniques followed by the manual revision of the generated themes. Second, a thematic analysis was performed on the keyword-related dataset, using AI-assisted techniques followed by the manual revision of the generated themes. In total, 29.75% of alcohol-related; 22.22% of caffeine-related; and 23.08% of nicotine-related comments clearly stated a cessation of the intake of these substances following the start of GLP-1 RAs prescription. Conversely, mixed results were found for cannabis intake, and only limited, anecdotal data were made available for cocaine, entactogens, and dissociative drugs' misuse. Regarding behavioral addictions, 21.35% of comments reported a compulsive shopping interruption, whilst the sexual drive/libido elements reportedly increased in several users. The current mixed-methods approach appeared to be a useful tool in gaining insight into complex topics such as the effects of GLP-1 RAs on substance and non-substance addiction-related disorders; some GLP-1 RA-related mental health benefits could also be inferred from here. Overall, it appeared that GLP-1 RAs may show the potential to target both substance craving and maladaptive/addictive behaviors, although further empirical research is needed.
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Affiliation(s)
- Davide Arillotta
- Department of Neurosciences, Psychology, Drug Research and Child Health, Section of Pharmacology and Toxicology, University of Florence, 50121 Florence, Italy
| | - Giuseppe Floresta
- Department of Drug and Health Sciences, University of Catania, 95124 Catania, Italy;
| | - G. Duccio Papanti Pelletier
- Tolmezzo Community Mental Health Centre, ASUFC Mental Health Department, Via Giuliano Bonanni, 2, 33028 Tolmezzo, Italy;
| | - Amira Guirguis
- Pharmacy, Faculty of Medicine, Health and Life Science, Swansea University, Singleton Campus, Swansea SA2 8PP, Wales, UK;
| | - John Martin Corkery
- Psychopharmacology, Drug Misuse, and Novel Psychoactive Substances Research Unit, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, UK; (J.M.C.); (F.S.)
| | - Giovanni Martinotti
- Department of Neurosciences, Imaging and Clinical Sciences, University of Chieti-Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), Institute of Advanced Biomedical Technology (ITAB), University of Chieti-Pescara, Via dei Vestini 21, 66100 Chieti, Italy
| | - Fabrizio Schifano
- Psychopharmacology, Drug Misuse, and Novel Psychoactive Substances Research Unit, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, UK; (J.M.C.); (F.S.)
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14
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Mustapha T, B S, Zubair T, Patil RB, Bhongade BA, Sangshetti JN, Mali A, Babalola BJ, Moin AT, Islam T. In vitro and in silico investigation of effects of antimicrobial peptides from Solanaceae plants against rice sheath blight pathogen Rhizoctinia solani. PLoS One 2024; 19:e0302440. [PMID: 38870165 PMCID: PMC11175423 DOI: 10.1371/journal.pone.0302440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 04/01/2024] [Indexed: 06/15/2024] Open
Abstract
Rhizoctonia solani, the causative agent of sheath blight disease in rice, poses a significant threat to agricultural productivity. Traditional management approaches involving chemical fungicides have been effective but come with detrimental consequences for the ecosystem. This study aimed to investigate sustainable alternatives in the form of antifungal peptides derived from Solanaceous plant species as potential agents against R. solani. Peptide extracts were obtained using an optimized antimicrobial peptide (AMP) extraction method and desalted using the solid-phase extraction technique. The antifungal potential of peptide-rich extracts from Solanum tuberosum and Capsicum annum was assessed through in vitro tests employing the agar well diffusion method. Furthermore, peptide-protein docking analysis was performed on HPEPDOCK and HDOCK server; and molecular dynamics simulations (MDS) of 100 ns period were performed using the Gromacs 2020.4. The results demonstrated significant inhibition zones for both extracts at concentrations of 100 mg/mL. Additionally, the extracts of Solanum tuberosum and Capsicum annum had minimum inhibitory concentrations of 50 mg/mL and 25 mg/mL, respectively with minimum fungicidal concentrations of 25 mg/mL. Insights into the potential mechanisms of key peptides inhibiting R. solani targets were gleaned from in-silico studies. Notably, certain AMPs exhibited favorable free energy of binding against pathogenicity-related targets, including histone demethylase, sortin nexin, and squalene synthase, in protein-peptide docking simulations. Extended molecular dynamics simulations lasting 100 ns and MM-PBSA calculations were performed on select protein-peptide complexes. AMP10 displayed the most favorable binding free energy against all target proteins, with AMP3, AMP12b, AMP6, and AMP15 also exhibiting promising results against specific targets of R. solani. These findings underscore the potential of peptide extracts from S. tuberosum and C. annum as effective antifungal agents against rice sheath blight caused by R. solani.
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Affiliation(s)
- Tijjani Mustapha
- Department of Biological Sciences, Federal University, Dutse, Nigeria
| | - Shefin B
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Trivandrum, India
| | | | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Vadgaon (Bk), Pune, Maharashtra, India
| | - Bhoomendra A. Bhongade
- Department of Pharmaceutical Chemistry, RAK College of Pharmacy, RAK Medical & Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Jaiprakash N. Sangshetti
- Y. B. Chavan College of Pharmacy, Dr. Rafiq Zakaria Campus, Rauza Baugh, Aurangabad, (MS), India
| | - Aniket Mali
- Cancer Research Lab, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, Maharashtra, India
| | | | - Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, University of Chittagong, Chattogram, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
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15
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Durojaye OA, Yekeen AA, Idris MO, Okoro NO, Odiba AS, Nwanguma BC. Investigation of the MDM2-binding potential of de novo designed peptides using enhanced sampling simulations. Int J Biol Macromol 2024; 269:131840. [PMID: 38679255 DOI: 10.1016/j.ijbiomac.2024.131840] [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: 02/14/2024] [Revised: 04/13/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
The tumor suppressor p53 plays a crucial role in cellular responses to various stresses, regulating key processes such as apoptosis, senescence, and DNA repair. Dysfunctional p53, prevalent in approximately 50 % of human cancers, contributes to tumor development and resistance to treatment. This study employed deep learning-based protein design and structure prediction methods to identify novel high-affinity peptide binders (Pep1 and Pep2) targeting MDM2, with the aim of disrupting its interaction with p53. Extensive all-atom molecular dynamics simulations highlighted the stability of the designed peptide in complex with the target, supported by several structural analyses, including RMSD, RMSF, Rg, SASA, PCA, and free energy landscapes. Using the steered molecular dynamics and umbrella sampling simulations, we elucidate the dissociation dynamics of p53, Pep1, and Pep2 from MDM2. Notable differences in interaction profiles were observed, emphasizing the distinct dissociation patterns of each peptide. In conclusion, the results of our umbrella sampling simulations suggest Pep1 as a higher-affinity MDM2 binder compared to p53 and Pep2, positioning it as a potential inhibitor of the MDM2-p53 interaction. Using state-of-the-art protein design tools and advanced MD simulations, this study provides a comprehensive framework for rational in silico design of peptide binders with therapeutic implications in disrupting MDM2-p53 interactions for anticancer interventions.
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Affiliation(s)
- Olanrewaju Ayodeji Durojaye
- MOE Key Laboratory of Membraneless Organelle and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui 230027, China; School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China; Department of Chemical Sciences, Coal City University, Emene, Enugu State, Nigeria.
| | - Abeeb Abiodun Yekeen
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | | | - Nkwachukwu Oziamara Okoro
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka 410001, Nigeria
| | - Arome Solomon Odiba
- Department of Molecular Genetics and Biotechnology, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State 410001, Nigeria.
| | - Bennett Chima Nwanguma
- Department of Molecular Genetics and Biotechnology, University of Nigeria, Nsukka, Enugu State 410001, Nigeria; Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Enugu State 410001, Nigeria.
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16
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Chen Z, Wang R, Guo J, Wang X. The role and future prospects of artificial intelligence algorithms in peptide drug development. Biomed Pharmacother 2024; 175:116709. [PMID: 38713945 DOI: 10.1016/j.biopha.2024.116709] [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: 03/10/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024] Open
Abstract
Peptide medications have been more well-known in recent years due to their many benefits, including low side effects, high biological activity, specificity, effectiveness, and so on. Over 100 peptide medications have been introduced to the market to treat a variety of illnesses. Most of these peptide medications are developed on the basis of endogenous peptides or natural peptides, which frequently required expensive, time-consuming, and extensive tests to confirm. As artificial intelligence advances quickly, it is now possible to build machine learning or deep learning models that screen a large number of candidate sequences for therapeutic peptides. Therapeutic peptides, such as those with antibacterial or anticancer properties, have been developed by the application of artificial intelligence algorithms.The process of finding and developing peptide drugs is outlined in this review, along with a few related cases that were helped by AI and conventional methods. These resources will open up new avenues for peptide drug development and discovery, helping to meet the pressing needs of clinical patients for disease treatment. Although peptide drugs are a new class of biopharmaceuticals that distinguish them from chemical and small molecule drugs, their clinical purpose and value cannot be ignored. However, the traditional peptide drug research and development has a long development cycle and high investment, and the creation of peptide medications will be substantially hastened by the AI-assisted (AI+) mode, offering a new boost for combating diseases.
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Affiliation(s)
- Zhiheng Chen
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Ruoxi Wang
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Junqi Guo
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China.
| | - Xiaogang Wang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, Guangdong 510630, China.
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17
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Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024; 56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Many drug formulations containing small active molecules are used for the treatment of coronary artery disease, which affects a significant part of the world's population. However, the inadequate profile of these molecules in terms of therapeutic efficacy has led to the therapeutic use of protein and peptide-based biomolecules with superior properties, such as target-specific affinity and low immunogenicity, in critical diseases. Protein‒protein interactions, as a consequence of advances in molecular techniques with strategies involving the combined use of in silico methods, have enabled the design of therapeutic peptides to reach an advanced dimension. In particular, with the advantages provided by protein/peptide structural modeling, molecular docking for the study of their interactions, molecular dynamics simulations for their interactions under physiological conditions and machine learning techniques that can work in combination with all these, significant progress has been made in approaches to developing therapeutic peptides that can modulate the development and progression of coronary artery diseases. In this scope, this review discusses in silico methods for the development of peptide therapeutics for the treatment of coronary artery disease and strategies for identifying the molecular mechanisms that can be modulated by these designs and provides a comprehensive perspective for future studies.
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Affiliation(s)
- Ayca Aslan
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey
| | - Selcen Ari Yuka
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, Esenler, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Esenler, Istanbul, Turkey.
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18
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Bayarsaikhan B, Zsidó BZ, Börzsei R, Hetényi C. Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols. Int J Mol Sci 2024; 25:5945. [PMID: 38892133 PMCID: PMC11172440 DOI: 10.3390/ijms25115945] [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: 04/24/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Histones are keys to many epigenetic events and their complexes have therapeutic and diagnostic importance. The determination of the structures of histone complexes is fundamental in the design of new drugs. Computational molecular docking is widely used for the prediction of target-ligand complexes. Large, linear peptides like the tail regions of histones are challenging ligands for docking due to their large conformational flexibility, extensive hydration, and weak interactions with the shallow binding pockets of their reader proteins. Thus, fast docking methods often fail to produce complex structures of such peptide ligands at a level appropriate for drug design. To address this challenge, and improve the structural quality of the docked complexes, post-docking refinement has been applied using various molecular dynamics (MD) approaches. However, a final consensus has not been reached on the desired MD refinement protocol. In this present study, MD refinement strategies were systematically explored on a set of problematic complexes of histone peptide ligands with relatively large errors in their docked geometries. Six protocols were compared that differ in their MD simulation parameters. In all cases, pre-MD hydration of the complex interface regions was applied to avoid the unwanted presence of empty cavities. The best-performing protocol achieved a median of 32% improvement over the docked structures in terms of the change in root mean squared deviations from the experimental references. The influence of structural factors and explicit hydration on the performance of post-docking MD refinements are also discussed to help with their implementation in future methods and applications.
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Affiliation(s)
- Bayartsetseg Bayarsaikhan
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Rita Börzsei
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, H-7624 Pécs, Hungary; (B.B.); (B.Z.Z.); (R.B.)
- National Laboratory for Drug Research and Development, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
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19
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Thongtak A, Yutisayanuwat K, Harnkit N, Noikaew T, Chumnanpuen P. Computational Screening for the Dipeptidyl Peptidase-IV Inhibitory Peptides from Putative Hemp Seed Hydrolyzed Peptidome as a Potential Antidiabetic Agent. Int J Mol Sci 2024; 25:5730. [PMID: 38891918 PMCID: PMC11171819 DOI: 10.3390/ijms25115730] [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: 04/18/2024] [Revised: 05/19/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Dipeptidyl peptidase-IV (DPPIV) inhibitory peptides are a class of antihyperglycemic drugs used in the treatment of type 2 diabetes mellitus, a metabolic disorder resulting from reduced levels of the incretin hormone GLP-1. Given that DPPIV degrades incretin, a key regulator of blood sugar levels, various antidiabetic medications that inhibit DPPIV, such as vildagliptin, sitagliptin, and linagliptin, are employed. However, the potential side effects of these drugs remain a matter of debate. Therefore, we aimed to investigate food-derived peptides from Cannabis sativa (hemp) seeds. Our developed bioinformatics pipeline was used to identify the putative hydrolyzed peptidome of three highly abundant proteins: albumin, edestin, and vicilin. These proteins were subjected to in silico digestion by different proteases (trypsin, chymotrypsin, and pepsin) and then screened for DPPIV inhibitory peptides using IDPPIV-SCM. To assess potential adverse effects, several prediction tools, namely, TOXINpred, AllerCatPro, and HemoPred, were employed to evaluate toxicity, allergenicity, and hemolytic effects, respectively. COPID was used to determine the amino acid composition. Molecular docking was performed using GalaxyPepDock and HPEPDOCK, 3D visualizations were conducted using the UCSF Chimera program, and MD simulations were carried out with AMBER20 MD software. Based on the predictive outcomes, FNVDTE from edestin and EAQPST from vicilin emerged as promising candidates for DPPIV inhibitors. We anticipate that our findings may pave the way for the development of alternative DPPIV inhibitors.
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Affiliation(s)
- Arisa Thongtak
- Mahidol Wittayanusorn School, 364 Salaya, Phuttamonthon District, Nakhon Pathom 73170, Thailand; (A.T.); (K.Y.)
| | - Kulpariya Yutisayanuwat
- Mahidol Wittayanusorn School, 364 Salaya, Phuttamonthon District, Nakhon Pathom 73170, Thailand; (A.T.); (K.Y.)
| | - Nathaphat Harnkit
- Medicinal Plant Research Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand;
| | - Tipanart Noikaew
- Department of Biology and Health Science, Mahidol Wittayanusorn School, 364 Salaya, Phuttamonthon District, Nakhon Pathom 73170, Thailand;
| | - Pramote Chumnanpuen
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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20
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Zhu C, Zhang C, Shang T, Zhang C, Zhai S, Cao L, Xu Z, Su Z, Song Y, Su A, Li C, Duan H. GAPS: a geometric attention-based network for peptide binding site identification by the transfer learning approach. Brief Bioinform 2024; 25:bbae297. [PMID: 38990514 PMCID: PMC11238429 DOI: 10.1093/bib/bbae297] [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: 02/11/2024] [Revised: 04/28/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
Protein-peptide interactions (PPepIs) are vital to understanding cellular functions, which can facilitate the design of novel drugs. As an essential component in forming a PPepI, protein-peptide binding sites are the basis for understanding the mechanisms involved in PPepIs. Therefore, accurately identifying protein-peptide binding sites becomes a critical task. The traditional experimental methods for researching these binding sites are labor-intensive and time-consuming, and some computational tools have been invented to supplement it. However, these computational tools have limitations in generality or accuracy due to the need for ligand information, complex feature construction, or their reliance on modeling based on amino acid residues. To deal with the drawbacks of these computational algorithms, we describe a geometric attention-based network for peptide binding site identification (GAPS) in this work. The proposed model utilizes geometric feature engineering to construct atom representations and incorporates multiple attention mechanisms to update relevant biological features. In addition, the transfer learning strategy is implemented for leveraging the protein-protein binding sites information to enhance the protein-peptide binding sites recognition capability, taking into account the common structure and biological bias between proteins and peptides. Consequently, GAPS demonstrates the state-of-the-art performance and excellent robustness in this task. Moreover, our model exhibits exceptional performance across several extended experiments including predicting the apo protein-peptide, protein-cyclic peptide and the AlphaFold-predicted protein-peptide binding sites. These results confirm that the GAPS model is a powerful, versatile, stable method suitable for diverse binding site predictions.
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Affiliation(s)
- Cheng Zhu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Chengyun Zhang
- AI Department, Shanghai Highslab Therapeutics. Inc, Zhangheng Road, Pudong New Area, Shanghai 201203, China
| | - Tianfeng Shang
- AI Department, Shanghai Highslab Therapeutics. Inc, Zhangheng Road, Pudong New Area, Shanghai 201203, China
| | - Chenhao Zhang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Silong Zhai
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Lujing Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Zhenyu Xu
- AI Department, Shanghai Highslab Therapeutics. Inc, Zhangheng Road, Pudong New Area, Shanghai 201203, China
| | - Zhihao Su
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Ying Song
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - An Su
- College of Chemical Engineering, Zhejiang University of Technology, Chaowang Road, Gongshu District, Hangzhou 310014, China
| | - Chengxi Li
- College of Chemical and Biological Engineering, Zhejiang University, Yuhangtang Road, Xihu District, Hangzhou 310027, China
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, R. de Luís Gonzaga Gomes, Macao 999078, China
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Karagiannis TC, Ververis K, Liang JJ, Pitsillou E, Liu S, Bresnehan SM, Xu V, Wijoyo SJ, Duan X, Ng K, Hung A, Goebel E, El-Osta A. Identification and Evaluation of Olive Phenolics in the Context of Amine Oxidase Enzyme Inhibition and Depression: In Silico Modelling and In Vitro Validation. Molecules 2024; 29:2446. [PMID: 38893322 PMCID: PMC11173677 DOI: 10.3390/molecules29112446] [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: 05/03/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
The Mediterranean diet well known for its beneficial health effects, including mood enhancement, is characterised by the relatively high consumption of extra virgin olive oil (EVOO), which is rich in bioactive phenolic compounds. Over 200 phenolic compounds have been associated with Olea europaea, and of these, only a relatively small fraction have been characterised. Utilising the OliveNetTM library, phenolic compounds were investigated as potential inhibitors of the epigenetic modifier lysine-specific demethylase 1 (LSD1). Furthermore, the compounds were screened for inhibition of the structurally similar monoamine oxidases (MAOs) which are directly implicated in the pathophysiology of depression. Molecular docking highlighted that olive phenolics interact with the active site of LSD1 and MAOs. Protein-peptide docking was also performed to evaluate the interaction of the histone H3 peptide with LSD1, in the presence of ligands bound to the substrate-binding cavity. To validate the in silico studies, the inhibitory activity of phenolic compounds was compared to the clinically approved inhibitor tranylcypromine. Our findings indicate that olive phenolics inhibit LSD1 and the MAOs in vitro. Using a cell culture model system with corticosteroid-stimulated human BJ fibroblast cells, the results demonstrate the attenuation of dexamethasone- and hydrocortisone-induced MAO activity by phenolic compounds. The findings were further corroborated using human embryonic stem cell (hESC)-derived neurons stimulated with all-trans retinoic acid. Overall, the results indicate the inhibition of flavin adenine dinucleotide (FAD)-dependent amine oxidases by olive phenolics. More generally, our findings further support at least a partial mechanism accounting for the antidepressant effects associated with EVOO and the Mediterranean diet.
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Affiliation(s)
- Tom C. Karagiannis
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Katherine Ververis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia J. Liang
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Siyao Liu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Sarah M. Bresnehan
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
| | - Vivian Xu
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
| | - Stevano J. Wijoyo
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Xiaofei Duan
- Melbourne TrACEES Platform, School of Chemistry, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ken Ng
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Erik Goebel
- Occhem Labs, LLC, 3510 Hopkins Place North, Oakdale, MN 55128, USA
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, 3/F Lui Che Woo Clinical Sciences Building, 30-32 Ngan Shing Street, Sha Tin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong SAR, China
- Biomedical Laboratory Science, Department of Technology, Faculty of Health, University College Copenhagen, 1799 Copenhagen V, Denmark
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22
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Mortazavi B, Molaei A, Fard NA. Multi-epitopevaccines, from design to expression; an in silico approach. Hum Immunol 2024; 85:110804. [PMID: 38658216 DOI: 10.1016/j.humimm.2024.110804] [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: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The development of vaccines against a wide range of infectious diseases and pathogens often relies on multi-epitope strategies that can effectively stimulate both humoral and cellular immunity. Immunoinformatics tools play a pivotal role in designing such vaccines, enhancing immune response potential, and minimizing the risk of failure. This review presents a comprehensive overview of practical tools for epitope prediction and the associated immune responses. These immunoinformatics tools facilitate the selection of epitopes based on parameters such as antigenicity, absence of toxic and allergenic sequences, secondary and tertiary structures, sequence conservation, and population coverage. The chosen epitopes can be tailored for B-cells or T-cells, both of which require further assessments covered in this study. We offer a range of suitable linkers that effectively separate cytotoxic T lymphocyte and helper T lymphocyte epitopes while preserving their functionality. Additionally, we identify various adjuvants for specific purposes. We delve into the evaluation of MHC-epitope interactions, MHC clusters, and the simulation of final constructs through molecular docking techniques. We provide diverse linkers and adjuvants optimized for epitope functions to bolster immune responses through epitope attachment. By leveraging these comprehensive tools, the development of multi-epitope vaccines holds the promise of robust immunity and a significant reduction in experimental costs.
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Affiliation(s)
- Behnam Mortazavi
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Molaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Najaf Allahyari Fard
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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23
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Mudgil P, Al Dhaheri MKO, Alsubousi MSM, Khan H, Redha AA, Yap PG, Gan CY, Maqsood S. Molecular docking studies on α-amylase inhibitory peptides from milk of different farm animals. J Dairy Sci 2024; 107:2633-2652. [PMID: 38101739 DOI: 10.3168/jds.2023-24118] [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: 08/23/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023]
Abstract
Milk-derived peptides have emerged as a popular mean to manage various lifestyle disorders such as diabetes. Fermentation is being explored as one of the faster and efficient way of producing peptides with antidiabetic potential. Therefore, in this study, an attempt was made to comparatively investigate the pancreatic α-amylase (PAA) inhibitory properties of peptides derived from milk of different farm animals through probiotic fermentation. Peptide's identification was carried out using liquid chromatography-quadrupole time-of-flight mass spectrometry and inhibition mechanisms were characterized by molecular docking. Results obtained showed a PAA-IC50 value (the amount of protein equivalent needed to inhibit 50% of enzymes) between 2.39 and 36.1 µg protein equivalent for different fermented samples. Overall, Pediococcus pentosaceus MF000957-derived fermented milk from all animals indicated higher PAA inhibition than other probiotic derived fermented milk (PAA-IC50 values of 6.01, 3.53, 15.6, and 10.8 µg protein equivalent for bovine, camel, goat, and sheep fermented milk). Further, molecular docking analysis indicated that camel milk-derived peptide IMEQQQTEDEQQDK and goat milk-derived peptide DQHQKAMKPWTQPK were the most potent PAA inhibitory peptides. Overall, the study concluded that fermentation derived peptides may prove useful in for managing diabetes via inhibition of carbohydrate digesting enzyme PAA.
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Affiliation(s)
- Priti Mudgil
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Mouza Khamis Obaid Al Dhaheri
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Maitha Saif Mohammed Alsubousi
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Hina Khan
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, 15551, United Arab Emirates
| | - Ali Ali Redha
- The Department of Public Health and Sport Sciences, University of Exeter Medical School, Faculty of Health and Life Sciences, University of Exeter, Exeter, EX1 2LU, United Kingdom; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Pei-Gee Yap
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
| | - Chee-Yuen Gan
- Analytical Biochemistry Research Centre (ABrC), Universiti Sains Malaysia, 11800, USM, Penang, Malaysia
| | - Sajid Maqsood
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, 15551, United Arab Emirates; Zayed Centre of Health Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates.
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24
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Dey S, Pratibha M, Singh Dagur H, Rajakumara E. Characterization of host receptor interaction with envelop protein of Kyasanur forest disease virus and predicting suitable epitopes for vaccine candidate. J Biomol Struct Dyn 2024; 42:4110-4120. [PMID: 37272880 DOI: 10.1080/07391102.2023.2218924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Kyasanur forest disease (KFD) is a zoonotic disease that is endemic to southern India and caused by KFD virus (KFDV) belonging to the family Flaviviridae. Humans are the dead-end host of the KFDV life cycle. The absence of effective treatment strategies against KFD can be attributed to a lack of studies on the mechanistic part of the spread of the disease. Hypothesizing molecular etiological similarity of KFDV to other well characterized flaviviruses, such as dengue virus (DENV), we focused on predicting the target receptor protein(s) in host and provided molecular basis of receptor-mediated recognition of the human host by KFDV envelop protein (EKFDV), drawing from the extant knowledge on the dengue counterpart, EDENV. Indeed, in silico approach helped to identify that the EKFDV structure closely resembles the EDENV structure and indicated DC-SIGN and/or Mannose receptors to be the plausible target host receptors. Immune-informatics approach aided in predicting 10 epitopes from E, NS1, NS2A, and NS2B proteins of the KFDV-P9605 genotype for vaccine design against KFDV. Further, molecular dynamics simulation (MDS) analyses of their complexes with human leukocyte antigens (HLAs) identified the epitopes DISLTCRVT and YAMEIRPVH as two high ranking candidates for vaccine design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sreenath Dey
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, India
| | - Manickavasagam Pratibha
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, India
| | - Hanuman Singh Dagur
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology, Hyderabad, Kandi, India
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25
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Huang F, Dai Q, Zheng K, Ma Q, Liu Y, Jiang S, Jiang W, Yan X. Exploring the inhibitory potential of KPHs-AL-derived GLLF peptide on pancreatic lipase and cholesterol esterase activities. Food Chem 2024; 439:138108. [PMID: 38061297 DOI: 10.1016/j.foodchem.2023.138108] [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: 09/15/2023] [Revised: 11/25/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024]
Abstract
The effective modulation of pancreatic lipase and cholesterol esterase activities proves critical in maintaining circulatory triglycerides and cholesterol levels within physiological boundaries. In this study, peptides derived from KPHs-AL, produced through the enzymatic hydrolysis of skipjack tuna dark muscle using alkaline protease, have a specific inhibitory effect on pancreatic lipase and cholesterol esterase. It is hypothesized that these peptides target and modulate the activities of enzymes by inducing conformational changes within their binding pockets, potentially impacting the catalytic functions of both pancreatic lipase and cholesterol esterase. Results revealed these peptides including AINDPFIDL, FLGM, GLLF and WGPL, were found to nestle into the binding site groove of pancreatic lipase and cholesterol esterase. Among these, GLLF stood out, demonstrating potent inhibition with IC50 values of 0.1891 mg/mL and 0.2534 mg/mL for pancreatic lipase and cholesterol esterase, respectively. The kinetics studies suggested that GLLF competed effectively with substrates for the enzyme active sites. Spectroscopic analyses, including ultraviolet-visible, fluorescence quenching, and circular dichroism, indicated that GLLF binding induced conformational changes within the enzymes, likely through hydrogen bond formation and hydrophobic interactions, thereby increasing structural flexibility. Molecular docking and molecular dynamics simulations supported these findings, showing GLLF's stable interaction with vital active site residues. These findings position GLLF as a potent inhibitor of key digestive enzymes, offering insights into its role in regulating lipid metabolism and highlighting its potential as functional ingredient.
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Affiliation(s)
- Fangfang Huang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China; Zhejiang Provincial Engineering Technology Research Center of Marine Biomedical Products, School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
| | - Qingfei Dai
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Kewei Zheng
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Qingbao Ma
- Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Yu Liu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China
| | - Shuoqi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China
| | - Wei Jiang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China.
| | - Xiaojun Yan
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, China; Institute of Innovation and Application, Zhejiang Ocean University, Zhoushan, China; Key Laboratory of Key Technical Factors in Zhejiang Seafood Health Hazards, College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, China
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26
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Pipaliya R, Basaiawmoit B, Sakure AA, Maurya R, Bishnoi M, Kondepudi KK, Singh BP, Paul S, Liu Z, Sarkar P, Patel A, Hati S. Peptidomics-based identification of antihypertensive and antidiabetic peptides from sheep milk fermented using Limosilactobacillus fermentum KGL4 MTCC 25515 with anti-inflammatory activity: in silico, in vitro, and molecular docking studies. Front Chem 2024; 12:1389846. [PMID: 38746020 PMCID: PMC11091447 DOI: 10.3389/fchem.2024.1389846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 05/16/2024] Open
Abstract
This study investigated the synthesis of bioactive peptides from sheep milk through fermentation with Limosilactobacillus fermentum KGL4 MTCC 25515 strain and assessed lipase inhibition, ACE inhibition, α-glucosidase inhibition, and α-amylase inhibition activities during the fermentation process. The study observed the highest activities, reaching 74.82%, 70.02%, 72.19%, and 67.08% (lipase inhibition, ACE inhibition, α-glucosidase inhibition, and α-amylase inhibition) after 48 h at 37°C, respectively. Growth optimization experiments revealed that a 2.5% inoculation rate after 48 h of fermentation time resulted in the highest proteolytic activity at 9.88 mg/mL. Additionally, fractions with less than 3 kDa of molecular weight exhibited superior ACE-inhibition and anti-diabetic activities compared to other fractions. Fermentation of sheep milk with KGL4 led to a significant reduction in the excessive production of NO, TNF-α, IL-6, and IL-1β produced in RAW 267.4 cells upon treatment with LPS. Peptides were purified utilizing SDS-PAGE and electrophoresis on 2D gels, identifying a maximum number of proteins bands ranging 10-70 kDa. Peptide sequences were cross-referenced with AHTPDB and BIOPEP databases, confirming potential antihypertensive and antidiabetic properties. Notably, the peptide (GPFPILV) exhibited the highest HPEPDOCK score against both α-amylase and ACE.
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Affiliation(s)
- Rinkal Pipaliya
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand, Gujarat, India
| | - Bethsheba Basaiawmoit
- Department of Rural Development and Agricultural Production, North-Eastern Hill University, Tura Campus, Chasingre, Meghalaya, India
| | - Amar A. Sakure
- Departmentof Agriculture Biotechnology, Anand Agricultural University, Anand, Gujarat, India
| | - Ruchika Maurya
- Regional Center for Biotechnology, Faridabad, Haryana, India
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, India
| | - Mahendra Bishnoi
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, India
| | - Kanthi Kiran Kondepudi
- Healthy Gut Research Group, Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute, SAS Nagar, Punjab, India
| | - Brij Pal Singh
- Department of Microbiology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
| | - Souparno Paul
- Department of Microbiology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, India
| | - Zhenbin Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | - Preetam Sarkar
- Department of Food Process Engineering, National Institute of Technology, Rourkela, India
| | - Ashish Patel
- Department of Animal Genetics and Breeding, College of Veterinary Science, Kamdhenu University, Anand, Gujarat, India
| | - Subrota Hati
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand, Gujarat, India
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Durinova A, Smutna L, Barta P, Kamaraj R, Smutny T, Schmierer B, Pavek P, Trejtnar F. Radiolabeled 15-mer peptide internalization is mediated by megalin (LRP2 receptor) in a CRISPR/Cas9-based LRP2 knockout human kidney cell model. EJNMMI Radiopharm Chem 2024; 9:32. [PMID: 38637347 PMCID: PMC11026318 DOI: 10.1186/s41181-024-00262-2] [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: 02/09/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Megalin (LRP2 receptor) mediates the endocytosis of radiolabeled peptides into proximal tubular kidney cells, which may cause nephrotoxicity due to the accumulation of a radioactive tracer. The study aimed to develop a cellular model of human kidney HK2 cells with LRP2 knockout (KO) using CRISPR/Cas9 technique. This model was employed for the determination of the megalin-mediated accumulation of 68Ga- and 99mTc-labeled 15-mer peptide developed to target the vascular endothelial growth factor (VEGF) receptor in oncology radiodiagnostics. RESULTS The gene editing in the LRP2 KO model was verified by testing two well-known megalin ligands when higher viability of KO cells was observed after gentamicin treatment at cytotoxic concentrations and lower FITC-albumin internalization by the KO cells was detected in accumulation studies. Fluorescent-activated cell sorting was used to separate genetically modified LRP2 KO cell subpopulations. Moreover, flow cytometry with a specific antibody against megalin confirmed LRP2 knockout. The verified KO model identified both 68Ga- and 99mTc-radiolabeled 15-mer peptides as megalin ligands in accumulation studies. We found that both radiolabeled 15-mers enter LRP2 KO HK2 cells to a lesser extent compared to parent cells. Differences in megalin-mediated cellular uptake depending on the radiolabeling were not observed. Using biomolecular docking, the interaction site of the 15-mer with megalin was also described. CONCLUSION The CRISPR/Cas9 knockout of LRP2 in human kidney HK2 cells is an effective approach for the determination of radiopeptide internalization mediated by megalin. This in vitro method provided direct molecular evidence for the cellular uptake of radiolabeled anti-VEGFR 15-mer peptides via megalin.
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Affiliation(s)
- Anna Durinova
- Division of Radiopharmacy, Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Lucie Smutna
- Division of Radiopharmacy, Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic.
| | - Pavel Barta
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Rajamanikkam Kamaraj
- Division of Radiopharmacy, Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Tomas Smutny
- Division of Radiopharmacy, Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Bernhard Schmierer
- SciLifeLab and Department of Medical Biochemistry and Biophysics, CRISPR Functional Genomics, Karolinska Institutet, Solna, Sweden
| | - Petr Pavek
- Division of Radiopharmacy, Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Frantisek Trejtnar
- Division of Radiopharmacy, Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
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28
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Rapp PB, Baccile JA, Galimidi RP, Vielmetter J. Engineering Antigen-Specific Tolerance to an Artificial Protein Hydrogel. ACS Biomater Sci Eng 2024; 10:2188-2199. [PMID: 38479351 DOI: 10.1021/acsbiomaterials.3c01430] [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] [Indexed: 04/09/2024]
Abstract
Artificial protein hydrogels are an emerging class of biomaterials with numerous prospective applications in tissue engineering and regenerative medicine. These materials are likely to be immunogenic due to their frequent incorporation of novel amino acid sequence domains, which often serve a functional role within the material itself. We engineered injectable "self" and "nonself" artificial protein hydrogels, which were predicted to have divergent immune outcomes in vivo on the basis of their primary amino acid sequence. Following implantation in mouse, the nonself gels raised significantly higher antigel antibody titers than the corresponding self gels. Prophylactic administration of a fusion antibody targeting the nonself hydrogel epitopes to DEC-205, an endocytic receptor involved in Treg induction, fully suppressed the elevated antibody titer against the nonself gels. These results suggest that the clinical immune response to artificial protein biomaterials, including those that contain highly antigenic sequence domains, can be tuned through the induction of antigen-specific tolerance.
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Affiliation(s)
- Peter B Rapp
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Joshua A Baccile
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Rachel P Galimidi
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
| | - Jost Vielmetter
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, California 91125, United States
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Piloto JV, Dias RVR, Mazucato WSA, Fossey MA, de Melo FA, Almeida FCL, de Souza FP, Caruso IP. Computational Insights into the Interaction of the Conserved Cysteine-Noose Domain of the Human Respiratory Syncytial Virus G Protein with the Canonical Fractalkine Binding site of Transmembrane Receptor CX3CR1 Isoforms. MEMBRANES 2024; 14:84. [PMID: 38668112 PMCID: PMC11052111 DOI: 10.3390/membranes14040084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/23/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024]
Abstract
The human Respiratory Syncytial Virus (hRSV) stands as one of the most common causes of acute respiratory diseases. The infectivity of this virus is intricately linked to its membrane proteins, notably the attachment glycoprotein (G protein). The latter plays a key role in facilitating the attachment of hRSV to respiratory tract epithelial cells, thereby initiating the infection process. The present study aimed to characterize the interaction of the conserved cysteine-noose domain of hRSV G protein (cndG) with the transmembrane CX3C motif chemokine receptor 1 (CX3CR1) isoforms using computational tools of molecular modeling, docking, molecular dynamics simulations, and binding free energy calculations. From MD simulations of the molecular system embedded in the POPC lipid bilayer, we showed a stable interaction of cndG with the canonical fractalkine binding site in the N-terminal cavity of the CX3CR1 isoforms and identified that residues in the extracellular loop 2 (ECL2) region and Glu279 of this receptor are pivotal for the stabilization of CX3CR1/cndG binding, corroborating what was reported for the interaction of the chemokine fractalkine with CX3CR1 and its structure homolog US28. Therefore, the results presented here contribute by revealing key structural points for the CX3CR1/G interaction, allowing us to better understand the biology of hRSV from its attachment process and to develop new strategies to combat it.
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Affiliation(s)
- João Victor Piloto
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
| | - Raphael Vinicius Rodrigues Dias
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
| | - Wan Suk Augusto Mazucato
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
| | - Marcelo Andres Fossey
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
| | - Fernando Alves de Melo
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
| | - Fabio Ceneviva Lacerda Almeida
- Institute of Medical Biochemistry (IBqM), National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil;
| | - Fatima Pereira de Souza
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
| | - Icaro Putinhon Caruso
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São Jose do Rio Preto 15054-000, Brazil; (J.V.P.); (R.V.R.D.); (W.S.A.M.); (M.A.F.); (F.A.d.M.); (F.P.d.S.)
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Zeng J, Loi GWZ, Saipuljumri EN, Romero Durán MA, Silva-García O, Perez-Aguilar JM, Baizabal-Aguirre VM, Lo CH. Peptide-based allosteric inhibitor targets TNFR1 conformationally active region and disables receptor-ligand signaling complex. Proc Natl Acad Sci U S A 2024; 121:e2308132121. [PMID: 38551841 PMCID: PMC10998571 DOI: 10.1073/pnas.2308132121] [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: 05/15/2023] [Accepted: 01/23/2024] [Indexed: 04/02/2024] Open
Abstract
Tumor necrosis factor (TNF) receptor 1 (TNFR1) plays a pivotal role in mediating TNF induced downstream signaling and regulating inflammatory response. Recent studies have suggested that TNFR1 activation involves conformational rearrangements of preligand assembled receptor dimers and targeting receptor conformational dynamics is a viable strategy to modulate TNFR1 signaling. Here, we used a combination of biophysical, biochemical, and cellular assays, as well as molecular dynamics simulation to show that an anti-inflammatory peptide (FKCRRWQWRMKK), which we termed FKC, inhibits TNFR1 activation allosterically by altering the conformational states of the receptor dimer without blocking receptor-ligand interaction or disrupting receptor dimerization. We also demonstrated the efficacy of FKC by showing that the peptide inhibits TNFR1 signaling in HEK293 cells and attenuates inflammation in mice with intraperitoneal TNF injection. Mechanistically, we found that FKC binds to TNFR1 cysteine-rich domains (CRD2/3) and perturbs the conformational dynamics required for receptor activation. Importantly, FKC increases the frequency in the opening of both CRD2/3 and CRD4 in the receptor dimer, as well as induces a conformational opening in the cytosolic regions of the receptor. This results in an inhibitory conformational state that impedes the recruitment of downstream signaling molecules. Together, these data provide evidence on the feasibility of targeting TNFR1 conformationally active region and open new avenues for receptor-specific inhibition of TNFR1 signaling.
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Affiliation(s)
- Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore308232, Singapore
| | - Gavin Wen Zhao Loi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore308232, Singapore
| | - Eka Norfaishanty Saipuljumri
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore308232, Singapore
- School of Applied Science, Republic Polytechnic, Singapore738964, Singapore
| | - Marco Antonio Romero Durán
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia58893, México
| | - Octavio Silva-García
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia58893, México
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla, University City, Puebla72570, México
| | - Víctor M. Baizabal-Aguirre
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia58893, México
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore308232, Singapore
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Naha A, Ramaiah S. Novel Antimicrobial Peptide SAAP Mutant as a Better Adjuvant to Sulbactam-Based Treatments Against Clinical Strains of XDR Acinetobacter baumannii. Probiotics Antimicrob Proteins 2024; 16:459-473. [PMID: 36971982 DOI: 10.1007/s12602-023-10067-5] [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] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
The production of extended spectrum β-lactamases (ESBLs) in extensively drug-resistant (XDR) strains of Acinetobacter baumannii has created havoc amongst clinicians making the treatment procedure challenging. Carbapenem-resistant strains have displayed total ineffectiveness towards newer combinations of β-lactam-β-lactamase inhibitors (βL-βLI) in tertiary healthcare settings. Therefore, the present study was aimed to design potential β-lactamase antimicrobial peptide (AMP) inhibitors against ESBLs produced by the strains. We have constructed an AMP mutant library with higher antimicrobial efficacy (range: ~ 15 to 27%) than their parent peptides. The mutants were thoroughly screened based on different physicochemical and immunogenic properties revealing three peptides, namely SAAP-148, HFIAP-1, myticalin-C6 and their mutants with safe pharmacokinetics profile. Molecular docking highlighted SAAP-148_M15 displaying maximum inhibitory potential with lowest binding energies against NDM1 (- 1148.7 kcal/mol), followed by OXA23 (- 1032.5 kcal/mol) and OXA58 (- 925.3 kcal/mol). The intermolecular interaction profiles displayed SAAP-148_M15 exhibiting hydrogen bonds and van der Waals hydrophobic interactions with the crucial residues of metallo β-lactamase [IPR001279] and penicillin-binding transpeptidase [IPR001460] domains. Coarse-grained clustering and molecular dynamics simulations (MDS) further validated the stable backbone profile and minimal residue-level fluctuations of the protein-peptide complex that were maintained throughout the simulation timeframe. The present study hypothesised that the combination of sulbactam (βL) with SAAP-148_M15 (βLI) holds immense potential in inhibiting the ESBLs alongside restoration of sulbactam activity. The current in silico findings upon further experimental validations can pave path towards designing of successful therapeutic strategy against XDR strains of A. baumannii.
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Affiliation(s)
- Aniket Naha
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Tamil Nadu, Vellore, 632014, India
- Department of Bio-Medical Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Tamil Nadu, Vellore, 632014, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Tamil Nadu, Vellore, 632014, India.
- Department of Bio-Sciences, School of Bio-Sciences and Technology, Vellore Institute of Technology (VIT), Tamil Nadu, Vellore, 632014, India.
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32
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Martineau-Côté D, Achouri A, Karboune S, L’Hocine L. Antioxidant and Angiotensin-Converting Enzyme Inhibitory Activity of Faba Bean-Derived Peptides After In Vitro Gastrointestinal Digestion: Insight into Their Mechanism of Action. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6432-6443. [PMID: 38470110 PMCID: PMC10979453 DOI: 10.1021/acs.jafc.4c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Faba bean flour, after in vitro gastrointestinal digestion, showed important antioxidant and angiotensin-converting enzyme (ACE) inhibitory activities. In the present study, 11 faba bean- derived peptides were synthesized to confirm their bioactivities and provide a deeper understanding of their mechanisms of action. The results revealed that 7 peptides were potent antioxidants, namely, NYDEGSEPR, TETWNPNHPEL, TETWNPNHPE, VIPTEPPH, VIPTEPPHA, VVIPTEPPHA, and VVIPTEPPH. Among them, TETWNPNHPEL had the highest activity in the ABTS (EC50 = 0.5 ± 0.2 mM) and DPPH (EC50 = 2.1 ± 0.1 mM) assays (p < 0.05), whereas TETWNPNHPE had the highest activity (p < 0.05) in the ORAC assay (2.84 ± 0.08 mM Trolox equivalent/mM). Synergistic and/or additive effects were found when selected peptides (TETWNPNHPEL, NYDEGSEPR, and VVIPTEPPHA) were combined. Four peptides were potent ACE inhibitors, where VVIPTEPPH (IC50 = 43 ± 1 μM) and VVIPTEPPHA (IC50 = 50 ± 5 μM) had the highest activity (p < 0.05), followed by VIPTEPPH (IC50 = 90 ± 10 μM) and then VIPTEPPHA (IC50 = 123 ± 5 μM) (p < 0.05). These peptides were noncompetitive inhibitors, as supported by kinetic studies and a molecular docking investigation. This study demonstrated that peptides derived from faba beans have multifunctional bioactivities, making them a promising food-functional and nutraceutical ingredient.
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Affiliation(s)
- Delphine Martineau-Côté
- Agriculture
and Agri-Food Canada, Saint-Hyacinthe Research
and Development Centre, Saint-Hyacinthe, Quebec J2S 8E3, Canada
- Department
of Food Science and Agricultural Chemistry, Macdonald Campus, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Allaoua Achouri
- Agriculture
and Agri-Food Canada, Saint-Hyacinthe Research
and Development Centre, Saint-Hyacinthe, Quebec J2S 8E3, Canada
| | - Salwa Karboune
- Department
of Food Science and Agricultural Chemistry, Macdonald Campus, McGill University, Sainte-Anne-de-Bellevue, Quebec H9X 3 V9, Canada
| | - Lamia L’Hocine
- Agriculture
and Agri-Food Canada, Saint-Hyacinthe Research
and Development Centre, Saint-Hyacinthe, Quebec J2S 8E3, Canada
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Bautista E, Jung YH, Jaramillo M, Ganesh H, Varma A, Savsani K, Dakshanamurthy S. AutoPepVax, a Novel Machine-Learning-Based Program for Vaccine Design: Application to a Pan-Cancer Vaccine Targeting EGFR Missense Mutations. Pharmaceuticals (Basel) 2024; 17:419. [PMID: 38675381 PMCID: PMC11053815 DOI: 10.3390/ph17040419] [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: 03/03/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The current epitope selection methods for peptide vaccines often rely on epitope binding affinity predictions, prompting the need for the development of more sophisticated in silico methods to determine immunologically relevant epitopes. Here, we developed AutoPepVax to expedite and improve the in silico epitope selection for peptide vaccine design. AutoPepVax is a novel program that automatically identifies non-toxic and non-allergenic epitopes capable of inducing tumor-infiltrating lymphocytes by considering various epitope characteristics. AutoPepVax employs random forest classification and linear regression machine-learning-based models, which are trained with datasets derived from tumor samples. AutoPepVax, along with documentation on how to run the program, is freely available on GitHub. We used AutoPepVax to design a pan-cancer peptide vaccine targeting epidermal growth factor receptor (EGFR) missense mutations commonly found in lung adenocarcinoma (LUAD), colorectal adenocarcinoma (CRAD), glioblastoma multiforme (GBM), and head and neck squamous cell carcinoma (HNSCC). These mutations have been previously targeted in clinical trials for EGFR-specific peptide vaccines in GBM and LUAD, and they show promise but lack demonstrated clinical efficacy. Using AutoPepVax, our analysis of 96 EGFR mutations identified 368 potential MHC-I-restricted epitope-HLA pairs from 49,113 candidates and 430 potential MHC-II-restricted pairs from 168,669 candidates. Notably, 19 mutations presented viable epitopes for MHC I and II restrictions. To evaluate the potential impact of a pan-cancer vaccine composed of these epitopes, we used our program, PCOptim, to curate a minimal list of epitopes with optimal population coverage. The world population coverage of our list ranged from 81.8% to 98.5% for MHC Class II and Class I epitopes, respectively. From our list of epitopes, we constructed 3D epitope-MHC models for six MHC-I-restricted and four MHC-II-restricted epitopes, demonstrating their epitope binding potential and interaction with T-cell receptors. AutoPepVax's comprehensive approach to in silico epitope selection addresses vaccine safety, efficacy, and broad applicability. Future studies aim to validate the AutoPepVax-designed vaccines with murine tumor models that harbor the studied mutations.
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Affiliation(s)
- Enrico Bautista
- Georgetown University School of Medicine, Washington, DC 20007, USA
| | | | | | - Harrish Ganesh
- Virginia Commonwealth University, Richmond, VA 22043, USA
| | - Aryaan Varma
- The George Washington University, Washington, DC 20052, USA
| | - Kush Savsani
- Virginia Commonwealth University, Richmond, VA 22043, USA
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
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Vásquez-Suárez A, Muñoz-Flores C, Ortega L, Roa F, Castillo C, Romero A, Parra N, Sandoval F, Macaya L, González-Chavarría I, Astuya A, Starck MF, Villegas MF, Agurto N, Montesino R, Sánchez O, Valenzuela A, Toledo JR, Acosta J. Design and functional characterization of Salmo salar TLR5 agonist peptides derived from high mobility group B1 acidic tail. FISH & SHELLFISH IMMUNOLOGY 2024; 146:109373. [PMID: 38272332 DOI: 10.1016/j.fsi.2024.109373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/21/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Toll-like receptor 5 (TLR5) responds to the monomeric form of flagellin and induces the MyD88-depending signaling pathway, activating proinflammatory transcription factors such as NF-κB and the consequent induction of cytokines. On the other hand, HMGB1 is a highly conserved non-histone chromosomal protein shown to interact with and activate TLR5. The present work aimed to design and characterize TLR5 agonist peptides derived from the acidic tail of Salmo salar HMGB1 based on the structural knowledge of the TLR5 surface using global molecular docking platforms. Peptide binding poses complexed on TLR5 ectodomain model from each algorithm were filtrated based on docking scoring functions and predicted theoretical binding affinity of the complex. Circular dichroism spectra were recorded for each peptide selected for synthesis. Only intrinsically disordered peptides (6W, 11W, and SsOri) were selected for experimental functional assay. The functional characterization of the peptides was performed by NF-κB activation assays, RT-qPCR gene expression assays, and Piscirickettsia salmonis challenge in SHK-1 cells. The 6W and 11W peptides increased the nuclear translation of p65 and phosphorylation. In addition, the peptides induced the expression of genes related to the TLR5 pathway activation, pro- and anti-inflammatory response, and differentiation and activation of T lymphocytes towards phenotypes such as TH1, TH17, and TH2. Finally, it was shown that the 11W peptide protects immune cells against infection with P. salmonis bacteria. Overall, the results indicate the usefulness of novel peptides as potential immunostimulants in salmonids.
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Affiliation(s)
- Aleikar Vásquez-Suárez
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Carolina Muñoz-Flores
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Leonardo Ortega
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Francisco Roa
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Carolina Castillo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Alex Romero
- Laboratorio de Inmunología y Estrés de Organismos Acuáticos, Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile; Centro FONDAP, Interdisciplinary Center for Aquaculture Research (INCAR), Universidad de Concepción, Concepción, Chile
| | - Natalie Parra
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Felipe Sandoval
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Luis Macaya
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Iván González-Chavarría
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Allisson Astuya
- Laboratorio de Genómica Marina y Cultivo Celular, Departamento de Oceanografía y COPAS Sur-Austral, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - María Francisca Starck
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Milton F Villegas
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Niza Agurto
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Raquel Montesino
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Oliberto Sánchez
- Laboratorio de Biofármacos Recombinantes, Departamento de Farmacología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Ariel Valenzuela
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Jorge R Toledo
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Jannel Acosta
- Laboratorio de Biotecnología y Biofármacos, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
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Agrawal A, Varshney R, Gattani A, Kirthika P, Gupta R, Kumar D, Singh RP, Singh P. SLAM (CD150) receptor homologous peptides block the peste des petits ruminants virus entry into B95a cells. Proteins 2024; 92:356-369. [PMID: 37881117 DOI: 10.1002/prot.26595] [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: 03/23/2023] [Revised: 08/19/2023] [Accepted: 09/07/2023] [Indexed: 10/27/2023]
Abstract
The fusion of haemagglutinin-neuraminidase (HN) protein of peste des petits ruminant (PPR) virus with signaling lymphocyte activation molecules (SLAM) host cell receptor consequences the virus entry and multiplication inside the host cell. The use of synthetic SLAM homologous peptides (i.e., molecular decoy for HN protein of PPR virus) may check PPR infection at the preliminary stage. Hence, the predicted SLAM homologous peptides using bioinformatics tools were synthesized by solid phase chemistry with standard Merrifield's 9-fluorenylmethoxycarbonyl (Fmoc) chemistry and were purified by reverse phase high performance liquid chromatography. The secondary structures of synthesized peptides were elucidated by circular dichroism spectroscopy. The in vitro interactions of these peptides were studied through indirect Enzyme Linked Immuno Sorbent Assay (ELISA) and visual surface plasmon UV-visible spectroscopy. The SLAM homologous peptides were able to interact with the peste des petits ruminant virus (PPRV) with varying binding efficiency. The interaction of SLAM homologous peptide with the PPR virus was ascertained by the change in the plasmon color from red wine to purple during visual detection and also by bathochromic shift in absorbance spectra under UV-visible spectrophotometry. The cytotoxic and anti-PPRV effect of these peptides were also evaluated in B95a cell line using PPR virus (Sungri/96). The cytotoxic concentration 50 (CC50 ) value of each peptide was greater than 1000 μg mL-1 . The anti-PPRV efficiency of SLAM-22 was relatively high among SLAM homologous peptides, SLAM-22 at 25 μg mL-1 concentration showed a reduction of more than log10 3 virus titer by priming of B95a cell line while the use of SLAM-15 and Muco-17 at the same concentration dropped virus titer from log10 4.8 to log10 2.5 and log10 3.1 respectively. The concentration of SLAM homologous peptide (25 μg mL-1 ) to exert its anti-PPRV effect was much less than its CC50 level (>1000 μg mL-1 ). Therefore, the synthetic SLAM homologous peptides may prove to be better agents to target PPRV.
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Affiliation(s)
- Aditya Agrawal
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal Husbandry, Rewa, Madhya Pradesh, India
| | - Rajat Varshney
- Department of Veterinary Microbiology, Faculty of Veterinary and Animal Sciences, Rajiv Gandhi South Campus, Banaras Hindu University, Mirzapur, Uttar Pradesh, India
- Division of Bacteriology and Mycology, ICAR-IVRI, Bareilly, Uttar Pradesh, India
| | - Anil Gattani
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Department of Veterinary Biochemistry, NDVSU, Jabalpur, Madhya Pradesh, India
| | - Perumalraja Kirthika
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rohini Gupta
- Department of Veterinary Medicine, NDVSU, Jabalpur, Madhya Pradesh, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, Uttar Pradesh, India
| | | | - Praveen Singh
- Division of Biochemistry, ICAR-IVRI, Bareilly, Uttar Pradesh, India
- Biophysics Section, ICAR-IVRI, Bareilly, Uttar Pradesh, India
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Day M, Tetik B, Parlak M, Almeida-Hernández Y, Räschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D. TopBP1 utilises a bipartite GINS binding mode to support genome replication. Nat Commun 2024; 15:1797. [PMID: 38413589 PMCID: PMC10899662 DOI: 10.1038/s41467-024-45946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for replication origin firing, and as such for faithful genetic inheritance. Our biochemical and structural studies demonstrate that the helicase activator GINS interacts with TopBP1 through two separate binding surfaces, the first involving a stretch of highly conserved amino acids in the TopBP1-GINI region, the second a surface on TopBP1-BRCT4. The two surfaces bind to opposite ends of the A domain of the GINS subunit Psf1. Mutation analysis reveals that either surface is individually able to support TopBP1-GINS interaction, albeit with reduced affinity. Consistently, either surface is sufficient for replication origin firing in Xenopus egg extracts and becomes essential in the absence of the other. The TopBP1-GINS interaction appears sterically incompatible with simultaneous binding of DNA polymerase epsilon (Polε) to GINS when bound to Mcm2-7-Cdc45, although TopBP1-BRCT4 and the Polε subunit PolE2 show only partial competitivity in binding to Psf1. Our TopBP1-GINS model improves the understanding of the recently characterised metazoan pre-loading complex. It further predicts the coordination of three molecular origin firing processes, DNA polymerase epsilon arrival, TopBP1 ejection and GINS integration into Mcm2-7-Cdc45.
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Affiliation(s)
- Matthew Day
- School of Biological and Behavioural Sciences, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Bilal Tetik
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Milena Parlak
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Räschle
- Molecular Genetics, Technical University Kaiserslautern, Paul-Ehrlich Straße 24, 67663, Kaiserslautern, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Heike Siegert
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Anika Marko
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Kaiser
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Isabel A Barker
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Dominik Boos
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany.
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37
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Zhang TY, Chen YQ, Tan JC, Zhou JA, Chen WN, Jiang T, Zha JY, Zeng XK, Li BW, Wei LQ, Zou Y, Zhang LY, Hong YM, Wang XL, Zhu RZ, Xu WX, Xi J, Wang QQ, Pan L, Zhang J, Luan Y, Zhu RX, Wang H, Chen C, Liu NN. Global fungal-host interactome mapping identifies host targets of candidalysin. Nat Commun 2024; 15:1757. [PMID: 38413612 PMCID: PMC10899660 DOI: 10.1038/s41467-024-46141-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Candidalysin, a cytolytic peptide toxin secreted by the human fungal pathogen Candida albicans, is critical for fungal pathogenesis. Yet, its intracellular targets have not been extensively mapped. Here, we performed a high-throughput enhanced yeast two-hybrid (HT-eY2H) screen to map the interactome of all eight Ece1 peptides with their direct human protein targets and identified a list of potential interacting proteins, some of which were shared between the peptides. CCNH, a regulatory subunit of the CDK-activating kinase (CAK) complex involved in DNA damage repair, was identified as one of the host targets of candidalysin. Mechanistic studies revealed that candidalysin triggers a significantly increased double-strand DNA breaks (DSBs), as evidenced by the formation of γ-H2AX foci and colocalization of CCNH and γ-H2AX. Importantly, candidalysin binds directly to CCNH to activate CAK to inhibit DNA damage repair pathway. Loss of CCNH alleviates DSBs formation under candidalysin treatment. Depletion of candidalysin-encoding gene fails to induce DSBs and stimulates CCNH upregulation in a murine model of oropharyngeal candidiasis. Collectively, our study reveals that a secreted fungal toxin acts to hijack the canonical DNA damage repair pathway by targeting CCNH and to promote fungal infection.
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Affiliation(s)
- Tian-Yi Zhang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yao-Qi Chen
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing-Cong Tan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jin-An Zhou
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wan-Ning Chen
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Tong Jiang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jin-Yin Zha
- State Key Laboratory of Systems Medicine for Cancer, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Xiang-Kang Zeng
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Science, Shanghai, China
| | - Bo-Wen Li
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lu-Qi Wei
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yun Zou
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lu-Yao Zhang
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yue-Mei Hong
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiu-Li Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Run-Ze Zhu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Wan-Xing Xu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jing Xi
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qin-Qin Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lei Pan
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Science, Shanghai, China
| | - Jian Zhang
- State Key Laboratory of Systems Medicine for Cancer, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Yang Luan
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Rui-Xin Zhu
- Department of Gastroenterology, The Shanghai Tenth People's Hospital, Department of Bioinformatics, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hui Wang
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Changbin Chen
- The Center for Microbes, Development, and Health, Key Laboratory of Molecular Virology and Immunology, Unit of Pathogenic Fungal Infection & Host Immunity, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Ning-Ning Liu
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
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Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
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39
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Munna MMR, Islam MA, Shanta SS, Monty MA. Structural, functional, molecular docking analysis of a hypothetical protein from Talaromyces marneffei and its molecular dynamic simulation: an in-silico approach. J Biomol Struct Dyn 2024:1-20. [PMID: 38345137 DOI: 10.1080/07391102.2024.2314264] [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: 07/31/2023] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
Telaromyces marneffei (formerly Penicillium marneffei) is an endemic pathogenic fungus in Southern China and Southeast Asia. It can cause disease in patients with travel-related exposure to this organism and high morbidity and mortality in acquired immune deficiency syndrome (AIDS). In this study, we analyzed the structure and function of a hypothetical protein from T. marneffei using several bioinformatics tools and servers to unveil novel pharmacological targets and design a peptide vaccine against specific epitopes. A total of seven functional epitopes were screened on the protein, and 'STGVDMWSV' was the most antigenic, non-allergenic and non-toxic. Molecular docking showed stronger affinity between the CTL epitope 'STGVDMWSV' and the MHC I allele HLA-A*02:01, a higher docking score -234.98 kcal/mol, revealed stable interactions during a 100 ns molecular dynamic simulation. Overall, the results of this study revealed that this hypothetical protein is crucial for comprehending biochemical, physiological pathways and identifying novel therapeutic targets for human health. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Masudur Rahman Munna
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Md Ariful Islam
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, PR China
| | - Saima Sajnin Shanta
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Masuma Akter Monty
- Institute of Biomedical Engineering and Technology, Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, PR China
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40
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Wang F, Zhang Z, Mao M, Yang Y, Xu P, Lu S. COSMIC-based mutation database enhances identification efficiency of HLA-I immunopeptidome. J Transl Med 2024; 22:144. [PMID: 38336780 PMCID: PMC10858511 DOI: 10.1186/s12967-023-04821-0] [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: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Neoantigens have emerged as a promising area of focus in tumor immunotherapy, with several established strategies aiming to enhance their identification. Human leukocyte antigen class I molecules (HLA-I), which present intracellular immunopeptides to T cells, provide an ideal source for identifying neoantigens. However, solely relying on a mutation database generated through commonly used whole exome sequencing (WES) for the identification of HLA-I immunopeptides, may result in potential neoantigens being missed due to limitations in sequencing depth and sample quality. METHOD In this study, we constructed and evaluated an extended database for neoantigen identification, based on COSMIC mutation database. This study utilized mass spectrometry-based proteogenomic profiling to identify the HLA-I immunopeptidome enriched from HepG2 cell. HepG2 WES-based and the COSMIC-based mutation database were generated and utilized to identify HepG2-specific mutant immunopeptides. RESULT The results demonstrated that COSMIC-based database identified 5 immunopeptides compared to only 1 mutant peptide identified by HepG2 WES-based database, indicating its effectiveness in identifying mutant immunopeptides. Furthermore, HLA-I affinity of the mutant immunopeptides was evaluated through NetMHCpan and peptide-docking modeling to validate their binding to HLA-I molecules, demonstrating the potential of mutant peptides identified by the COSMIC-based database as neoantigens. CONCLUSION Utilizing the COSMIC-based mutation database is a more efficient strategy for identifying mutant peptides from HLA-I immunopeptidome without significantly increasing the false positive rate. HepG2 specific WES-based database may exclude certain mutant peptides due to WES sequencing depth or sample heterogeneity. The COSMIC-based database can effectively uncover potential neoantigens within the HLA-I immunopeptidomes.
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Affiliation(s)
- Fangzhou Wang
- Medical School of Chinese People's Liberation Army (PLA), Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
| | - Mingsong Mao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yudai Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China.
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- School of Medicine, Guizhou University, Guiyang, China.
| | - Shichun Lu
- Medical School of Chinese People's Liberation Army (PLA), Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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Rivera K, Tanaka KJ, Buechel ER, Origel O, Harrison A, Mason KM, Pinkett HW. Antimicrobial Peptide Recognition Motif of the Substrate Binding Protein SapA from Nontypeable Haemophilus influenzae. Biochemistry 2024; 63:294-311. [PMID: 38189237 PMCID: PMC10851439 DOI: 10.1021/acs.biochem.3c00562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024]
Abstract
Nontypeable Haemophilus influenzae (NTHi) is an opportunistic pathogen associated with respiratory diseases, including otitis media and exacerbations of chronic obstructive pulmonary disease. NTHi exhibits resistance to killing by host antimicrobial peptides (AMPs) mediated by SapA, the substrate binding protein of the sensitivity to antimicrobial peptides (Sap) transporter. However, the specific mechanisms by which SapA selectively binds various AMPs such as defensins and cathelicidin are unknown. In this study, we report mutational analyses of both defensin AMPs and the SapA binding pocket to define the specificity of AMP recognition. Bactericidal assays revealed that NTHi lacking SapA are more susceptible to human beta defensins and LL-37, while remaining highly resistant to a human alpha defensin. In contrast to homologues, our research underscores the distinct specificity of NTHi SapA, which selectively recognizes and binds to peptides containing the charged-hydrophobic motif PKE and RRY. These findings provide valuable insight into the divergence of SapA among bacterial species and NTHi SapA's ability to selectively interact with specific AMPs to mediate resistance.
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Affiliation(s)
- Kristen
G. Rivera
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Kari J. Tanaka
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Evan R. Buechel
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Octavio Origel
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
| | - Alistair Harrison
- The
Center for Microbial Pathogenesis, The Abigail Wexner Research Institute
at Nationwide Children’s Hospital and College of Medicine,
Department of Pediatrics, The Ohio State
University, Columbus, Ohio 43205, United States
| | - Kevin M. Mason
- The
Center for Microbial Pathogenesis, The Abigail Wexner Research Institute
at Nationwide Children’s Hospital and College of Medicine,
Department of Pediatrics, The Ohio State
University, Columbus, Ohio 43205, United States
| | - Heather W. Pinkett
- Department
of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, United States
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Ayoub MA, Yap PG, Mudgil P, Khan FB, Anwar I, Muhammad K, Gan CY, Maqsood S. Invited review: Camel milk-derived bioactive peptides and diabetes-Molecular view and perspectives. J Dairy Sci 2024; 107:649-668. [PMID: 37709024 DOI: 10.3168/jds.2023-23733] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/20/2023] [Indexed: 09/16/2023]
Abstract
In dairy science, camel milk (CM) constitutes a center of interest for scientists due to its known beneficial effect on diabetes as demonstrated in many in vitro, in vivo, and clinical studies and trials. Overall, CM had positive effects on various parameters related to glucose transport and metabolism as well as the structural and functional properties of the pancreatic β-cells and insulin secretion. Thus, CM consumption may help manage diabetes; however, such a recommendation will become rationale and clinically conceivable only if the exact molecular mechanisms and pathways involved at the cellular levels are well understood. Moreover, the application of CM as an alternative antidiabetic tool may first require the identification of the exact bioactive molecules behind such antidiabetic properties. In this review, we describe the advances in our knowledge of the molecular mechanisms reported to be involved in the beneficial effects of CM in managing diabetes using different in vitro and in vivo models. This mainly includes the effects of CM on the different molecular pathways controlling (1) insulin receptor signaling and glucose uptake, (2) the pancreatic β-cell structure and function, and (3) the activity of key metabolic enzymes in glucose metabolism. Moreover, we described the current status of the identification of CM-derived bioactive peptides and their structure-activity relationship study and characterization in the context of molecular markers related to diabetes. Such an overview will not only enrich our scientific knowledge of the plausible mode of action of CM in diabetes but should ultimately rationalize the claim of the potential application of CM against diabetes. This will pave the way toward new directions and ideas for developing a new generation of antidiabetic products taking benefits from the chemical composition of CM.
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Affiliation(s)
- Mohammed Akli Ayoub
- Department of Biological Sciences, College of Medicine and Health Sciences, Khalifa University, 127788, Abu Dhabi, United Arab Emirates.
| | - Pei-Gee Yap
- Analytical Biochemistry Research Centre (ABrC), University Innovation Incubator (i2U) Building, SAINS@USM Campus, Universiti Sains Malaysia, Lebuh Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Priti Mudgil
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Farheen Badrealam Khan
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Irfa Anwar
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
| | - Chee-Yuen Gan
- Analytical Biochemistry Research Centre (ABrC), University Innovation Incubator (i2U) Building, SAINS@USM Campus, Universiti Sains Malaysia, Lebuh Bukit Jambul, 11900 Bayan Lepas, Penang, Malaysia
| | - Sajid Maqsood
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, 15551, Al Ain, United Arab Emirates
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [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: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Lee SH, Kim MA, Sohn YC. Crustacean cardioactive peptide signaling system in the gastropod mollusk Pacific abalone. Comp Biochem Physiol A Mol Integr Physiol 2024; 288:111552. [PMID: 37956901 DOI: 10.1016/j.cbpa.2023.111552] [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: 09/19/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
Crustacean cardioactive peptide (CCAP) signaling systems have been characterized in a diverse range of protostomes, representatively in arthropods. The cyclic CX5C-type CCAP regulates various biological activities through CCAP receptors (CCAPRs), which are orthologous to neuropeptide S receptors (NPSRs) in deuterostomes. However, the CCAPRs of the lophotrochozoa remain poorly characterized; therefore, the relationship between the CCAP, NPS, and CX4C-type oxytocin/vasopressin (OT/VP) signaling systems is unclear. In this study, we identified a CCAP precursor and two CCAPR isoforms in the Pacific abalone (Haliotis discus hannai; Hdh). The Hdh-CCAP precursor was found to harbor three CX5C-type and one CX4C-type CCAPs. The Hdh-CCAPRs displayed homology with protostome CCAPRs and deuterostome NPSRs, having characteristics of the rhodopsin-type G protein-coupled receptors. Phylogenetic analysis showed that lophotrochozoan CCAPRs, including Hdh-CCAPRs, form a monophyletic group distinct from arthropod CCAPRs. Reporter assays demonstrated that all examined Hdh-CCAPs and insect CCAP-induced intracellular Ca2+ mobilization and cAMP accumulation in Hdh-CCAPR-expressing HEK293 cells, whereas none of the CCAP peptides inhibited the forskolin-stimulated cAMP signaling pathway even at micromolar concentrations. In silico ligand-receptor docking models showed that the N-terminal FCN motifs of Hdh-CCAPs are deeply inserted inside the binding pocket of Hdh-CCAPR, forming extensive hydrophobic interactions. In mature Pacific abalone, the transcripts for Hdh-CCAP precursor and Hdh-CCAPR were highly expressed in the neural ganglia compared to the peripheral tissues. Collectively, this study characterized the first CCAP signaling system linked to both Ca2+/PKC and cAMP/PKA signal transduction pathways in gastropod mollusks and gives insights into the evolutional origins of deuterostomian NPS and OT/VP signaling systems.
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Affiliation(s)
- Sang Hyuck Lee
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Mi Ae Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea; East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Gangwon-do, Republic of Korea.
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Ma S, Shi S, Xu B, Liu M, Xie L, Su Y, Li J, Liang Q, Ye S, Wang Y. Host serine protease ACOT2 assists DENV proliferation by hydrolyzing viral polyproteins. mSystems 2024; 9:e0097323. [PMID: 38112462 PMCID: PMC10804956 DOI: 10.1128/msystems.00973-23] [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: 09/11/2023] [Accepted: 11/12/2023] [Indexed: 12/21/2023] Open
Abstract
Dengue fever is a mosquito-borne tropical disease caused by the dengue virus (DENV). The replication of DENV relies on the processing of its genome-encoded polyprotein by both viral protease NS3 (NS3pro) and host proteases. However, the impact of host proteases on DENV proliferation is not well understood. In this study, we utilized fluorophosphonate-based probes (FPs) to investigate the up-regulation of host serine proteases during DENV infection in detail. Among the identified proteases, acyl-CoA thioesterase 2 (ACOT2), an enzyme that hydrolyzes acyl-CoA molecules to generate fatty acids and free CoA, exhibited cleavage activity against DENV polypeptide substrates. Enzymatic assays and virological experiments confirmed that ACOT2 contributes to DENV propagation during the replication stage by cleaving the viral polyprotein. Docking models provided insights into the binding pocket of viral polypeptides and the catalytic mechanism of ACOT2. Notably, this study is the first to demonstrate that ACOT2 functions as a serine protease to hydrolyze protein substrates. These findings offer novel insights into DENV infection, host response, as well as the potential development of innovative antiviral strategies.IMPORTANCEDENV, one of the major pathogens of Dengue fever, remains a significant public health concern in tropical and subtropical regions worldwide. How DENV efficiently hijacks the host and accesses its life cycle with delicate interaction remains to be elucidated. Here, we deconvoluted that the host protease ACOT2 assists the DENV replication and characterized the ACOT2 as a serine protease involved in the hydrolysis of the DENV polypeptide substrate. Our results not only further the understanding of the DENV life cycle but also provide a possibility for the usage of activity-based proteomics to reveal host-virus interactions.
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Affiliation(s)
- Sen Ma
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Sai Shi
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Binghong Xu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Meijun Liu
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Lei Xie
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Yang Su
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jiachen Li
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Qinqin Liang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Sheng Ye
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Yaxin Wang
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
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Song H, Huang W, Jia F, Wang Z, Zhang J, Qian R, Nie G, Wang H. Targeted Degradation of Signal Transduction and Activator of Transcription 3 by Chaperone-Mediated Autophagy Targeting Chimeric Nanoplatform. ACS NANO 2024; 18:1599-1610. [PMID: 38157218 DOI: 10.1021/acsnano.3c09536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Chaperone-mediated autophagy (CMA) is a lysosomal-dependent proteolysis pathway for the degradation of cytosolic proteins. However, exploiting CMA-mediated proteolysis to degrade proteins of interest in cancer therapy has not been widely applied. In this study, we develop a CMA-targeting chimera (CMATAC) to efficiently and specifically degrade signal transduction and activator of transcription 3 (STAT3) in tumor cells. CMATAC consists of STAT3 and heat shock cognate 70 kDa protein (HSC70) targeting peptides connected by a linker. To efficiently deliver CMATACs into tumor cells, lipid nanoparticles (LNPs) are used to encapsulate CMATACs (nCMATACs) and decorated with an insulin-like growth factor 2 receptor (IGF2R) targeting peptide (InCMATACs) to achieve tumor targeting and precise delivery. The CMA pathway is activated in tumor cells by a fasting-mimicking diet (FMD). Furthermore, FMD treatment strongly enhances the cellular uptake and tumor accumulation of InCMATACs by upregulating the IGF2R expression. As a result, InCMATACs efficiently degrade STAT3 protein in both A549 and HCC827 tumor cells and inhibit tumor growths in vivo. This study demonstrates that InCMATACs can be used for selective proteolysis in cancer therapy.
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Affiliation(s)
- Haohao Song
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- Henan Institutes of Advanced Technology, Zhengzhou University, Zhengzhou 450052, China
| | - Wenping Huang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuhao Jia
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhihang Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruihao Qian
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Gungjun Nie
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Liu Y, Zhao W, Jiang Y, Xing S, Li W. Study on the Mechanism of Interaction between Dipeptidyl Peptidase 4 and Inhibitory Peptides Based on Gaussian Accelerated Molecular Dynamic Simulation. Int J Mol Sci 2024; 25:839. [PMID: 38255913 PMCID: PMC10815451 DOI: 10.3390/ijms25020839] [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: 11/24/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Dipeptidyl peptidase 4 (DPP4) inhibitors can effectively inhibit the activity of DPP4, increasing the concentrations of glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), which allows for them to effectively contribute to the reduction of blood sugar levels. Leu-Pro-Ala-Val-Thr-Ile-Arg (LPAVTIR) and Leu-Pro-Pro-Glu-His-Asp-Trp-Arg (LPPEHDWR) were the two peptides with the strongest inhibitory activity against DPP4 selected from silkworm pupa proteins. In this study, four systems were established: Apo (ligand-free DPP4), IPI (IPI-bound DPP4), LPAVTIR (LPAVTIR-bound DPP4), LPPEHDWR (LPPEHDWR-bound DPP4), and Gaussian accelerated molecular dynamic (GaMD) simulation was conducted to investigate the mechanism of action of two inhibitory peptides binding to DPP4. Our study revealed that the LPAVTIR peptide possessed a more stable structure and exhibited a tighter binding to the Ser630 active site in DPP4, thus exhibiting a favorable competitive inhibition effect. In contrast, the LPPEHDWR peptide caused the horizontal α-helix (residues 201-215) composed of Glu205 and Glu206 residues in DPP4 to disappear. The spatial arrangement of active sites Ser630 relative to Glu205 and Glu206 was disrupted, resulting in enzyme inactivation. Moreover, the size of the substrate channel and cavity volume was significantly reduced after the binding of the inhibitory peptide to the protein, which was an important factor in the inhibition of the enzyme activity. A similar effect was also found from IPI (our positive control). By stabilizing the active site of DPP4, the IPI peptide induced the disappearance of the horizontal α-helix and a notable reduction in the active cavity volume. In conclusion, our study provided a solid theoretical foundation for the inhibitory mechanisms of IPI, LPAVTIR, and LPPEHDWR on DPP4, offering valuable insights for advancing the development of drug targets for type 2 diabetes.
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Affiliation(s)
- Yuyang Liu
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (W.Z.)
| | - Wencheng Zhao
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (W.Z.)
| | - Yongxin Jiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China;
| | - Shu Xing
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (W.Z.)
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Changchun 130012, China; (Y.L.); (W.Z.)
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Vásquez-Suárez A, Ortega L, González-Chavarría I, Valenzuela A, Muñoz-Flores C, Altamirano C, Acosta J, Toledo JR. Agonistic effect of peptides derived from a truncated HMGB1 acidic tail sequence in TLR5 from Salmo salar. FISH & SHELLFISH IMMUNOLOGY 2024; 144:109219. [PMID: 37952850 DOI: 10.1016/j.fsi.2023.109219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/24/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
Based on the structural knowledge of TLR5 surface and using blind docking platforms, peptides derived from a truncated HMGB1 acidic tail from Salmo salar was designed as TLR5 agonistic. Additionally, a template peptide with the native N-terminal of the acidic tail sequence as a reference was included (SsOri). Peptide binding poses complexed on TLR5 ectodomain model from each algorithm were filtrated based on docking scoring functions and predicted theoretical binding affinity of the complex. The best peptides, termed 6WK and 5LWK, were selected for chemical synthesis and experimental functional assay. The agonist activity by immunoblotting and immunocytochemistry was determined following the NF-κBp65 phosphorylation (p-NF-κBp65) and the nuclear translocation of the NF-κBp65 subunit from the cytosol, respectively. HeLa cells stably expressing a S. salar TLR5 chimeric form (TLR5c7) showed increased p-NF-κBp65 levels regarding extracts from flagellin-treated cells. No statistically significant differences (p > 0.05) were found in the detected p-NF-κBp65 levels between cellular extracts treated with peptides or flagellin by one-way ANOVA. The image analysis of NF-κBp65 immunolabeled cells obtained by confocal microscopy showed increased nuclear NF-κBp65 co-localization in cells both 5LWK and flagellin stimulated, while 6WK and SsOri showed less effect on p65 nuclear translocation (p < 0.05). Also, an increased transcript expression profile of proinflammatory cytokines such as TNFα, IL-1β, and IL-8 in HKL cells isolated from Salmo salar was evidenced in 5LWK - stimulated by RT-PCR analysis. Overall, the result indicates the usefulness of novel peptides as a potential immunostimulant in S. salar.
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Affiliation(s)
- Aleikar Vásquez-Suárez
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Leonardo Ortega
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Iván González-Chavarría
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Ariel Valenzuela
- Laboratorio de Piscicultura y Patología Acuática, Departamento de Oceanografía, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Carolina Muñoz-Flores
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Claudia Altamirano
- Laboratorio de Cultivos Celulares, Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, 2362803, Valparaíso, Chile
| | - Jannel Acosta
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile
| | - Jorge R Toledo
- Biotechnology and Biopharmaceuticals Laboratory, Departamento de Fisiopatología, Facultad de Ciencias Biológicas, Universidad de Concepción, Víctor Lamas 1290, Concepción, CP. 4030000, Chile.
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Singh BP, Paul S, Goel G. Shotgun proteomics and molecular simulations on multifunctional bioactive peptides derived from the whey of unexplored "Gaddi" goat of Himalayas. Food Chem 2024; 430:137075. [PMID: 37549618 DOI: 10.1016/j.foodchem.2023.137075] [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: 05/24/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
The very first time, whey protein from the Himalayan goat breed "Gaddi" was hydrolyzed with alcalase, flavourzyme, and a combination of both in this study. The degree of hydrolysis (DH) ranged from 28 to 53%, with sequential hydrolysis by combination achieving the highest DH. The sequential hydrolysis demonstrated antimicrobial activity against all pathogens used with 3 kDa permeate showed significantly higher (p < 0.05) activity against S. aureus, E. coli, B. cereus and C. sakazakii. The antioxidant activity was in the range of IC50 = 0.49 to 2.00 mg protein/mL, flavourzyme and sequential hydrolysates showed significant ABTS radical and FRAP inhibition. The α-amylase inhibitory activity was highest in 3 kDa permeate of flavourzyme with IC50 values of 0.34 mg protein/mL. Bioactive peptides DDSPDLPK, EMPFPK and TPEVDKEALEK were identified most significant in the hydrolysates. In molecular docking, the DDSPDLPK interacted most efficiently with enzymes involved in microbial growth, oxidative stress, and hyperglycemia.
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Affiliation(s)
- Brij Pal Singh
- Department of Microbiology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh 123031, India.
| | - Souparno Paul
- Department of Microbiology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh 123031, India
| | - Gunjan Goel
- Department of Microbiology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh 123031, India.
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Patel KN, Chavda D, Manna M. Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies. Methods Mol Biol 2024; 2780:165-201. [PMID: 38987470 DOI: 10.1007/978-1-0716-3985-6_11] [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] [Indexed: 07/12/2024]
Abstract
Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).
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Affiliation(s)
- Keyur N Patel
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dhruvil Chavda
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Moutusi Manna
- Applied Phycology and Biotechnology Division, CSIR Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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