51
|
Rui M, Zhang W, Mi K, Ni H, Ji W, Yu X, Qin J, Feng C. Design and evaluation of α-helix-based peptide inhibitors for blocking PD-1/PD-L1 interaction. Int J Biol Macromol 2023; 253:126811. [PMID: 37690647 DOI: 10.1016/j.ijbiomac.2023.126811] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
The current research in tumor immunotherapy indicates that blocking the protein-protein interaction (PPI) between PD-1 and its ligand, PD-L1, may be one of the most effective treatments for cancer patients. The α-helix is a common elements of protein secondary structure and is often involved in protein interaction. Thus, α-helix-based peptides could mimic proteins involved in such interactions and are also capable of modulating PPI in vivo. In this study, starting from a potential α-helix-rich protein, we designed a series of α-helix-based peptide candidates to block PD-1/PD-L1 interaction. These candidates were first screened using molecular docking and molecular dynamics simulations, and then their capacities to inhibit PD-1/PD-L1 interactions and to restore antitumor immune activities were investigated using the HTRF assay, SPR assay, cellular co-culture experiments and animal model experiments. Two peptides exhibited the best anti-tumor effects and the strong ability to restore the immunity of tumor-infiltrating T-cells. Further D-amino acid substitution was employed to improve the serum stability of peptide candidate, making the intravenous administration easier while maintaining the therapeutic efficacy. The resultant peptides showed promise as checkpoint inhibitors for application in tumor immunotherapy. These findings suggested that our strategy for developing peptides starting from an α-helical structure could be used in the design of bioactive inhibitors to potential block protein-protein interactions.
Collapse
Affiliation(s)
- Mengjie Rui
- Department of Pharmaceutics, School of Pharmacy, Jiangsu University, Zhenjiang, PR China
| | - Wen Zhang
- Department of Pharmaceutics, School of Pharmacy, Jiangsu University, Zhenjiang, PR China
| | - Ke Mi
- Department of Pharmaceutics, School of Pharmacy, Jiangsu University, Zhenjiang, PR China
| | - Hairong Ni
- Department of Pharmaceutics, School of Pharmacy, Jiangsu University, Zhenjiang, PR China
| | - Wei Ji
- Department of Pharmaceutics, School of Pharmacy, Jiangsu University, Zhenjiang, PR China
| | - Xuefei Yu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Hangzhou, PR China
| | - Jiangjiang Qin
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, PR China
| | - Chunlai Feng
- Department of Pharmaceutics, School of Pharmacy, Jiangsu University, Zhenjiang, PR China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration, Tongji University, Ministry of Education, Shanghai, PR China.
| |
Collapse
|
52
|
André S, Verteneuil S, Ris L, Kahvecioglu ZC, Nonclercq D, De Winter J, Vander Elst L, Laurent S, Muller RN, Burtea C. Modulation of Cytosolic Phospholipase A2 as a Potential Therapeutic Strategy for Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:1395-1426. [PMID: 38225969 PMCID: PMC10789292 DOI: 10.3233/adr-230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024] Open
Abstract
Background Alzheimer's disease (AD) is a neurodegenerative disorder lacking any curative treatment up to now. Indeed, actual medication given to the patients alleviates only symptoms. The cytosolic phospholipase A2 (cPLA2-IVA) appears as a pivotal player situated at the center of pathological pathways leading to AD and its inhibition could be a promising therapeutic approach. Objective A cPLA2-IVA inhibiting peptide was identified in the present work, aiming to develop an original therapeutic strategy. Methods We targeted the cPLA2-IVA using the phage display technology. The hit peptide PLP25 was first validated in vitro (arachidonic acid dosage [AA], cPLA2-IVA cellular translocation) before being tested in vivo. We evaluated spatial memory using the Barnes maze, amyloid deposits by MRI and immunohistochemistry (IHC), and other important biomarkers such as the cPLA2-IVA itself, the NMDA receptor, AβPP and tau by IHC after i.v. injection in APP/PS1 mice. Results Showing a high affinity for the C2 domain of this enzyme, the peptide PLP25 exhibited an inhibitory effect on cPLA2-IVA activity by blocking its binding to its substrate, resulting in a decreased release of AA. Coupled to a vector peptide (LRPep2) in order to optimize brain access, we showed an improvement of cognitive abilities of APP/PS1 mice, which also exhibited a decreased number of amyloid plaques, a restored expression of cPLA2-IVA, and a favorable effect on NMDA receptor expression and tau protein phosphorylation. Conclusions cPLA2-IVA inhibition through PLP25 peptide could be a promising therapeutic strategy for AD.
Collapse
Affiliation(s)
- Séverine André
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
| | - Sébastien Verteneuil
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
| | - Laurence Ris
- Department of Neurosciences, University of Mons, Research Institute for Health Science and Technologies, Mons, Belgium
| | - Zehra-Cagla Kahvecioglu
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
| | | | - Julien De Winter
- Organic Synthesis and Mass Spectrometry Laboratory (SMOs), University of Mons-UMONS, Mons, Belgium
| | - Luce Vander Elst
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
| | - Sophie Laurent
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
- Center for Microscopy and Molecular Imaging, Gosselies, Belgium
| | - Robert N. Muller
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
- Center for Microscopy and Molecular Imaging, Gosselies, Belgium
| | - Carmen Burtea
- General, Organic and Biomedical Chemistry Unit, NMR and Molecular Imaging Laboratory, University of Mons, Mons, Belgium
| |
Collapse
|
53
|
Zerihun M, Qvit N. Selective inhibitors targeting Fis1/Mid51 protein-protein interactions protect against hypoxia-induced damage in cardiomyocytes. Front Pharmacol 2023; 14:1275370. [PMID: 38192411 PMCID: PMC10773907 DOI: 10.3389/fphar.2023.1275370] [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: 08/09/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Cardiovascular diseases (CVDs) are the most common non-communicable diseases globally. An estimated 17.9 million people died from CVDs in 2019, representing 32% of all global deaths. Mitochondria play critical roles in cellular metabolic homeostasis, cell survival, and cell death, as well as producing most of the cell's energy. Protein-protein interactions (PPIs) have a significant role in physiological and pathological processes, and aberrant PPIs are associated with various diseases, therefore they are potential drug targets for a broad range of therapeutic areas. Due to their ability to mimic natural interaction motifs and cover relatively larger interaction region, peptides are very promising as PPI inhibitors. To expedite drug discovery, computational approaches are widely used for screening potential lead compounds. Here, we developed peptides that inhibit mitochondrial fission 1 (Fis1)/mitochondrial dynamics 51 kDa (Mid51) PPI to reduce the cellular damage that can lead to various human pathologies, such as CVDs. Based on a rational design approach we developed peptide inhibitors of the Fis1/Mid51 PPI. In silico and in vitro studies were done to evaluate the biological activity and molecular interactions of the peptides. Two peptides, CVP-241 and CVP-242 were identified based on low binding energy and molecular dynamics simulations. These peptides inhibit Fis1/Mid51 PPI (-1324.9 kcal mol-1) in docking calculations (CVP-241, -741.3 kcal mol-1, and CVP-242, -747.4 kcal mol-1), as well as in vitro experimental studies Fis1/Mid51 PPI (KD 0.054 µM) Fis1/Mid51 PPI + CVP-241 (KD 3.43 µM), and Fis1/Mid51 PPI + CVP-242 (KD 44.58 µM). Finally, these peptides have no toxicity to H9c2 cells, and they increase cell viability in cardiomyocytes (H9c2 cells). Consequently, the identified inhibitor peptides could serve as potent molecules in basic research and as leads for therapeutic development.
Collapse
Affiliation(s)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| |
Collapse
|
54
|
Zerihun M, Rubin SJS, Silnitsky S, Qvit N. An Update on Protein Kinases as Therapeutic Targets-Part II: Peptides as Allosteric Protein Kinase C Modulators Targeting Protein-Protein Interactions. Int J Mol Sci 2023; 24:17504. [PMID: 38139336 PMCID: PMC10743673 DOI: 10.3390/ijms242417504] [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: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Human protein kinases are highly-sought-after drug targets, historically harnessed for treating cancer, cardiovascular disease, and an increasing number of autoimmune and inflammatory conditions. Most current treatments involve small molecule protein kinase inhibitors that interact orthosterically with the protein kinase ATP-binding pocket. As a result, these compounds are often poorly selective and highly toxic. Part I of this series reviews the role of PKC isoforms in various human diseases, featuring cancer and cardiovascular disease, as well as translational examples of PKC modulation applied to human health and disease. In the present Part II, we discuss alternative allosteric binding mechanisms for targeting PKC, as well as novel drug platforms, such as modified peptides. A major goal is to design protein kinase modulators with enhanced selectivity and improved pharmacological properties. To this end, we use molecular docking analysis to predict the mechanisms of action for inhibitor-kinase interactions that can facilitate the development of next-generation PKC modulators.
Collapse
Affiliation(s)
- Mulate Zerihun
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| | - Samuel J. S. Rubin
- Department of Medicine, School of Medicine, Stanford University, 300 Pasteur Drive, Stanford, CA 94305, USA;
| | - Shmuel Silnitsky
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, P.O. Box 1589, Safed 1311502, Israel; (M.Z.); (S.S.)
| |
Collapse
|
55
|
Côco LZ, Aires R, Carvalho GR, Belisário EDS, Yap MKK, Amorim FG, Conde-Aranda J, Nogueira BV, Vasquez EC, Pereira TDMC, Campagnaro BP. Unravelling the Gastroprotective Potential of Kefir: Exploring Antioxidant Effects in Preventing Gastric Ulcers. Cells 2023; 12:2799. [PMID: 38132119 PMCID: PMC10742242 DOI: 10.3390/cells12242799] [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: 10/30/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
The present study was conducted to evaluate the protective effect of milk kefir against NSAID-induced gastric ulcers. Male Swiss mice were divided into three groups: control (Vehicle; UHT milk at a dose of 0.3 mL/100 g), proton pump inhibitor (PPI; lansoprazole 30 mg/kg), and 4% milk kefir (Kefir; 0.3 mL/100 g). After 14 days of treatment, gastric ulcer was induced by oral administration of indomethacin (40 mg/kg). Reactive oxygen species (ROS), nitric oxide (NO), DNA content, cellular apoptosis, IL-10 and TNF-α levels, and myeloperoxidase (MPO) enzyme activity were determined. The interaction networks between NADPH oxidase 2 and kefir peptides 1-35 were determined using the Residue Interaction Network Generator (RING) webserver. Pretreatment with kefir for 14 days prevented gastric lesions. In addition, kefir administration reduced ROS production, DNA fragmentation, apoptosis, and TNF-α systemic levels. Simultaneously, kefir increased NO bioavailability in gastric cells and IL-10 systemic levels. A total of 35 kefir peptides showed affinity with NADPH oxidase 2. These findings suggest that the gastroprotective effect of kefir is due to its antioxidant and anti-inflammatory properties. Kefir could be a promising natural therapy for gastric ulcers, opening new perspectives for future research.
Collapse
Affiliation(s)
- Larissa Zambom Côco
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Rafaela Aires
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Glaucimeire Rocha Carvalho
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Eduarda de Souza Belisário
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | | | - Fernanda Gobbi Amorim
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, 4000 Liège, Belgium;
| | - Javier Conde-Aranda
- Molecular and Cellular Gastroenterology, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain;
| | - Breno Valentim Nogueira
- Department of Morphology, Health Sciences Center, Federal University of Espírito Santo (UFES), Vitoria 29047-105, ES, Brazil;
| | - Elisardo Corral Vasquez
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Thiago de Melo Costa Pereira
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| | - Bianca Prandi Campagnaro
- Laboratory of Translational Physiology and Pharmacology, Pharmaceutical Sciences Graduate Program, Vila Velha University (UVV), Vila Velha 29102-920, ES, Brazil; (L.Z.C.); (R.A.); (G.R.C.); (E.d.S.B.); (E.C.V.); (T.d.M.C.P.)
| |
Collapse
|
56
|
Pitsillou E, Logothetis ANO, Liang JJ, El-Osta A, Hung A, AbuMaziad AS, Karagiannis TC. Identification of Potential Modulators of a Pathogenic G Protein-Gated Inwardly Rectifying K + Channel 4 Mutant: In Silico Investigation in the Context of Drug Discovery for Hypertension. Molecules 2023; 28:7946. [PMID: 38138436 PMCID: PMC10745636 DOI: 10.3390/molecules28247946] [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: 11/10/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Genetic abnormalities have been associated with primary aldosteronism, a major cause of secondary hypertension. This includes mutations in the KCNJ5 gene, which encodes G protein-gated inwardly rectifying K+ channel 4 (GIRK4). For example, the substitution of glycine with glutamic acid gives rise to the pathogenic GIRK4G151E mutation, which alters channel selectivity, making it more permeable to Na+ and Ca2+. While tertiapin and tertiapin-Q are well-known peptide inhibitors of the GIRK4WT channel, clinically, there is a need for the development of selective modulators of mutated channels, including GIRK4G151E. Using in silico methods, including homology modeling, protein-peptide docking, ligand-binding site prediction, and molecular docking, we aimed to explore potential modulators of GIRK4WT and GIRK4G151E. Firstly, protein-peptide docking was performed to characterize the binding site of tertiapin and its derivative to the GIRK4 channels. In accordance with previous studies, the peptide inhibitors preferentially bind to the GIRK4WT channel selectivity filter compared to GIRK4G151E. A ligand-binding site analysis was subsequently performed, resulting in the identification of two potential regions of interest: the central cavity and G-loop gate. Utilizing curated chemical libraries, we screened over 700 small molecules against the central cavity of the GIRK4 channels. Flavonoids, including luteolin-7-O-rutinoside and rutin, and the macrolides rapamycin and troleandomycin bound strongly to the GIRK4 channels. Similarly, xanthophylls, particularly luteoxanthin, bound to the central cavity with a strong preference towards the mutated GIRK4G151E channel compared to GIRK4WT. Overall, our findings suggest potential lead compounds for further investigation, particularly luteoxanthin, that may selectively modulate GIRK4 channels.
Collapse
Affiliation(s)
- Eleni Pitsillou
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Alexander N. O. Logothetis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Julia J. Liang
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
| | - 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, Denmark
| | - Andrew Hung
- School of Science, STEM College, RMIT University, Melbourne, VIC 3001, Australia
| | - Asmaa S. AbuMaziad
- Department of Pediatrics, College of Medicine Tucson, The University of Arizona, Tucson, AZ 85724, USA
| | - Tom C. Karagiannis
- Epigenomic Medicine Laboratory at prospED Polytechnic, Carlton, VIC 3053, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
- Epigenetics in Human Health and Disease Program, Baker Heart and Diabetes Institute, 75 Commercial Road, Prahran, VIC 3004, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, VIC 3010, Australia
| |
Collapse
|
57
|
Choi S, Son SH, Kim MY, Na I, Uversky VN, Kim CG. Improved prediction of protein-protein interactions by a modified strategy using three conventional docking software in combination. Int J Biol Macromol 2023; 252:126526. [PMID: 37633550 DOI: 10.1016/j.ijbiomac.2023.126526] [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: 06/30/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Proteins play a crucial role in many biological processes, where their interaction with other proteins are integral. Abnormal protein-protein interactions (PPIs) have been linked to various diseases including cancer, and thus targeting PPIs holds promise for drug development. However, experimental confirmation of the peculiarities of PPIs is challenging due to their dynamic and transient nature. As a complement to experimental technologies, multiple computational molecular docking (MD) methods have been developed to predict the structures of protein-protein complexes and their dynamics, still requiring further improvements in several issues. Here, we report an improved MD method, namely three-software docking (3SD), by employing three popular protein-peptide docking software (CABS-dock, HPEPDOCK, and HADDOCK) in combination to ensure constant quality for most targets. We validated our 3SD performance in known protein-peptide interactions (PpIs). We also enhanced MD performance in proteins having intrinsically disordered regions (IDRs) by applying the modified 3SD strategy, the three-software docking after removing random coiled IDR (3SD-RR), to the comparable crystal PpI structures. At the end, we applied 3SD-RR to the AlphaFold2-predicted receptors, yielding an efficient prediction of PpI pose with high relevance to the experimental data regardless of the presence of IDRs or the availability of receptor structures. Our study provides an improved solution to the challenges in studying PPIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery. SIGNIFICANCE STATEMENT: Protein-protein interactions (PPIs) are integral to life, and abnormal PPIs are associated with diseases such as cancer. Studying protein-peptide interactions (PpIs) is challenging due to their dynamic and transient nature. Here we developed improved docking methods (3SD and 3SD-RR) to predict the PpI poses, ensuring constant quality in most targets and also addressing issues like intrinsically disordered regions (IDRs) and artificial intelligence-predicted structures. Our study provides an improved solution to the challenges in studying PpIs through computational docking and has the potential to contribute to PPIs-targeted drug discovery.
Collapse
Affiliation(s)
- Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Insung Na
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida; Tampa, FL 33612, USA.
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea; CGK Biopharma Co. Ltd., 222 Wangshipri-ro, Sungdong-gu, Seoul 04763, Republic of Korea.
| |
Collapse
|
58
|
Chen J, Gu Z, Lai L, Pei J. In silico protein function prediction: the rise of machine learning-based approaches. MEDICAL REVIEW (2021) 2023; 3:487-510. [PMID: 38282798 PMCID: PMC10808870 DOI: 10.1515/mr-2023-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/11/2023] [Indexed: 01/30/2024]
Abstract
Proteins function as integral actors in essential life processes, rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation. Within the context of protein research, an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings. Due to the exorbitant costs and limited throughput inherent in experimental investigations, computational models offer a promising alternative to accelerate protein function annotation. In recent years, protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks. This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction. In this review, we elucidate the historical evolution and research paradigms of computational methods for predicting protein function. Subsequently, we summarize the progress in protein and molecule representation as well as feature extraction techniques. Furthermore, we assess the performance of machine learning-based algorithms across various objectives in protein function prediction, thereby offering a comprehensive perspective on the progress within this field.
Collapse
Affiliation(s)
- Jiaxiao Chen
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Zhonghui Gu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Luhua Lai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Research Unit of Drug Design Method, Chinese Academy of Medical Sciences (2021RU014), Beijing, China
| | - Jianfeng Pei
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Research Unit of Drug Design Method, Chinese Academy of Medical Sciences (2021RU014), Beijing, China
| |
Collapse
|
59
|
Agrawal A, Varshney R, Gattani A, Hira Khan M, Gupta R, Solanki KS, Patel SK, Singh RP, Singh P. Development of Hemagglutinin-Neuraminidase Homologous Peptides as Novel Promising Therapeutic Agents Against Peste des Petits Ruminants Virus. Protein J 2023; 42:685-697. [PMID: 37421558 DOI: 10.1007/s10930-023-10134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
The lack of specific antiviral therapy and complications associated with the existing peste des petits ruminants (PPR) vaccines accentuates the search of novel antiviral blocking agents in order to curtail the PPR infection at initial level. The synthetic hemagglutinin-neuraminidase (HN) homologous peptides may compete with the natural HN protein of PPR virus for binding to signaling lymphocytic activation molecule (SLAM) receptor, consequently, may disrupt peste des petits ruminants virus (PPRV) at entry level. Therefore, insilico analysis, synthesis, purification and subsequent characterization of HN homologous peptides were conducted in this study. The HN homologous peptides were synthesized by means of solid phase chemistry and were purified by reversed-phase-high performance liquid chromatography. The mass as well as sequence of HN homologous peptides were assessed by mass spectroscopy while its secondary structure was elucidated by circular dichroism spectroscopy. The binding (interaction) efficacy of HN homologous peptides with PPRV antibodies was assessed via indirect enzyme linked immunosorbent assay, visual detection test (red wine to purple), bathochromic shift under UV-Vis spectrophotometry and lateral flow immunochromatographic strip test. The antiviral properties and cytotoxicity of these peptides were also assessed in B95a cell line with changes in cytopathic effect and titer of PPRV (Sungri/96). The presence of green fluorescein isothiocyanate over the B95a cell surface pointed towards the binding of HN homologous peptides with surface SLAM receptor. Moreover, the intact beta sheet configuration in water and lower cytotoxicity [cytotoxic concentration 50 (CC50) > 1000 µg/ml] of these peptides signifies its in vivo use. Among HN homologous peptides, the binding efficacy and antiviral properties of pep A was relatively high in comparison to pep B and Pep ppr peptides. The prerequisite concentration of HN homologous peptides (pep A = 12.5 µg/ml; pep B = 25 µg/ml; pep ppr = 25 µg/ml) to exemplify its antiviral effect was much lower than its CC50 level. Hence, this study signifies the therapeutic potential of synthetic HN homologous peptides.
Collapse
Affiliation(s)
- Aditya Agrawal
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India.
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal husbandry, NDVSU, Rewa, Jabalpur, 486001, India.
| | - Rajat Varshney
- Department of Veterinary Microbiology, BHU, Mirzapur, U.P., 231001, India
- Division of Bacteriology and Mycology, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| | - Anil Gattani
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal husbandry, NDVSU, Jabalpur, 486001, India
| | - Mahvash Hira Khan
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Science and Animal husbandry, NDVSU, Jabalpur, 486001, India
| | - Rohini Gupta
- Department of Veterinary Medicine, College of Veterinary Science and Animal husbandry, NDVSU, Jabalpur, 486001, India
| | - Khushal Singh Solanki
- Division of Veterinary Biotechnology, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| | - Shailesh Kumar Patel
- Department of Veterinary Pathology, College of Veterinary Science and Animal husbandry, NDVSU, Rewa, Jabalpur, 486001, India
| | - R P Singh
- Division of Bacteriology and Mycology, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| | - Praveen Singh
- Division of Animal Biochemistry, IVRI, Izatnagar, Bareilly, U.P., 243122, India
| |
Collapse
|
60
|
Pitou M, Papachristou E, Bratsios D, Kefala GM, Tsagkarakou AS, Leonidas DD, Aggeli A, Papadopoulos GE, Papi RM, Choli-Papadopoulou T. In Vitro Chondrogenesis Induction by Short Peptides of the Carboxy-Terminal Domain of Transforming Growth Factor β1. Biomedicines 2023; 11:3182. [PMID: 38137403 PMCID: PMC10740954 DOI: 10.3390/biomedicines11123182] [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: 09/17/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 12/24/2023] Open
Abstract
Τransforming growth factor β1 (TGF-β1) comprises a key regulator protein in many cellular processes, including in vivo chondrogenesis. The treatment of human dental pulp stem cells, separately, with Leu83-Ser112 (C-terminal domain of TGF-β1), as well as two very short peptides, namely, 90-YYVGRKPK-97 (peptide 8) and 91-YVGRKP-96 (peptide 6) remarkably enhanced the chondrogenic differentiation capacity in comparison to their full-length mature TGF-β1 counterpart either in monolayer cultures or 3D scaffolds. In 3D scaffolds, the reduction of the elastic modulus and viscous modulus verified the production of different amounts and types of ECM components. Molecular dynamics simulations suggested a mode of the peptides' binding to the receptor complex TβRII-ALK5 and provided a possible structural explanation for their role in inducing chondrogenesis, along with endogenous TGF-β1. Further experiments clearly verified the aforementioned hypothesis, indicating the signal transduction pathway and the involvement of TβRII-ALK5 receptor complex. Real-time PCR experiments and Western blot analysis showed that peptides favor the ERK1/2 and Smad2 pathways, leading to an articular, extracellular matrix formation, while TGF-β1 also favors the Smad1/5/8 pathway which leads to the expression of the metalloproteinases ADAMTS-5 and MMP13 and, therefore, to a hypertrophic chondrocyte phenotype. Taken together, the two short peptides, and, mainly, peptide 8, could be delivered with a scaffold to induce in vivo chondrogenesis in damaged articular cartilage, constituting, thus, an alternative therapeutic approach for osteoarthritis.
Collapse
Affiliation(s)
- Maria Pitou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece
| | - Eleni Papachristou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece
| | - Dimitrios Bratsios
- Laboratory of Biomedical Engineering, School of Chemical Engineering, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece
| | - Georgia-Maria Kefala
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Anastasia S. Tsagkarakou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Demetrios D. Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Amalia Aggeli
- Laboratory of Biomedical Engineering, School of Chemical Engineering, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece
| | - Georgios E. Papadopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Rigini M. Papi
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece
| | - Theodora Choli-Papadopoulou
- Laboratory of Biochemistry, School of Chemistry, Aristotle University of Thessaloniki (AUTh), 54124 Thessaloniki, Greece
| |
Collapse
|
61
|
Chaudhuri D, Majumder S, Datta J, Giri K. In silico designing of an epitope-based peptide vaccine cocktail against Nipah virus: an Indian population-based epidemiological study. Arch Microbiol 2023; 205:380. [PMID: 37955744 DOI: 10.1007/s00203-023-03717-3] [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: 09/20/2023] [Revised: 10/09/2023] [Accepted: 10/21/2023] [Indexed: 11/14/2023]
Abstract
Nipah virus, a zoonotic virus from the family Paramyxoviridae has led to significant loss of lives till date with the most recent outbreak in India reported in Kerala. The virus has a considerably high mortality rate along with lack of characteristic symptoms which results in the delay of the virus detection. No specific vaccine is available for the virus although monoclonal antibody treatment has been seen to be effective along with favipiravir. The high mortality and complications caused by the virus underscores the necessity to develop alternative modes of vaccination. One such method has been designed in this study using peptide cocktail consisting of the immunologically important epitopes for use as vaccine. The human leucocytic antigens that are used for the study were analyzed for their presence in various ethnic Indian populations. This study may serve as a new avenue for development of more efficient peptide cocktail vaccines in recent future based on the population genetics and ethnicity.
Collapse
Affiliation(s)
- Dwaipayan Chaudhuri
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Satyabrata Majumder
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Joyeeta Datta
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India
| | - Kalyan Giri
- Department of Life Sciences, Presidency University, 86/1 College Street, Kolkata, 700073, India.
| |
Collapse
|
62
|
Balakrishnan N, Katkar R, Pham PV, Downey T, Kashyap P, Anastasiu DC, Ramasubramanian AK. Prospection of Peptide Inhibitors of Thrombin from Diverse Origins Using a Machine Learning Pipeline. Bioengineering (Basel) 2023; 10:1300. [PMID: 38002424 PMCID: PMC10669389 DOI: 10.3390/bioengineering10111300] [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: 09/14/2023] [Revised: 10/30/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Thrombin is a key enzyme involved in the development and progression of many cardiovascular diseases. Direct thrombin inhibitors (DTIs), with their minimum off-target effects and immediacy of action, have greatly improved the treatment of these diseases. However, the risk of bleeding, pharmacokinetic issues, and thrombotic complications remain major concerns. In an effort to increase the effectiveness of the DTI discovery pipeline, we developed a two-stage machine learning pipeline to identify and rank peptide sequences based on their effective thrombin inhibitory potential. The positive dataset for our model consisted of thrombin inhibitor peptides and their binding affinities (KI) curated from published literature, and the negative dataset consisted of peptides with no known thrombin inhibitory or related activity. The first stage of the model identified thrombin inhibitory sequences with Matthew's Correlation Coefficient (MCC) of 83.6%. The second stage of the model, which covers an eight-order of magnitude range in KI values, predicted the binding affinity of new sequences with a log room mean square error (RMSE) of 1.114. These models also revealed physicochemical and structural characteristics that are hidden but unique to thrombin inhibitor peptides. Using the model, we classified more than 10 million peptides from diverse sources and identified unique short peptide sequences (<15 aa) of interest, based on their predicted KI. Based on the binding energies of the interaction of the peptide with thrombin, we identified a promising set of putative DTI candidates. The prediction pipeline is available on a web server.
Collapse
Affiliation(s)
- Nivedha Balakrishnan
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Rahul Katkar
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Peter V. Pham
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - Taylor Downey
- Department of Computer Science and Engineering, Santa Clara University, Santa Clara, CA 95053, USA (D.C.A.)
| | - Prarthna Kashyap
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| | - David C. Anastasiu
- Department of Computer Science and Engineering, Santa Clara University, Santa Clara, CA 95053, USA (D.C.A.)
| | - Anand K. Ramasubramanian
- Department of Chemical and Materials Engineering, San José State University, San Jose, CA 95192, USA (P.K.)
| |
Collapse
|
63
|
Holmes SG, Desai UR. Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins. Biomolecules 2023; 13:1633. [PMID: 38002315 PMCID: PMC10669598 DOI: 10.3390/biom13111633] [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: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Although molecular docking has evolved dramatically over the years, its application to glycosaminoglycans (GAGs) has remained challenging because of their intrinsic flexibility, highly anionic character and rather ill-defined site of binding on proteins. GAGs have been treated as either fully "rigid" or fully "flexible" in molecular docking. We reasoned that an intermediate semi-rigid docking (SRD) protocol may be better for the recapitulation of native heparin/heparan sulfate (Hp/HS) topologies. Herein, we study 18 Hp/HS-protein co-complexes containing chains from disaccharide to decasaccharide using genetic algorithm-based docking with rigid, semi-rigid, and flexible docking protocols. Our work reveals that rigid and semi-rigid protocols recapitulate native poses for longer chains (5→10 mers) significantly better than the flexible protocol, while 2→4-mer poses are better predicted using the semi-rigid approach. More importantly, the semi-rigid docking protocol is likely to perform better when no crystal structure information is available. We also present a new parameter for parsing selective versus non-selective GAG-protein systems, which relies on two computational parameters including consistency of binding (i.e., RMSD) and docking score (i.e., GOLD Score). The new semi-rigid protocol in combination with the new computational parameter is expected to be particularly useful in high-throughput screening of GAG sequences for identifying promising druggable targets as well as drug-like Hp/HS sequences.
Collapse
Affiliation(s)
- Samuel G. Holmes
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
| | - Umesh R. Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA;
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, 800 E. Leigh Street, Suite 212, Richmond, VA 23219, USA
| |
Collapse
|
64
|
Wang L, Wu L, Du Y, Wang X, Yang B, Guo S, Zhou Y, Xu Y, Yang S, Zhang Y, Ren J. DNA-dependent protein kinase catalytic subunit (DNA-PKcs) drives angiotensin II-induced vascular remodeling through regulating mitochondrial fragmentation. Redox Biol 2023; 67:102893. [PMID: 37741045 PMCID: PMC10520570 DOI: 10.1016/j.redox.2023.102893] [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: 09/01/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
BACKGROUND DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is a novel instigator for mitochondrial dysfunction, and plays an important role in the pathogenesis of cardiovascular diseases. However, the role and mechanism of DNA-PKcs in angiotensin II (Ang II)-induced vascular remodeling remains obscure. METHODS Rat aortic smooth muscle cells (SMC) and VSMC-specific DNA-PKcs knockout (DNA-PKcsΔVSMC) mice were employed to examine the role of DNA-PKcs in vascular remodeling and the underlying mechanisms. Blood pressure of mice was monitored using the tail-cuff and telemetry methods. The role of DNA-PKcs in vascular function was evaluated using vascular relaxation assessment. RESULTS In the tunica media of remodeled mouse thoracic aortas, and renal arteries from hypertensive patients, elevated DNA-PKcs expression was observed along with its cytoplasmic translocation from nucleus, suggesting a role for DNA-PKcs in vascular remodeling. We then infused wild-type (DNA-PKcsfl/fl) and DNA-PKcsΔVSMC mice with Ang II for 14 days to establish vascular remodeling, and demonstrated that DNA-PKcsΔVSMC mice displayed attenuated vascular remodeling through inhibition of dedifferentiation of VSMCs. Moreover, deletion of DNA-PKcs in VSMCs alleviated Ang II-induced vasodilation dysfunction and hypertension. Mechanistic investigations denoted that Ang II-evoked rises in cytoplasmic DNA-PKcs interacted with dynamin-related protein 1 (Drp1) at its TQ motif to phosphorylate Drp1S616, subsequently promoting mitochondrial fragmentation and dysfunction, as well as reactive oxygen species (ROS) production. Treatment of irbesartan, an Ang II type 1 receptor (AT1R) blocker, downregulated DNA-PKcs expression in VSMCs and aortic tissues following Ang II administration. CONCLUSION Our data revealed that cytoplasmic DNA-PKcs in VSMCs accelerated Ang II-induced vascular remodeling by interacting with Drp1 at its TQ motif and phosphorylating Drp1S616 to provoke mitochondrial fragmentation. Maneuvers targeting DNA-PKcs might be a valuable therapeutic option for the treatment of vascular remodeling and hypertension.
Collapse
Affiliation(s)
- Litao Wang
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai, 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Lin Wu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai, 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Yuxin Du
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai, 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Xiang Wang
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai, 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China
| | - Bingsheng Yang
- Department of Orthopedics, Guangdong Provincial Key Laboratory of Bone and Cartilage Regenerative Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Shuai Guo
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
| | - Yiming Xu
- School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Shuofei Yang
- Department of Vascular Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.
| | - Yingmei Zhang
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai, 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
| | - Jun Ren
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai, 200032, China; National Clinical Research Center for Interventional Medicine, Shanghai, 200032, China.
| |
Collapse
|
65
|
Khatooni Z, Teymourian N, Wilson HL. Using a novel structure/function approach to select diverse swine major histocompatibility complex 1 alleles to predict epitopes for vaccine development. Bioinformatics 2023; 39:btad590. [PMID: 37740287 PMCID: PMC10551226 DOI: 10.1093/bioinformatics/btad590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 07/26/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023] Open
Abstract
MOTIVATION Swine leukocyte antigens (SLAs) (i.e. swine major histocompatibility complex proteins) conduct a fundamental role in swine immunity. To generate a protective vaccine across an outbred species, such as pigs, it is critical that epitopes that bind to diverse SLA alleles are used in the vaccine development process. We introduced a new strategy for epitope prediction. RESULTS We employed molecular dynamics simulation to identify key amino acids for interactions with epitopes. We developed an algorithm wherein each SLA-1 is compared to a crystalized reference allele with unique weighting for non-conserved amino acids based on R group and position. We then performed homology modeling and electrostatic contact mapping to visualize how relatively small changes in sequences impacted the charge distribution in the binding site. We selected eight diverse SLA-1 alleles and performed homology modeling followed, by protein-peptide docking and binding affinity analyses, to identify porcine reproductive and respiratory syndrome virus matrix protein epitopes that bind with high affinity to these alleles. We also performed docking analysis on the epitopes identified as strong binders using NetMHCpan 4.1. Epitopes predicted to bind to our eight SLA-1 alleles had equivalent or higher energetic interactions than those predicted to bind to the NetMHCpan 4.1 allele repertoire. This approach of selecting diverse SLA-1 alleles, followed by homology modeling, and docking simulations, can be used as a novel strategy for epitope prediction that complements other available tools and is especially useful when available tools do not offer a prediction for SLAs/major histocompatibility complex. AVAILABILITY AND IMPLEMENTATION The data underlying this article are available in the online Supplementary Material.
Collapse
Affiliation(s)
- Zahed Khatooni
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Computer Science, University of Kurdistan, Sanandaj, Iran
| | - Navid Teymourian
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Heather L Wilson
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Computer Science, University of Kurdistan, Sanandaj, Iran
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| |
Collapse
|
66
|
Qu L, Liu M, Zheng L, Wang X, Xue H. Data-independent acquisition-based global phosphoproteomics reveal the diverse roles of casein kinase 1 in plant development. Sci Bull (Beijing) 2023; 68:2077-2093. [PMID: 37599176 DOI: 10.1016/j.scib.2023.08.017] [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: 06/02/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023]
Abstract
Casein kinase 1 (CK1) is serine/threonine protein kinase highly conserved among eukaryotes, and regulates multiple developmental and signaling events through phosphorylation of target proteins. Arabidopsis early flowering 1 (EL1)-like (AELs) are plant-specific CK1s with varied functions, but identification and validation of their substrates is a major bottleneck in elucidating their physiological roles. Here, we conducted a quantitative phosphoproteomic analysis in data-independent acquisition mode to systematically identify CK1 substrates. We extracted proteins from seedlings overexpressing individual AEL genes (AEL1/2/3/4-OE) or lacking AEL function (all ael single mutants and two triple mutants) to identify the high-confidence phosphopeptides with significantly altered abundance compared to wild-type Col-0. Among these, we selected 3985 phosphopeptides with higher abundance in AEL-OE lines or lower abundance in ael mutants compared with Col-0 as AEL-upregulated phosphopeptides, and defined 1032 phosphoproteins. Eight CK1s substrate motifs were enriched among AEL-upregulated phosphopeptides and verified, which allowed us to predict additional candidate substrates and functions of CK1s. We functionally characterized a newly identified substrate C3H17, a CCCH-type zinc finger transcription factor, through biochemical and genetic analyses, revealing a role for AEL-promoted C3H17 protein stability and transactivation activity in regulating embryogenesis. As CK1s are highly conserved across eukaryotes, we searched the rice, mouse, and human protein databases using newly identified CK1 substrate motifs, yielding many more candidate substrates than currently known, largely expanding our understanding of the common and distinct functions exerted by CK1s in Arabidopsis and humans, facilitating future mechanistic studies of CK1-mediated phosphorylation in different species.
Collapse
Affiliation(s)
- Li Qu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Moyang Liu
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingli Zheng
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hongwei Xue
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
67
|
Verma J, Kaushal N, Manish M, Subbarao N, Shakirova V, Martynova E, Liu R, Hamza S, Rizvanov AA, Khaiboullina SF, Baranwal M. Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein. J Biomol Struct Dyn 2023:1-17. [PMID: 37750540 DOI: 10.1080/07391102.2023.2260484] [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: 05/21/2023] [Accepted: 09/13/2023] [Indexed: 09/27/2023]
Abstract
The emergence of the new SARS-CoV-2 variants has led to major concern regarding the efficacy of approved vaccines. Nucleocapsid is a conserved structural protein essential for replication of the virus. This study focuses on identifying conserved epitopes on the nucleocapsid (N) protein of SARS-CoV-2. Using 510 unique amino acid sequences of SARS-CoV-2 N protein, two peptides (193 and 215 aa) with 90% conservancy were selected for T cell epitope prediction. Three immunogenic peptides containing multiple T cell epitopes were identified which were devoid of autoimmune and allergic immune response. These peptides were also conserved (100%) in recent Omicron variants reported in Jan-August 2023. HLA analysis reveals that these peptides are predicted as binding to large number of HLA alleles and 71-90% population coverage in six continents. Identified peptides displayed good binding score with both HLA class I and HLA class II molecules in the docking study. Also, a vaccine construct docked with TLR-4 receptor displays strong interaction with 20 hydrogen bonds and molecular simulation analysis reveals that docked complex are stable. Additionally, the immunogenicity of these N protein peptides was confirmed using SARS-CoV-2 convalescent serum samples. We conclude that the identified N protein peptides contain highly conserved and antigenic epitopes which could be used as a target for the future vaccine development against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jigyasa Verma
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Neha Kaushal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Manish Manish
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Venera Shakirova
- Department of Infectious Diseases, Kazan State Medical Academy, Kazan, Russia
| | - Ekaterina Martynova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Rongzeng Liu
- Department of Immunology, School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, China
| | - Shaimaa Hamza
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Albert A Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | | | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| |
Collapse
|
68
|
Kim MA, Kim TH, Kannan P, Kho KH, Park K, Sohn YC. Functional Characterization of Gonadotropin-Releasing Hormone and Corazonin Signaling Systems in Pacific Abalone: Toward Reclassification of Invertebrate Neuropeptides. Neuroendocrinology 2023; 114:64-89. [PMID: 37703838 DOI: 10.1159/000533662] [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: 05/09/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023]
Abstract
INTRODUCTION The proposed evolutionary origins and corresponding nomenclature of bilaterian gonadotropin-releasing hormone (GnRH)-related neuropeptides have changed tremendously with the aid of receptor deorphanization. However, the reclassification of the GnRH and corazonin (CRZ) signaling systems in Lophotrochozoa remains unclear. METHODS We characterized GnRH and CRZ receptors in the mollusk Pacific abalone, Haliotis discus hannai (Hdh), by phylogenetic and gene expression analyses, bioluminescence-based reporter, Western blotting, substitution of peptide amino acids, in vivo neuropeptide injection, and RNA interference assays. RESULTS Two Hdh CRZ-like receptors (Hdh-CRZR-A and Hdh-CRZR-B) and three Hdh GnRH-like receptors (Hdh-GnRHR1-A, Hdh-GnRHR1-B, and Hdh-GnRHR2) were identified. In phylogenetic analysis, Hdh-CRZR-A and -B grouped within the CRZ-type receptors, whereas Hdh-GnRHR1-A/-B and Hdh-GnRHR2 clustered within the GnRH/adipokinetic hormone (AKH)/CRZ-related peptide-type receptors. Hdh-CRZR-A/-B and Hdh-GnRHR1-A were activated by Hdh-CRZ (pQNYHFSNGWHA-NH2) and Hdh-GnRH (pQISFSPNWGT-NH2), respectively. Hdh-CRZR-A/-B dually coupled with the Gαq and Gαs signaling pathways, whereas Hdh-GnRHR1-A was linked only with Gαq signaling. Analysis of substituted peptides, [I2S3]Hdh-CRZ and [N2Y3H4]Hdh-GnRH, and in silico docking models revealed that the N-terminal amino acids of the peptides are critical for the selectivity of Hdh-CRZR and Hdh-GnRHR. Two precursor transcripts for Hdh-CRZ and Hdh-GnRH peptides and their receptors were mainly expressed in the neural ganglia, and their levels increased in starved abalones. Injection of Hdh-CRZ peptide into abalones decreased food consumption, whereas Hdh-CRZR knockdown increased food consumption. Moreover, Hdh-CRZ induced germinal vesicle breakdown in mature oocytes. CONCLUSION Characterization of Hdh-CRZRs and Hdh-GnRHRs and their cognate peptides provides new insight into the evolutionary route of GnRH-related signaling systems in bilaterians.
Collapse
Affiliation(s)
- Mi Ae Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Tae Ha Kim
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Priyadharshini Kannan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Kang Hee Kho
- Department of Fisheries Science, Chonnam National University, Yeosu, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, Republic of Korea
| | - Young Chang Sohn
- Department of Marine Bioscience, Gangneung-Wonju National University, Gangneung, Republic of Korea
- East Coast Life Sciences Institute, Gangneung-Wonju National University, Gangneung, Republic of Korea
| |
Collapse
|
69
|
Zsidó BZ, Bayarsaikhan B, Börzsei R, Hetényi C. Construction of Histone-Protein Complex Structures by Peptide Growing. Int J Mol Sci 2023; 24:13831. [PMID: 37762134 PMCID: PMC10530865 DOI: 10.3390/ijms241813831] [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: 08/21/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The structures of histone complexes are master keys to epigenetics. Linear histone peptide tails often bind to shallow pockets of reader proteins via weak interactions, rendering their structure determination challenging. In the present study, a new protocol, PepGrow, is introduced. PepGrow uses docked histone fragments as seeds and grows the full peptide tails in the reader-binding pocket, producing atomic-resolution structures of histone-reader complexes. PepGrow is able to handle the flexibility of histone peptides, and it is demonstrated to be more efficient than linking pre-docked peptide fragments. The new protocol combines the advantages of popular program packages and allows fast generation of solution structures. AutoDock, a force-field-based program, is used to supply the docked peptide fragments used as structural seeds, and the building algorithm of Modeller is adopted and tested as a peptide growing engine. The performance of PepGrow is compared to ten other docking methods, and it is concluded that in situ growing of a ligand from a seed is a viable strategy for the production of complex structures of histone peptides at atomic resolution.
Collapse
Affiliation(s)
| | | | | | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti Út 12, 7624 Pécs, Hungary; (B.Z.Z.); (B.B.); (R.B.)
| |
Collapse
|
70
|
Talukder A, Rahman MM, Masum MHU. Biocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae: a molecular docking and simulation study. J Biomol Struct Dyn 2023; 41:7204-7223. [PMID: 36039775 DOI: 10.1080/07391102.2022.2118167] [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: 04/29/2022] [Accepted: 08/23/2022] [Indexed: 10/14/2022]
Abstract
The principal objective of this study was to delineate the potentiality of the MBO_200107 protein from the Mycobacterium tuberculosis variant caprae in cancer research. It is a cytoplasmic protein, comprised of a 354-long amino acid chain, alkaline, had a molecular weight of 39089.37 Da, an isoelectric point of 9.62 and a grand average of hydropathicity of -0.345. One of the functional domains was predicted as Gammaglutamylcyclotransferase (GGCT). Among tertiary structures, the Modeller and Phyre2 model satisfied all the quality parameters, though they are truncated; contrarily, the I-TASSER model is full length and contains the sequence for the GGCT domain, though it did not meet all the quality parameters. It also has significant sequence similarities (47.5% by EMBOSS Water and 72.4% by EMBOSS Matcher) with a human GGCT, and the conserved sequences are confined to the GGCT domain of the MBO_200107. According to molecular docking analyses, the protein has a binding affinity of -4.8 kcal/mol by Autodock Vina and -56.465 kcal/mol by HPEPDOCK to the human glutathione (GSH), an essential metabolite for GGCT metabolism. The Molecular dynamic simulation of the docked complex showed the binding efficiency of the GSH to MBO_200107 with a minimal structural alteration. The in silico findings mentioned above revealed that the protein could be used as a supplementary tool in cancer research, such as designing vaccines or drugs where the role of GGCT has been implicated. Further, we recommend fully characterising the protein and conducting essential in vitro and in vivo experiments to determine its detailed usefulness.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Asma Talukder
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Mijanur Rahman
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
- Menzies Health Institute Queensland, School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia
| | - Md Habib Ullah Masum
- Microbiology, Cancer and Bioinformatics Research Group, Noakhali Science and Technology University, Noakhali, Bangladesh
- Department of Microbiology, Noakhali Science and Technology University, Noakhali, Bangladesh
| |
Collapse
|
71
|
Stincarelli MA, Quagliata M, Di Santo A, Pacini L, Fernandez FR, Arvia R, Rinaldi S, Papini AM, Rovero P, Giannecchini S. SARS-CoV-2 inhibitory activity of a short peptide derived from internal fusion peptide of S2 subunit of spike glycoprotein. Virus Res 2023; 334:199170. [PMID: 37422270 PMCID: PMC10384657 DOI: 10.1016/j.virusres.2023.199170] [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: 04/18/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike glycoprotein of SARS-CoV-2 to design new inhibitory peptides. Among the 11 overlapping peptides (9-23-mer), PN19, a 19-mer peptide, exhibited a powerful inhibitory activity against different SARS-CoV-2 clinical isolate variants in absence of cytotoxicity. The PN19 inhibitory activity was found to be dependent on conservation of the central Phe and C-terminal Tyr residues in the peptide sequence. Circular dichroism spectra of the active peptide exhibited an alpha-helix propensity, confirmed by secondary structure prediction analysis. The PN19 inhibitory activity, exerted in the first step of virus infection, was reduced after peptide adsorption treatment with virus-cell substrate during fusion interaction. Additionally, PN19 inhibitory activity was reduced by adding S2 membrane-proximal region derived peptides. PN19 showed binding ability to the S2 membrane proximal region derived peptides, confirmed by molecular modelling, playing a role in the mechanism of action. Collectively, these results confirm that the internal fusion peptide region is a good candidate on which develop peptidomimetic anti SARS-CoV-2 antivirals.
Collapse
Affiliation(s)
- Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Andrea Di Santo
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Feliciana Real Fernandez
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Silvia Rinaldi
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy.
| |
Collapse
|
72
|
Kuo K, Liu J, Pavlova A, Gumbart JC. Drug Binding to BamA Targets Its Lateral Gate. J Phys Chem B 2023; 127:7509-7517. [PMID: 37587651 PMCID: PMC10476194 DOI: 10.1021/acs.jpcb.3c04501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/30/2023] [Indexed: 08/18/2023]
Abstract
BamA, the core component of the β-barrel assembly machinery (BAM) complex, is an outer-membrane protein (OMP) in Gram-negative bacteria. Its function is to insert and fold substrate OMPs into the outer membrane (OM). Evidence suggests that BamA follows the asymmetric hybrid-barrel model where the first and last strands of BamA separate, a process known as lateral gate opening, to allow nascent substrate OMP β-strands to sequentially insert and fold through β-augmentation. Recently, multiple lead compounds that interfere with BamA's function have been identified. We modeled and then docked one of these compounds into either the extracellular loops of BamA or the open lateral gate. With the compound docked in the loops, we found that the lateral gate remains closed during 5 μs molecular dynamics simulations. The same compound when docked in the open lateral gate stays bound to the β16 strand of BamA during the simulation, which would prevent substrate OMP folding. In addition, we simulated mutants of BamA that are resistant to one or more of the identified lead compounds. In these simulations, we observed a differing degree and/or frequency of opening of BamA's lateral gate compared to BamA-apo, suggesting that the mutations grant resistance by altering the dynamics at the gate. We conclude that the compounds act by inhibiting BamA lateral gate opening and/or binding of substrate, thus preventing subsequent OMP folding and insertion.
Collapse
Affiliation(s)
- Katie
M. Kuo
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Jinchan Liu
- Department
of Molecular Biophysics and Biochemistry (MB&B), Yale University, New Haven, Connecticut 06510, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
73
|
Ramalingam PS, Arumugam S. Reverse vaccinology and immunoinformatics approaches to design multi-epitope based vaccine against oncogenic KRAS. Med Oncol 2023; 40:283. [PMID: 37644143 DOI: 10.1007/s12032-023-02160-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
Mutant KRAS-induced tumorigenesis is highly involved in the progression of pancreatic, lung, and breast cancer. Comparatively, KRAS G12D and KRAS G12C are the most frequent mutations that promote cancer progression and aggressiveness. Although KRAS mutant inhibitors exhibit significant therapeutic potential, day by day, they are becoming resistant among patients. Multi-epitope based cancer vaccines are a promising alternative strategy that induces an immune response against tumor antigens. In the present study, we have designed, constructed, and validated a novel multi-epitope vaccine construct against KRAS G12D and G12C mutants using reverse vaccinology and immunoinformatics approaches. In addition, the vaccine construct was structurally refined and showed significant physiochemical properties, and could induce an immune response. Furthermore, the optimized vaccine construct was cloned into a pET‑28a (+) expression vector through in silico cloning. Conclusively, the multi-epitope vaccine construct is structurally stable, soluble, antigenic, non‑allergic, and non‑toxic. Further, it has to be studied in in vitro and in vivo to evaluate its therapeutic efficacy against KRAS-mutated cancers in the near future.
Collapse
Affiliation(s)
| | - Sivakumar Arumugam
- Protein Engineering Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India.
| |
Collapse
|
74
|
Kang YA, Kim YJ, Jin SK, Choi HJ. Antioxidant, Collagenase Inhibitory, and Antibacterial Effects of Bioactive Peptides Derived from Enzymatic Hydrolysate of Ulva australis. Mar Drugs 2023; 21:469. [PMID: 37755082 PMCID: PMC10532848 DOI: 10.3390/md21090469] [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: 07/24/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
The protein extract of Ulva australis hydrolyzed with Alcalase and Flavourzyme was found to have multi-functional properties, including total antioxidant capacity (TAC), collagenase inhibitory, and antibacterial activities. The #5 fraction (SP5) and #7 fraction (SP7) of U. australis hydrolysate from cation-exchange chromatography displayed significantly high TAC, collagenase inhibitory, and antibacterial effects against Propionibacterium acnes, and only the Q3 fraction from anion-exchange chromatography displayed high multi-functional activities. Eight of 42 peptides identified by MALDI-TOF/MS and Q-TOF/MS/MS were selected from the results for screening with molecular docking on target proteins and were then synthesized. Thr-Gly-Thr-Trp (TGTW) displayed ABTS [2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid)] radical scavenging activity. The effect of TAC as Trolox equivalence was dependent on the concentration of TGTW. Asn-Arg-Asp-Tyr (NRDY) and Arg-Asp-Arg-Phe (RDRF) exhibited collagenase inhibitory activity, which increased according to the increase in concentration, and their IC50 values were 0.95 mM and 0.84 mM, respectively. Peptides RDRF and His-Ala-Val-Tyr (HAVY) displayed anti-P. Acnes effects, with IC50 values of 8.57 mM and 13.23 mM, respectively. These results suggest that the U. australis hydrolysate could be a resource for the application of effective nutraceuticals and cosmetics.
Collapse
Affiliation(s)
- You-An Kang
- Korea Beauty Industry Development Institute Co., Ltd., #501, Elite Bldg, Jeju Science Park, Cheomdanro 213-4, Jeju 63309, Republic of Korea;
| | - Ye-Jin Kim
- Oceanpep Co., Ltd., 105, Jinju Bioindustry Foundation, Musan-myeon, Jinju 52839, Republic of Korea;
| | - Sang-Keun Jin
- Division of Animal Science, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Hwa-Jung Choi
- Department of Beauty Art, Youngsan University, 142 Bansong Beltway (Bansong-dong), Busan 48015, Republic of Korea
| |
Collapse
|
75
|
Jiang M, Yang J, Yang L, Wang L, Wang T, Han S, Cheng Y, Chen Z, Su Y, Zhang L, Yang F, Chen SA, Zhang J, Xiong H, Wang L, Zhang Z, Ma L, Luo X, Xing Q. An association study of HLA with levofloxacin-induced severe cutaneous adverse drug reactions in Han Chinese. iScience 2023; 26:107391. [PMID: 37554438 PMCID: PMC10404721 DOI: 10.1016/j.isci.2023.107391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/21/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
Levofloxacin-induced severe cutaneous adverse drug reactions (LEV-SCARs) remain unexplored. An association study of human leukocyte antigen (HLA) alleles with LEV-SCARs among 12 patients, 806 healthy subjects, and 100 levofloxacin-tolerant individuals was performed. The carrier frequencies of HLA-B∗13:01 (odds ratio [OR]: 4.50; 95% confidence interval [CI]: 1.15-17.65; p = 0.043), HLA-B∗13:02 (OR: 6.14; 95% CI: 1.73-21.76; p = 0.0072), and serotype B13 (OR: 17.73; 95% CI: 3.61-86.95; p = 4.85 × 10-5) in patients with LEV-SCARs were significantly higher than those of levofloxacin-tolerant individuals. Molecular docking analysis suggested that levofloxacin formed more stable binding models with HLA-B∗13:01 and HLA-B∗13:02 than with non-risk HLA-B∗46:01. Mass spectrometry revealed that nonapeptides bound to HLA-B∗13:02 shifted at several positions after exposure to levofloxacin. Prospective screening for serotype B13 (sensitivity: 83%, specificity: 78%) and alternative drug treatment for carriers may significantly decrease the incidence of LEV-SCARs.
Collapse
Affiliation(s)
- Menglin Jiang
- Children’s Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai 200032, China
| | - Jin Yang
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Linlin Yang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Lina Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ting Wang
- Children’s Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai 200032, China
| | - Shengna Han
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Ye Cheng
- Children’s Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai 200032, China
| | - Zihua Chen
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Yu Su
- Children’s Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai 200032, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fanping Yang
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Sheng-an Chen
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jin Zhang
- Children’s Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai 200032, China
| | - Hao Xiong
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Lanting Wang
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhen Zhang
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Li Ma
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaoqun Luo
- Department of Allergy and Immunology, Huashan Hospital, Fudan University, Shanghai 200040, China
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Qinghe Xing
- Children’s Hospital of Fudan University and Institutes of Biomedical Sciences of Fudan University, Shanghai 200032, China
| |
Collapse
|
76
|
Jukič M, Kralj S, Kolarič A, Bren U. Design of Tetra-Peptide Ligands of Antibody Fc Regions Using In Silico Combinatorial Library Screening. Pharmaceuticals (Basel) 2023; 16:1170. [PMID: 37631085 PMCID: PMC10459493 DOI: 10.3390/ph16081170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Peptides, or short chains of amino-acid residues, are becoming increasingly important as active ingredients of drugs and as crucial probes and/or tools in medical, biotechnological, and pharmaceutical research. Situated at the interface between small molecules and larger macromolecular systems, they pose a difficult challenge for computational methods. We report an in silico peptide library generation and prioritization workflow using CmDock for identifying tetrapeptide ligands that bind to Fc regions of antibodies that is analogous to known in vitro recombinant peptide libraries' display and expression systems. The results of our in silico study are in accordance with existing scientific literature on in vitro peptides that bind to antibody Fc regions. In addition, we postulate an evolving in silico library design workflow that will help circumvent the combinatorial problem of in vitro comprehensive peptide libraries by focusing on peptide subunits that exhibit favorable interaction profiles in initial in silico peptide generation and testing.
Collapse
Affiliation(s)
- Marko Jukič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Sebastjan Kralj
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
| | - Anja Kolarič
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Engineering, University of Maribor, Smetanova ulica 17, SI-2000 Maribor, Slovenia
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška ulica 8, SI-6000 Koper, Slovenia
- Institute of Environmental Protection and Sensors, Beloruska ulica 7, SI-2000 Maribor, Slovenia
| |
Collapse
|
77
|
Zeng J, Lin C, Zhang S, Yin H, Deng K, Yang Z, Zhang Y, Liu Y, Hu C, Zhao YT. Isolation and Identification of a Novel Anti-Dry Eye Peptide from Tilapia Skin Peptides Based on In Silico, In Vitro, and In Vivo Approaches. Int J Mol Sci 2023; 24:12772. [PMID: 37628955 PMCID: PMC10454390 DOI: 10.3390/ijms241612772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Tilapia skin is a great source of collagen. Here, we aimed to isolate and identify the peptides responsible for combating dry eye disease (DED) in tilapia skin peptides (TSP). In vitro cell DED model was used to screen anti-DED peptides from TSP via Sephadex G-25 chromatography, LC/MS/MS, and in silico methods. The anti-DED activity of the screened peptide was further verified in the mice DED model. TSP was divided into five fractions (TSP-I, TSP-II, TSP-III, TSP-IV, and TSP-V), and TSP-II exerted an effective effect for anti-DED. A total of 131 peptides were identified using LC/MS/MS in TSP-II, and NGGPSGPR (NGG) was screened as a potential anti-DED fragment in TSP-II via in silico methods. In vitro, NGG restored cell viability and inhibited the expression level of Cyclooxygenase-2 (COX-2) protein in Human corneal epithelial cells (HCECs) induced by NaCl. In vivo, NGG increased tear production, decreased tear ferning score, prevented corneal epithelial thinning, alleviated conjunctival goblet cell loss, and inhibited the apoptosis of corneal epithelial cells in DED mice. Overall, NGG, as an anti-DED peptide, was successfully identified from TSP, and it may be devoted to functional food ingredients or medicine for DED.
Collapse
Affiliation(s)
- Jian Zeng
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - Cuixian Lin
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - Shilin Zhang
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - Haowen Yin
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
- College of Food Science and Engineering, Ocean University of China, Yu-Shan Road, Qingdao 266003, China
| | - Kaishu Deng
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - Zhiyou Yang
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - Yongping Zhang
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - You Liu
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| | - Chuanyin Hu
- Department of Biology, Guangdong Medical University, Zhanjiang 524023, China
| | - Yun-Tao Zhao
- College of Food Science and Technology, Modern Biochemistry Experimental Center, Guangdong Ocean University, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Zhanjiang 524088, China
| |
Collapse
|
78
|
Charoenjotivadhanakul S, Sakdee S, Imtong C, Li HC, Angsuthanasombat C. Conserved loop residues-Tyr 270 and Asn 372 near the catalytic site of the lysostaphin endopeptidase are essential for staphylolytic activity toward pentaglycine binding and catalysis. Biochem Biophys Res Commun 2023; 668:111-117. [PMID: 37245291 DOI: 10.1016/j.bbrc.2023.05.085] [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: 05/13/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Lysostaphin endopeptidase cleaves pentaglycine cross-bridges found in staphylococcal cell-wall peptidoglycans and proves very effective in combatting methicillin-resistant Staphylococcus aureus. Here, we revealed the functional importance of two loop residues, Tyr270 in loop 1 and Asn372 in loop 4, which are highly conserved among the M23 endopeptidase family and are found close to the Zn2+-coordinating active site. Detailed analyses of the binding groove architecture together with protein-ligand docking showed that these two loop residues potentially interact with the docked ligand-pentaglycine. Ala-substituted mutants (Y270A and N372A) were generated and over-expressed in Escherichia coli as a soluble form at levels comparable to the wild type. A drastic decrease in staphylolytic activity against S. aureus was observed for both mutants, suggesting an essential role of the two loop residues in lysostaphin function. Further substitutions with an uncharged polar Gln side-chain revealed that only the Y270Q mutation caused a dramatic reduction in bioactivity. In silico predicting the effect of binding site mutations revealed that all mutations displayed a large ΔΔGbind value, signifying requirements of the two loop residues for efficient binding to pentaglycine. Additionally, MD simulations revealed that Y270A and Y270Q mutations induced large flexibility of the loop 1 region, showing markedly increased RMSF values. Further structural analysis suggested that Tyr270 conceivably participated in the oxyanion stabilization of the enzyme catalysis. Altogether, our present study disclosed that two highly conserved loop residues, loop 1-Tyr270 and loop 4-Asn372, located near the lysostaphin active site are crucially involved in staphylolytic activity toward binding and catalysis of pentaglycine cross-links.
Collapse
Affiliation(s)
- Sathapat Charoenjotivadhanakul
- Bacterial Toxin Research Innovation Laboratory, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Somsri Sakdee
- Bacterial Toxin Research Innovation Laboratory, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand
| | - Chompounoot Imtong
- Laboratory of Cell Chemical Biology, Biophysics Institute for Research and Development (BIRD), Chiang Mai, 50110, Thailand
| | - Hui-Chun Li
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, 97004, Taiwan
| | - Chanan Angsuthanasombat
- Bacterial Toxin Research Innovation Laboratory, Institute of Molecular Biosciences, Mahidol University, Salaya Campus, Nakornpathom, 73170, Thailand; Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien, 97004, Taiwan; Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| |
Collapse
|
79
|
Cho H, Yoo T, Moon H, Kang H, Yang Y, Kang M, Yang E, Lee D, Hwang D, Kim H, Kim D, Kim JY, Kim E. Adnp-mutant mice with cognitive inflexibility, CaMKIIα hyperactivity, and synaptic plasticity deficits. Mol Psychiatry 2023; 28:3548-3562. [PMID: 37365244 PMCID: PMC10618100 DOI: 10.1038/s41380-023-02129-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/14/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023]
Abstract
ADNP syndrome, involving the ADNP transcription factor of the SWI/SNF chromatin-remodeling complex, is characterized by developmental delay, intellectual disability, and autism spectrum disorders (ASD). Although Adnp-haploinsufficient (Adnp-HT) mice display various phenotypic deficits, whether these mice display abnormal synaptic functions remain poorly understood. Here, we report synaptic plasticity deficits associated with cognitive inflexibility and CaMKIIα hyperactivity in Adnp-HT mice. These mice show impaired and inflexible contextual learning and memory, additional to social deficits, long after the juvenile-stage decrease of ADNP protein levels to ~10% of the newborn level. The adult Adnp-HT hippocampus shows hyperphosphorylated CaMKIIα and its substrates, including SynGAP1, and excessive long-term potentiation that is normalized by CaMKIIα inhibition. Therefore, Adnp haploinsufficiency in mice leads to cognitive inflexibility involving CaMKIIα hyperphosphorylation and excessive LTP in adults long after its marked expressional decrease in juveniles.
Collapse
Affiliation(s)
- Heejin Cho
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Taesun Yoo
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea
| | - Heera Moon
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Hyojin Kang
- Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Korea
| | - Yeji Yang
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanjiro, Ochang, Cheongju, Chungbuk, 28119, Korea
| | - MinSoung Kang
- Therapeutics & Biotechnology Division, Drug discovery platform research center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Korea
| | - Esther Yang
- Department of Anatomy and BK21 Graduate Program, Biomedical Sciences, College of Medicine, Korea University, Seoul, 02841, Korea
| | - Dowoon Lee
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Hyun Kim
- Department of Anatomy and BK21 Graduate Program, Biomedical Sciences, College of Medicine, Korea University, Seoul, 02841, Korea
| | - Doyoun Kim
- Therapeutics & Biotechnology Division, Drug discovery platform research center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, 34114, Korea
- Medicinal Chemistry and Pharmacology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Jin Young Kim
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, 162 Yeongudanjiro, Ochang, Cheongju, Chungbuk, 28119, Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology (KAIST), Daejeon, 34141, Korea.
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science (IBS), Daejeon, 34141, Korea.
| |
Collapse
|
80
|
Li J, Yin Y, Zou J, Zhang E, Li Q, Chen L, Li J. The adipose-derived stem cell peptide ADSCP2 alleviates hypertrophic scar fibrosis via binding with pyruvate carboxylase and remodeling the metabolic landscape. Acta Physiol (Oxf) 2023; 238:e14010. [PMID: 37366253 DOI: 10.1111/apha.14010] [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: 03/28/2023] [Revised: 05/29/2023] [Accepted: 06/04/2023] [Indexed: 06/28/2023]
Abstract
AIM The purpose of this study was to investigate the function and mechanism of a novel peptide derived from adipose-derived stem cell-conditioned medium (ADSC-CM). METHODS Mass spectrometry was applied to identify expressed peptides in ADSC-CM obtained at different time points. The cell counting kit-8 assay and quantitative reverse transcription polymerase chain reactions were performed to screen the functional peptides contained within ADSC-CM. RNA-seq, western blot, a back skin excisional model of BALB/c mice, the peptide pull-down assay, rescue experiments, untargeted metabolomics, and mixOmics analysis were performed to thoroughly understand the functional mechanism of selected peptide. RESULTS A total of 93, 827, 1108, and 631 peptides were identified in ADSC-CM at 0, 24, 48, and 72 h of conditioning, respectively. A peptide named ADSCP2 (DENREKVNDQAKL) derived from ADSC-CM inhibited collagen and ACTA2 mRNAs in hypertrophic scar fibroblasts. Moreover, ADSCP2 facilitated wound healing and attenuated collagen deposition in a mouse model. ADSCP2 bound with the pyruvate carboxylase (PC) protein and inhibited PC protein expression. Overexpressing PC rescued the reduction in collagen and ACTA2 mRNAs caused by ADSCP2. Untargeted metabolomics identified 258 and 447 differential metabolites in the negative and positive mode, respectively, in the ADSCP2-treated group. The mixOmics analysis, which integrated RNA-seq and untargeted metabolomics data, provided a more holistic view of the functions of ADSCP2. CONCLUSION Overall, a novel peptide derived from ADSC-CM, named ADSCP2, attenuated hypertrophic scar fibrosis in vitro and in vivo, and the novel peptide ADSCP2 might be a promising drug candidate for clinical scar therapy.
Collapse
Affiliation(s)
- Jingyun Li
- Nanjing Maternal and Child Health Medical Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yiliang Yin
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Jijun Zou
- Department of Burns and Plastic Surgery, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Enyuan Zhang
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Qian Li
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Ling Chen
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Jun Li
- Department of Plastic & Cosmetic Surgery, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| |
Collapse
|
81
|
Feng H, Wang F, Li N, Xu Q, Zheng G, Sun X, Hu M, Xing G, Zhang G. A Random Forest Model for Peptide Classification Based on Virtual Docking Data. Int J Mol Sci 2023; 24:11409. [PMID: 37511165 PMCID: PMC10380188 DOI: 10.3390/ijms241411409] [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: 06/06/2023] [Revised: 06/25/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
The affinity of peptides is a crucial factor in studying peptide-protein interactions. Despite the development of various techniques to evaluate peptide-receptor affinity, the results may not always reflect the actual affinity of the peptides accurately. The current study provides a free tool to assess the actual peptide affinity based on virtual docking data. This study employed a dataset that combined actual peptide affinity information (active and inactive) and virtual peptide-receptor docking data, and different machine learning algorithms were utilized. Compared with the other algorithms, the random forest (RF) algorithm showed the best performance and was used in building three RF models using different numbers of significant features (four, three, and two). Further analysis revealed that the four-feature RF model achieved the highest Accuracy of 0.714 in classifying an independent unknown peptide dataset designed with the PEDV spike protein, and it also revealed overfitting problems in the other models. This four-feature RF model was used to evaluate peptide affinity by constructing the relationship between the actual affinity and the virtual docking scores of peptides to their receptors.
Collapse
Affiliation(s)
- Hua Feng
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Fangyu Wang
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Ning Li
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qian Xu
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Guanming Zheng
- Public Health and Preventive Medicine Teaching and Research Center, Henan University of Chinese Medicine, Zhengzhou 450046, China
| | - Xuefeng Sun
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Man Hu
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Guangxu Xing
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Gaiping Zhang
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
- Longhu Modern Immunology Laboratory, Zhengzhou 450002, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
82
|
Ningrum A, Wardani DW, Vanidia N, Sarifudin A, Kumalasari R, Ekafitri R, Kristanti D, Setiaboma W, Munawaroh HSH. Evaluation of Antioxidant Activities from a Sustainable Source of Okara Protein Hydrolysate Using Enzymatic Reaction. Molecules 2023; 28:4974. [PMID: 37446636 DOI: 10.3390/molecules28134974] [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: 05/17/2023] [Revised: 06/11/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Okara is a solid byproduct created during the processing of soy milk. The production of protein hydrolysates utilizing enzymatic tests such as papain can result in the production of bioactive peptides (BPs), which are amino acid sequences that can also be produced from the okara protein by hydrolysis. The objective of this study was to investigate the antioxidant activities of okara hydrolysates using papain, based on the in silico and in vitro assays using the papain enzyme. We found that using the in silico assessment, the antioxidant peptides can be found from the precursor (glycinin and conglycinin) in okara. When used as a protease, papain provides the maximum degree of hydrolysis for antioxidative peptides. The highest-peptide-rank peptide sequence was predicted using peptide ranks such as proline-histidine-phenylalanine (PHF), alanine-aspartic acid-phenylalanine (ADF), tyrosine-tyrosine-leucine (YYL), proline-histidine-histidine (PHH), isoleucine-arginine (IR), and serine-valine-leucine (SVL). Molecular docking studies revealed that all peptides generated from the parent protein impeded substrate access to the active site of xanthine oxidase (XO). They have antioxidative properties and are employed in the in silico approach to the XO enzyme. We also use papain to evaluate the antioxidant activity by using in vitro tests for protein hydrolysate following proteolysis. The antioxidant properties of okara protein hydrolysates have been shown in vitro, utilizing DPPH and FRAP experiments. This study suggests that okara hydrolysates generated by papain can be employed as natural antioxidants in food and for further applications, such as active ingredients for antioxidants in packaging.
Collapse
Affiliation(s)
- Andriati Ningrum
- Department of Food and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Flora Street No. 1, Bulaksumur, Yogyakarta 55281, Indonesia
| | - Dian Wahyu Wardani
- Department of Food and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Flora Street No. 1, Bulaksumur, Yogyakarta 55281, Indonesia
| | - Nurul Vanidia
- Department of Food and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Flora Street No. 1, Bulaksumur, Yogyakarta 55281, Indonesia
| | - Achmat Sarifudin
- Research Centre for Appropriate Technology, National Research and Innovation Agency, KS. Tubun Street No. 5, Subang 41213, Indonesia
| | - Rima Kumalasari
- Research Centre for Appropriate Technology, National Research and Innovation Agency, KS. Tubun Street No. 5, Subang 41213, Indonesia
| | - Riyanti Ekafitri
- Research Centre for Appropriate Technology, National Research and Innovation Agency, KS. Tubun Street No. 5, Subang 41213, Indonesia
| | - Dita Kristanti
- Research Center for Food Technology and Processing, National Research and Innovation Agency, Jogja-Wonosari Street km 31, 5 Playen, Gunungkidul, Yogyakarta 55861, Indonesia
| | - Woro Setiaboma
- Research Center for Food Technology and Processing, National Research and Innovation Agency, Jogja-Wonosari Street km 31, 5 Playen, Gunungkidul, Yogyakarta 55861, Indonesia
| | - Heli Siti Helimatul Munawaroh
- Study Program of Chemistry, Department of Chemistry Education, Faculty of Mathematics and Science Education, Universitas Pendidikan Indonesia, Bandung 40154, Indonesia
| |
Collapse
|
83
|
Ruaro-Moreno M, Monterrubio-López GP, Reyes-Gastellou A, Castelán-Vega JA, Jiménez-Alberto A, Aparicio-Ozores G, Delgadillo-Gutiérrez K, González-Y-Merchand JA, Ribas-Aparicio RM. Design of a Multi-Epitope Vaccine against Tuberculosis from Mycobacterium tuberculosis PE_PGRS49 and PE_PGRS56 Proteins by Reverse Vaccinology. Microorganisms 2023; 11:1647. [PMID: 37512820 PMCID: PMC10385543 DOI: 10.3390/microorganisms11071647] [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: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis, representing the second leading cause of death by an infectious agent worldwide. The available vaccine against this disease has insufficient coverage and variable efficacy, accounting for a high number of cases worldwide. In fact, an estimated third of the world's population has a latent infection. Therefore, developing new vaccines is crucial to preventing it. In this study, the highly antigenic PE_PGRS49 and PE_PGRS56 proteins were analyzed. These proteins were used for predicting T- and B-cell epitopes and for human leukocyte antigen (HLA) protein binding efficiency. Epitopes GGAGGNGSLSS, FAGAGGQGGLGG, GIGGGTQSATGLG (PE_PGRS49), and GTGWNGGKGDTG (PE_PGRS56) were selected based on their best physicochemical, antigenic, non-allergenic, and non-toxic properties and coupled to HLA I and HLA II structures for in silico assays. A construct with an adjuvant (RS09) plus each epitope joined by GPGPG linkers was designed, and the stability of the HLA-coupled construct was further evaluated by molecular dynamics simulations. Although experimental and in vivo studies are still necessary to ensure its protective effect against the disease, this study shows that the vaccine construct is dynamically stable and potentially effective against tuberculosis.
Collapse
Affiliation(s)
- Maritriny Ruaro-Moreno
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gloria Paulina Monterrubio-López
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Abraham Reyes-Gastellou
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Juan Arturo Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Karen Delgadillo-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Jorge Alberto González-Y-Merchand
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| |
Collapse
|
84
|
Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 2023; 56:1376-1392.e8. [PMID: 37164013 DOI: 10.1016/j.immuni.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Phage-displayed immunoprecipitation sequencing (PhIP-seq) has enabled high-throughput profiling of human antibody repertoires. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is lacking. In this study, we investigated the effects of genetic, environmental, and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We detected individual-specificity, temporal consistency, and co-housing similarities in antibody repertoires. Genetic analyses showed the involvement of the HLA, IGHV, and FUT2 gene regions in antibody-bound peptide reactivity. Furthermore, we uncovered associations between phenotypic factors (including age, cell counts, sex, smoking behavior, and allergies, among others) and particular antibody-bound peptides. Our results indicate that human antibody epitope repertoires are shaped by both genetics and environmental exposures and highlight specific signatures of distinct phenotypes and genotypes.
Collapse
Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Angel J Ruiz-Moreno
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| |
Collapse
|
85
|
Guerrib F, Ning C, Mateos-Hernandéz L, Rakotobe S, Park Y, Hajdusek O, Perner J, Vancová M, Valdés JJ, Šimo L. Dual SIFamide receptors in Ixodes salivary glands. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023:103963. [PMID: 37257628 DOI: 10.1016/j.ibmb.2023.103963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/05/2023] [Accepted: 05/13/2023] [Indexed: 06/02/2023]
Abstract
Salivary glands are vital to tick feeding success and also play a crucial role in tick-borne pathogen transmission. In previous studies of Ixodes scapularis salivary glands, we demonstrated that saliva-producing type II and III acini are innervated by neuropeptidergic axons which release different classes of neuropeptides via their terminals (Šimo et al., 2009b, 2013). Among these, the neuropeptide SIFamide-along with its cognate receptor-were postulated to control the basally located acinar valve via basal epithelial and myoepithelial cells (Vancová et al., 2019). Here, we functionally characterized a second SIFamide receptor (SIFa_R2) from the I. scapularis genome and proved that it senses a low nanomolar level of its corresponding ligand. Insect SIFamide paralogs, SMYamides, also activated the receptor but less effectively compared to SIFamide. Bioinformatic and molecular dynamic analyses suggested that I. scapularis SIFamide receptors are class A GPCRs where the peptide amidated carboxy-terminus is oriented within the receptor binding cavity. The receptor was found to be expressed in Ixodes ricinus salivary glands, synganglia, midguts, trachea, and ovaries, but not in Malpighian tubules. Investigation of the temporal expression patterns suggests that the receptor transcript is highly expressed in unfed I. ricinus female salivary glands and then decreases during feeding. In synganglia, a significant transcript increase was detected in replete ticks. In salivary gland acini, an antibody targeting the second SIFamide receptor recognized basal epithelial cells, myoepithelial cells, and basal granular cells in close proximity to the SIFamide-releasing axon terminals. Immunoreactivity was also detected in specific neurons distributed throughout various I. ricinus synganglion locations. The current findings, alongside previous reports from our group, indicate that the neuropeptide SIFamide acts via two different receptors that regulate distinct or common cell types in the basal region of type II and III acini in I. ricinus salivary glands. The current study investigates the peptidergic regulation of the I. ricinus salivary gland in detail, emphasizing the complexity of this system.
Collapse
Affiliation(s)
- Fetta Guerrib
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Caina Ning
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Lourdes Mateos-Hernandéz
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Sabine Rakotobe
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France
| | - Yoonseong Park
- Entomolgy department, Kansas State University, 123 Waters Hall, 66506-4004, Manhattan, KS, USA
| | - Ondrej Hajdusek
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Jan Perner
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Marie Vancová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005, České Budějovice, Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice, 37005, Czech Republic
| | - James J Valdés
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Ladislav Šimo
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, 94700, Maisons-Alfort, France.
| |
Collapse
|
86
|
Sukumaran S, Tan M, Ben-Uliel SF, Zhang H, De Zotti M, Chua MS, So SK, Qvit N. Rational design, synthesis and structural characterization of peptides and peptidomimetics to target Hsp90/Cdc37 interaction for treating hepatocellular carcinoma. Comput Struct Biotechnol J 2023; 21:3159-3172. [PMID: 37304004 PMCID: PMC10250827 DOI: 10.1016/j.csbj.2023.05.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
Heat shock protein 90 (Hsp90) and cell division cycle 37 (Cdc37) work together as a molecular chaperone complex to regulate the activity of a multitude of client protein kinases. These kinases belong to a wide array of intracellular signaling networks that mediate multiple cellular processes including proliferation. As a result, Hsp90 and Cdc37 represent innovative therapeutic targets in various cancers (such as leukemia, multiple myeloma, and hepatocellular carcinoma (HCC)) in which their expression levels are elevated. Conventional small molecule Hsp90 inhibitors act by blocking the conserved adenosine triphosphate (ATP) binding site. However, by targeting less conserved sites in a more specific manner, peptides and peptidomimetics (modified peptides) hold potential as more efficacious and less toxic alternatives to the conventional small molecule inhibitors. Using a rational approach, we herein developed bioactive peptides targeting Hsp90/Cdc37 interaction. A six amino acid linear peptide derived from Cdc37, KTGDEK, was designed to target Hsp90. We used in silico computational docking to first define its mode of interaction, and binding orientation, and then conjugated the peptide with a cell penetrating peptide, TAT, and a fluorescent dye to confirm its ability to colocalize with Hsp90 in HCC cells. Based on the parent linear sequence, we developed a peptidomimetics library of pre-cyclic and cyclic derivatives. These peptidomimetics were evaluated for their binding affinity to Hsp90, and bioactivity in HCC cell lines. Among them, a pre-cyclic peptidomimetic demonstrates high binding affinity and bioactivity in HCC cells, causing reduced cell proliferation that is associated with induction of cell apoptosis, and down-regulation of phosphorylated MEK1/2. Overall, this generalized approach of rational design, structural optimization, and cellular validation of 'drug-like' peptidomimetics against Hsp90/Cdc37 offers a feasible and promising way to design novel therapeutic agents for malignancies and other diseases that are dependent on this molecular chaperone complex.
Collapse
Affiliation(s)
- Surya Sukumaran
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel
| | - Mingdian Tan
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, 1201 Welch Road, Palo Alto, CA 94305, USA
| | - Shulamit Fluss Ben-Uliel
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel
| | - Hui Zhang
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, 1201 Welch Road, Palo Alto, CA 94305, USA
| | - Marta De Zotti
- Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Mei-Sze Chua
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, 1201 Welch Road, Palo Alto, CA 94305, USA
| | - Samuel K. So
- Asian Liver Center, Department of Surgery, Stanford University School of Medicine, 1201 Welch Road, Palo Alto, CA 94305, USA
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed 1311502, Israel
| |
Collapse
|
87
|
Molteni C, Forni D, Cagliani R, Arrigoni F, Pozzoli U, De Gioia L, Sironi M. Selective events at individual sites underlie the evolution of monkeypox virus clades. Virus Evol 2023; 9:vead031. [PMID: 37305708 PMCID: PMC10256197 DOI: 10.1093/ve/vead031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/31/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
In endemic regions (West Africa and the Congo Basin), the genetic diversity of monkeypox virus (MPXV) is geographically structured into two major clades (Clades I and II) that differ in virulence and host associations. Clade IIb is closely related to the B.1 lineage, which is dominating a worldwide outbreak initiated in 2022. Lineage B.1 has however accumulated mutations of unknown significance that most likely result from apolipoprotein B mRNA editing catalytic polypeptide-like 3 (APOBEC3) editing. We applied a population genetics-phylogenetics approach to investigate the evolution of MPXV during historical viral spread in Africa and to infer the distribution of fitness effects. We observed a high preponderance of codons evolving under strong purifying selection, particularly in viral genes involved in morphogenesis and replication or transcription. However, signals of positive selection were also detected and were enriched in genes involved in immunomodulation and/or virulence. In particular, several genes showing evidence of positive selection were found to hijack different steps of the cellular pathway that senses cytosolic DNA. Also, a few selected sites in genes that are not directly involved in immunomodulation are suggestive of antibody escape or other immune-mediated pressures. Because orthopoxvirus host range is primarily determined by the interaction with the host immune system, we suggest that the positive selection signals represent signatures of host adaptation and contribute to the different virulence of Clade I and II MPXVs. We also used the calculated selection coefficients to infer the effects of mutations that define the predominant human MPXV1 (hMPXV1) lineage B.1, as well as the changes that have been accumulating during the worldwide outbreak. Results indicated that a proportion of deleterious mutations were purged from the predominant outbreak lineage, whose spread was not driven by the presence of beneficial changes. Polymorphic mutations with a predicted beneficial effect on fitness are few and have a low frequency. It remains to be determined whether they have any significance for ongoing virus evolution.
Collapse
Affiliation(s)
| | | | | | - Federica Arrigoni
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della scienza, Milan 20126, Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Via don Luigi Monza, Bosisio Parini 23842, Italy
| | - Luca De Gioia
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della scienza, Milan 20126, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Via don Luigi Monza, Bosisio Parini 23842, Italy
| |
Collapse
|
88
|
Masoudi-Sobhanzadeh Y, Pourseif MM, Khalili-Sani A, Jafari B, Salemi A, Omidi Y. Deciphering anti-biofilm property of Arthrospira platensis-origin peptides against Staphylococcusaureus. Comput Biol Med 2023; 160:106975. [PMID: 37146493 DOI: 10.1016/j.compbiomed.2023.106975] [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: 12/06/2022] [Revised: 04/17/2023] [Accepted: 04/22/2023] [Indexed: 05/07/2023]
Abstract
Arthrospira platensis is a valuable natural health supplement consisting of various types of vitamins, dietary minerals, and antioxidants. Although different studies have been conducted to explore the hidden benefits of this bacterium, its antimicrobial property has been poorly understood. To decipher this important feature, here, we extended our recently introduced optimization algorithm (Trader) for aligning amino acid sequences associated with the antimicrobial peptides (AMPs) of Staphylococcus aureus and A.platensis. As a result, similar amino acid sequences were identified, and several candidate peptides were generated accordingly. The obtained peptides were then filtered based on their potential biochemical and biophysical properties, and their 3D structures were simulated based on homology modeling techniques. Next, to investigate how the generated peptides can interact with S. aureus proteins (i.e., heptameric state of the hly and homodimeric form of the arsB), molecular docking approaches were used. The results indicated that four peptides included better molecular interactions relative to the other generated ones in terms of the number/average length of hydrogen bonds and hydrophobic interactions. Based on the outcomes, it can be concluded that the antimicrobial property of A.platensis might be associated with its capability in disturbing the membrane of pathogens and their functions.
Collapse
Affiliation(s)
- Yosef Masoudi-Sobhanzadeh
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad M Pourseif
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ava Khalili-Sani
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Computer Engineering, University College of Nabi Akram, Tabriz, Iran
| | - Behzad Jafari
- Department of Medicinal Chemistry, School of Pharmacy, Urmia University of Medical Sciences, Urmia, Iran
| | - Aysan Salemi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Florida, 33328, USA.
| |
Collapse
|
89
|
Castro-Amorim J, Oliveira A, Mukherjee AK, Ramos MJ, Fernandes PA. Unraveling the Reaction Mechanism of Russell's Viper Venom Factor X Activator: A Paradigm for the Reactivity of Zinc Metalloproteinases? J Chem Inf Model 2023. [PMID: 37092784 DOI: 10.1021/acs.jcim.2c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Snake venom metalloproteinases (SVMPs) are important drug targets against snakebite envenoming, the neglected tropical disease with the highest mortality worldwide. Here, we focus on Russell's viper (Daboia russelii), one of the "big four" snakes of the Indian subcontinent that, together, are responsible for ca. 50,000 fatalities annually. The "Russell's viper venom factor X activator" (RVV-X), a highly toxic metalloproteinase, activates the blood coagulation factor X (FX), leading to the prey's abnormal blood clotting and death. Given its tremendous public health impact, the WHO recognized an urgent need to develop efficient, heat-stable, and affordable-for-all small-molecule inhibitors, for which a deep understanding of the mechanisms of action of snake's principal toxins is fundamental. In this study, we determine the catalytic mechanism of RVV-X by using a density functional theory/molecular mechanics (DFT:MM) methodology to calculate its free energy profile. The results showed that the catalytic process takes place via two steps. The first step involves a nucleophilic attack by an in situ generated hydroxide ion on the substrate carbonyl, yielding an activation barrier of 17.7 kcal·mol-1, while the second step corresponds to protonation of the peptide nitrogen and peptide bond cleavage with an energy barrier of 23.1 kcal·mol-1. Our study shows a unique role played by Zn2+ in catalysis by lowering the pKa of the Zn2+-bound water molecule, enough to permit the swift formation of the hydroxide nucleophile through barrierless deprotonation by the formally much less basic Glu140. Without the Zn2+ cofactor, this step would be rate-limiting.
Collapse
Affiliation(s)
- Juliana Castro-Amorim
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ana Oliveira
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Ashis K Mukherjee
- Institute of Advanced Study in Science and Technology, Vigyan Path Garchuk, Paschim Boragaon, Guwahati 781035, Assam, India
| | - Maria J Ramos
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| | - Pedro A Fernandes
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, s/n, Porto 4169-007, Portugal
| |
Collapse
|
90
|
Patnaik SK, Swaroop AK, Naik MR, Selvaraj J, Chandrasekar MJN. Repurposing of FDA Approved Drugs and Neuropep peptides as Anticancer Agents Against ErbB1 and ErbB2. Drug Res (Stuttg) 2023. [PMID: 37068520 DOI: 10.1055/a-2030-4078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
ErbB1 and ErbB2 are the most important biological targets in cancer drug discovery and development of dual inhibitors for the cancer therapy. FDA approved drugs and Neuropep peptides were used to fit into the ATP binding site of the tyrosine kinases; ErbB1 and ErbB2 proteins. Cytoscape, iGEMDOCK, HPEPDOCK and DataWarrior softwares were used to study the role of these agents as anticancer drugs. Eleven FDA approved drugs and eleven Neuropep peptides showed the strongest 2D interactions and significant binding energy with the proteins. Invitro MTT anticancer assay revealed that, the test compounds, peptide YSFGL and doxorubicin showed significant IC50 value (µM) of 26.417±0.660 and 7.675±0.278 respectively which are compared with the lapatinib standard IC50 value (µM) of 2.380±0.357 against A549 cells and IC50 value (µM) of 39.047±0.770 and 8.313±0.435 respectively which are compared with the lapatinib standard IC50 value (µM) of 3.026±0.180 against MDA-MB-231 cells.
Collapse
Affiliation(s)
- Sunil Kumar Patnaik
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Tamilnadu, India
| | - Akey Krishna Swaroop
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Tamilnadu, India
| | - Mudavath Ravi Naik
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Tamilnadu, India
| | - Jubie Selvaraj
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Tamilnadu, India
| | - Moola Joghee Nanjan Chandrasekar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Tamilnadu, India
- School of Life Sciences, JSS Academy of Higher Education & Research(Ooty Campus), Longwood, Mysuru Road, Ooty-643001, Tamilnadu, India
| |
Collapse
|
91
|
Sioud M, Zhang Q. Precision Killing of M2 Macrophages with Phage-Displayed Peptide-Photosensitizer Conjugates. Cancers (Basel) 2023; 15:cancers15072009. [PMID: 37046671 PMCID: PMC10093000 DOI: 10.3390/cancers15072009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Among the immunosuppressive cells recruited to the tumor microenvironment, macrophages are particularly abundant and involved in angiogenesis, metastasis, and resistance to current cancer therapies. A strategy that simultaneously targets tumor cells and macrophages, particularly pro-tumoral M2 macrophages, would have significant clinical impact for various types of solid malignancies. By the use of phage display technology, we have recently developed a synthetic peptide, named NW, which binds to M1 and M2 macrophages with high affinity. Additional affinity selection on M2 macrophages identified only dominant peptides whose binding motifs are similar to that of the NW peptide. To reduce the frequency of selecting such dominating peptides, the peptide library was affinity selected on M2 macrophages blocked with NW peptide. This approach resulted in the selection of peptides that bind to M2, but not M1 macrophages. To explore the therapeutic potential of the selected peptides, the M13 phage-displayed peptides were conjugated to the photosensitizer IR700, which has been used for cancer photoimmunotherapy. The phage displaying a dominant peptide (SPILWLNAPPWA) killed both M1 and M2 macrophages, while those displaying the M2-specific peptides killed M2 macrophages only upon near-infrared light exposure. A significant fraction of the M2 macrophages were also killed with the untargeted M13 phage-IR700 conjugates. Hence, M2 macrophages can also be selectively targeted by the wild type M13 phage, which displayed a significant tropism to these cells. The benefits of this photoimmunotherapy include an automatic self-targeting ability of the wild type M13 phage, and the option of genetic manipulation of the phage genome to include tumor targeting peptides, allowing the killing of both M2 macrophages and cancer cells.
Collapse
Affiliation(s)
- Mouldy Sioud
- Department of Cancer Immunology, Division of Cancer Medicine, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway
- Correspondence:
| | - Qindong Zhang
- Department of Cancer Immunology, Division of Cancer Medicine, Oslo University Hospital, Radiumhospitalet, Ullernchausseen 70, 0379 Oslo, Norway
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Blindern, 0316 Oslo, Norway
| |
Collapse
|
92
|
Shkhyan R, Flynn C, Lamoure E, Sarkar A, Van Handel B, Li J, York J, Banks N, Van der Horst R, Liu NQ, Lee S, Bajaj P, Vadivel K, Harn HIC, Tassey J, Lozito T, Lieberman JR, Chuong CM, Hurtig MS, Evseenko D. Inhibition of a signaling modality within the gp130 receptor enhances tissue regeneration and mitigates osteoarthritis. Sci Transl Med 2023; 15:eabq2395. [PMID: 36947594 PMCID: PMC10792550 DOI: 10.1126/scitranslmed.abq2395] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 01/17/2023] [Indexed: 03/24/2023]
Abstract
Adult mammals are incapable of multitissue regeneration, and augmentation of this potential may shift current therapeutic paradigms. We found that a common co-receptor of interleukin 6 (IL-6) cytokines, glycoprotein 130 (gp130), serves as a major nexus integrating various context-specific signaling inputs to either promote regenerative outcomes or aggravate disease progression. Via genetic and pharmacological experiments in vitro and in vivo, we demonstrated that a signaling tyrosine 814 (Y814) within gp130 serves as a major cellular stress sensor. Mice with constitutively inactivated Y814 (F814) were resistant to surgically induced osteoarthritis as reflected by reduced loss of proteoglycans, reduced synovitis, and synovial fibrosis. The F814 mice also exhibited enhanced regenerative, not reparative, responses after wounding in the skin. In addition, pharmacological modulation of gp130 Y814 upstream of the SRC and MAPK circuit by a small molecule, R805, elicited a protective effect on tissues after injury. Topical administration of R805 on mouse skin wounds resulted in enhanced hair follicle neogenesis and dermal regeneration. Intra-articular administration of R805 to rats after medial meniscal tear and to canines after arthroscopic meniscal release markedly mitigated the appearance of osteoarthritis. Single-cell sequencing data demonstrated that genetic and pharmacological modulation of Y814 resulted in attenuation of inflammatory gene signature as visualized by the anti-inflammatory macrophage and nonpathological fibroblast subpopulations in the skin and joint tissue after injury. Together, our study characterized a molecular mechanism that, if manipulated, enhances the intrinsic regenerative capacity of tissues through suppression of a proinflammatory milieu and prevents pathological outcomes in injury and disease.
Collapse
Affiliation(s)
- Ruzanna Shkhyan
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Candace Flynn
- Ontario Veterinary College, Department of Clinical Studies, University of Guelph, ON N1G 2W1, Canada
| | - Emma Lamoure
- Ontario Veterinary College, Department of Clinical Studies, University of Guelph, ON N1G 2W1, Canada
| | - Arijita Sarkar
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Benjamin Van Handel
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Jinxiu Li
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Jesse York
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Nicholas Banks
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Robert Van der Horst
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Nancy Q. Liu
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Siyoung Lee
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Paul Bajaj
- UCLA Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
| | - Kanagasabai Vadivel
- UCLA Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA
| | - Hans I.-Chen Harn
- Department of Pathology, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
- International Research Center of Wound Repair and Regeneration (iWRR), National Cheng Kung University, Tainan 701401 Taiwan
| | - Jade Tassey
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Thomas Lozito
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Jay R. Lieberman
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Mark S. Hurtig
- Ontario Veterinary College, Department of Clinical Studies, University of Guelph, ON N1G 2W1, Canada
| | - Denis Evseenko
- Department of Orthopaedic Surgery, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
- Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| |
Collapse
|
93
|
Fatoki TH, Chukwuejim S, Udenigwe CC, Aluko RE. In Silico Exploration of Metabolically Active Peptides as Potential Therapeutic Agents against Amyotrophic Lateral Sclerosis. Int J Mol Sci 2023; 24:ijms24065828. [PMID: 36982902 PMCID: PMC10058213 DOI: 10.3390/ijms24065828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is regarded as a fatal neurodegenerative disease that is featured by progressive damage of the upper and lower motor neurons. To date, over 45 genes have been found to be connected with ALS pathology. The aim of this work was to computationally identify unique sets of protein hydrolysate peptides that could serve as therapeutic agents against ALS. Computational methods which include target prediction, protein-protein interaction, and peptide-protein molecular docking were used. The results showed that the network of critical ALS-associated genes consists of ATG16L2, SCFD1, VAC15, VEGFA, KEAP1, KIF5A, FIG4, TUBA4A, SIGMAR1, SETX, ANXA11, HNRNPL, NEK1, C9orf72, VCP, RPSA, ATP5B, and SOD1 together with predicted kinases such as AKT1, CDK4, DNAPK, MAPK14, and ERK2 in addition to transcription factors such as MYC, RELA, ZMIZ1, EGR1, TRIM28, and FOXA2. The identified molecular targets of the peptides that support multi-metabolic components in ALS pathogenesis include cyclooxygenase-2, angiotensin I-converting enzyme, dipeptidyl peptidase IV, X-linked inhibitor of apoptosis protein 3, and endothelin receptor ET-A. Overall, the results showed that AGL, APL, AVK, IIW, PVI, and VAY peptides are promising candidates for further study. Future work would be needed to validate the therapeutic properties of these hydrolysate peptides by in vitro and in vivo approaches.
Collapse
Affiliation(s)
| | - Stanley Chukwuejim
- Department of Biochemistry, Federal University Oye-Ekiti, PMB 373, Oye 371104, Nigeria
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Chibuike C Udenigwe
- Faculty of Health Sciences, School of Nutrition Sciences, University of Ottawa, Ottawa, ON K1H 8M5, Canada
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Richardson Centre for Food Technology and Research, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| |
Collapse
|
94
|
Exploring the Potential of Black Soldier Fly Larval Proteins as Bioactive Peptide Sources through in Silico Gastrointestinal Proteolysis: A Cheminformatic Investigation. Catalysts 2023. [DOI: 10.3390/catal13030605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Despite their potential as a protein source for human consumption, the health benefits of black soldier fly larvae (BSFL) proteins following human gastrointestinal (GI) digestion are poorly understood. This computational study explored the potential of BSFL proteins to release health-promoting peptides after human GI digestion. Twenty-six proteins were virtually proteolyzed with GI proteases. The resultant peptides were screened for high GI absorption and non-toxicity. Shortlisted peptides were searched against the BIOPEP-UWM and Scopus databases to identify their bioactivities. The potential of the peptides as inhibitors of myeloperoxidase (MPO), NADPH oxidase (NOX), and xanthine oxidase (XO), as well as a disruptor of Keap1–Nrf2 protein–protein interaction, were predicted using molecular docking and dynamics simulation. Our results revealed that about 95% of the 5218 fragments generated from the proteolysis of BSFL proteins came from muscle proteins. Dipeptides comprised the largest group (about 25%) of fragments arising from each muscular protein. Screening of 1994 di- and tripeptides using SwissADME and STopTox tools revealed 65 unique sequences with high GI absorption and non-toxicity. A search of the databases identified 16 antioxidant peptides, 14 anti-angiotensin-converting enzyme peptides, and 17 anti-dipeptidyl peptidase IV peptides among these sequences. Results from molecular docking and dynamic simulation suggest that the dipeptide DF has the potential to inhibit Keap1–Nrf2 interaction and interact with MPO within a short time frame, whereas the dipeptide TF shows promise as an XO inhibitor. BSFL peptides were likely weak NOX inhibitors. Our in silico results suggest that upon GI digestion, BSFL proteins may yield high-GI-absorbed and non-toxic peptides with potential health benefits. This study is the first to investigate the bioactivity of peptides liberated from BSFL proteins following human GI digestion. Our findings provide a basis for further investigations into the potential use of BSFL proteins as a functional food ingredient with significant health benefits.
Collapse
|
95
|
In Silico Identification of Peptides with PPARγ Antagonism in Protein Hydrolysate from Rice (Oryza sativa). Pharmaceuticals (Basel) 2023; 16:ph16030440. [PMID: 36986539 PMCID: PMC10057873 DOI: 10.3390/ph16030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/04/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
At least half the population in industrialized countries suffers from obesity due to excessive accumulation of adipose tissue. Recently, rice (Oryza sativa) proteins have been considered valuable sources of bioactive peptides with antiadipogenic potential. In this study, the digestibility and bioaccessibility in vitro of a novel protein concentrate (NPC) from rice were determined through INFOGEST protocols. Furthermore, the presence of prolamin and glutelin was evaluated via SDS-PAGE, and their potential digestibility and the bioactivity of ligands against peroxisome proliferator-activated receptor gamma (PPARγ) were explored by BIOPEP UWM and HPEPDOCK. For the top candidates, molecular simulations were conducted using Autodock Vina to evaluate their binding affinity against the antiadipogenic region of PPARγ and their pharmacokinetics and drug-likeness using SwissADME. Simulating gastrointestinal digestion showed a recovery of 43.07% and 35.92% bioaccessibility. The protein banding patterns showed the presence of prolamin (57 kDa) and glutelin (12 kDa) as the predominant proteins in the NPC. The in silico hydrolysis predicts the presence of three and two peptide ligands in glutelin and prolamin fraction, respectively, with high affinity for PPARγ (≤160). Finally, the docking studies suggest that the prolamin-derived peptides QSPVF and QPY (−6.38 & −5.61 kcal/mol, respectively) have expected affinity and pharmacokinetic properties to act as potential PPARγ antagonists. Hence, according to our results, bioactive peptides resulting from NPC rice consumption might have an antiadipogenic effect via PPARγ interactions, but further experimentation and validation in suitable biological model systems are necessary to gain more insight and to provide evidence to support our in silico findings.
Collapse
|
96
|
Agrahari AK, Srivastava M, Singh M, Asthana S. SARS-CoV-2 envelope protein attain K ac mediated dynamical interaction network to adopt 'histone mimic' at BRD4 interface. J Biomol Struct Dyn 2023; 41:15305-15319. [PMID: 36907648 DOI: 10.1080/07391102.2023.2188430] [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: 11/24/2022] [Accepted: 02/27/2023] [Indexed: 03/13/2023]
Abstract
Interface mimicry, achieved by recognition of host-pathogen interactions, is the basis by which pathogen proteins can hijack the host machinery. The envelope (E) protein of SARS-CoV-2 is reported to mimic the histones at the BRD4 surface via establishing the structural mimicry; however, the underlying mechanism of E protein mimicking the histones is still elusive. To explore the mimics at dynamic and structural residual network level an extensive docking, and MD simulations were carried out in a comparative manner between complexes of H3-, H4-, E-, and apo-BRD4. We identified that E peptide is able to attain an 'interaction network mimicry', as its acetylated lysine (Kac) achieves orientation and residual fingerprint similar to histones, including water-mediated interactions for both the Kac positions. We identified Y59 of E, playing an anchor role to escort lysine positioning inside the binding site. Furthermore, the binding site analysis confirms that E peptide needs a higher volume, similar to the H4-BRD4 where both the lysine's (Kac5 and Kac8) can accommodate nicely, however, the position of Kac8 is mimicked by two additional water molecules other than four water-mediated bridging's, strengthening the possibility that E peptide could hijack host BRD4 surface. These molecular insights seem pivotal for mechanistic understanding and BRD4-specific therapeutic intervention. KEY POINTSMolecular mimicry is reported in hijacking and then outcompeting the host counterparts so that pathogens can rewire their cellular function by overcoming the host defense mechanism.The molecular recognition process is the basis of molecular mimicry. The E peptide of SARS-CoV-2 is reported to mimic host histone at the BRD4 surface by utilizing its C-terminally placed acetylated lysine (Kac63) to mimic the N-terminally placed acetylated lysine Kac5GGKac8 histone (H4) by interaction network mimicry identified through microsecond molecular dynamics (MD) simulations and post-processing extensive analysis.There are two steps to mimic: firstly, tyrosine residues help E to anchor at the BRD4 surface to position Kac and increase the volume of the pocket. Secondary, after positioning of Kac, a common durable interaction network N140:Kac5; Kac5:W1; W1:Y97; W1:W2; W2:W3; W3:W4; W4:P82 is established between Kac5, with key residues P82, Y97, N140, and four water molecules through water mediate bridge. Furthermore, the second acetylated lysine Kac8 position and its interaction as polar contact with Kac5 were also mimicked by E peptide through interaction network P82:W5; W5:Kac63; W5:W6; W6:Kac63.The binding event at BRD4/BD1 seems an induced-fit mechanism as a bigger binding site volume was identified at H4-BRD4 on which E peptide attains its better stability than H3-BRD4.We identified the tyrosine residue Y59 of E that acts like an anchor on the BRD4 surface to position Kac inside the pocket and attain the interaction network by using aromatic residues of the BRD4 surface.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Mrityunjay Singh
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Haryana, India
| |
Collapse
|
97
|
Screening of EWI-2-Derived Peptides for Targeting Tetraspanin CD81 and Their Effect on Cancer Cell Migration. Biomolecules 2023; 13:biom13030510. [PMID: 36979448 PMCID: PMC10046862 DOI: 10.3390/biom13030510] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
CD81, a transmembrane protein belonging to the tetraspanin family, has recently been suggested as a therapeutic target for cancers. Here, we screened peptides that bind to the tetraspanin CD81 protein, and evaluated their inhibitory activity in cancer cell migration. To screen for CD81-binding peptides (CD81-BP), a peptide array membrane was prepared from the amino acid sequence of the EWI-2 protein, a major partner of CD81, before binding to fluorescently labeled CD81. As a result, four candidate CD81-BPs were identified and characterized. In particular, the CFMKRLRK peptide (called P152 in this study) was found to be the best candidate that preferentially binds to the extracellular loop of CD81, with an estimated dissociation constant of 0.91 µM. Since CD81 was reported to promote cancer cell migration, an initial step in metastasis, the Boyden chamber assay, was next performed to assess the effect of CD81-BP candidates on the migration of MDA-MB-231 human breast cancer cells. Interestingly, our result indicated that P152 could suppress MDA-MB-231 cell migration at the level comparable to that of an anti-human CD81 antibody (5A6). Thus, we propose these CD81-BPs with the anti-migration property against cancer cells for the development of novel therapeutic strategies.
Collapse
|
98
|
Sun Y, Chan J, Bose K, Tam C. Simultaneous control of infection and inflammation with keratin-derived antibacterial peptides targeting TLRs and co-receptors. Sci Transl Med 2023; 15:eade2909. [PMID: 36888696 PMCID: PMC10173409 DOI: 10.1126/scitranslmed.ade2909] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/10/2023] [Indexed: 03/10/2023]
Abstract
Controlling infection-driven inflammation is a major clinical dilemma because of limited therapeutic options and possible adverse effects on microbial clearance. Compounding this difficulty is the continued emergence of drug-resistant bacteria, where experimental strategies aiming to augment inflammatory responses for enhanced microbial killing are not applicable treatment options for infections of vulnerable organs. As with corneal infections, severe or prolonged inflammation jeopardizes corneal transparency, leading to devastating vision loss. We hypothesized that keratin 6a-derived antimicrobial peptides (KAMPs) may be a two-pronged remedy capable of tackling bacterial infection and inflammation at once. We used murine peritoneal neutrophils and macrophages, together with an in vivo model of sterile corneal inflammation, to find that nontoxic and prohealing KAMPs with natural 10- and 18-amino acid sequences suppressed lipoteichoic acid (LTA)- and lipopolysaccharide (LPS)-induced NFκB and IRF3 activation, proinflammatory cytokine production, and phagocyte recruitment independently of their bactericidal function. Mechanistically, KAMPs not only competed with bacterial ligands for cell surface Toll-like receptor (TLR) and co-receptors (MD2, CD14, and TLR2) but also reduced cell surface availability of TLR2 and TLR4 through promotion of receptor endocytosis. Topical KAMP treatment effectively alleviated experimental bacterial keratitis, as evidenced by substantial reductions of corneal opacification, inflammatory cell infiltration, and bacterial burden. These findings reveal the TLR-targeting activities of KAMPs and demonstrate their therapeutic potential as a multifunctional drug for managing infectious inflammatory disease.
Collapse
Affiliation(s)
- Yan Sun
- Department of Ophthalmic Research, Cole Eye Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jonathan Chan
- Department of Ophthalmic Research, Cole Eye Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Karthikeyan Bose
- Department of Ophthalmic Research, Cole Eye Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Connie Tam
- Department of Ophthalmic Research, Cole Eye Institute and Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| |
Collapse
|
99
|
Mudgil P, Gan CY, Affan Baig M, Hamdi M, Mohteshamuddin K, Aguilar-Toalá JE, Vidal-Limon AM, Liceaga AM, Maqsood S. In-depth peptidomic profile and molecular simulation studies on ACE-inhibitory peptides derived from probiotic fermented milk of different farm animals. Food Res Int 2023; 168:112706. [PMID: 37120189 DOI: 10.1016/j.foodres.2023.112706] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/22/2023]
Abstract
Investigations into ACE inhibitory properties of probiotic fermented bovine, camel, goat, and sheep milk were performed and studied for two weeks of refrigerated storage. Results from the degree of proteolysis suggested higher susceptibility of goat milk proteins, followed by sheep and camel milk proteins, to the probiotic-mediated proteolysis. ACE-inhibitory properties displayed continuous decline in ACE-IC50 values for two weeks of refrigerated storage. Overall, goat milk fermented with Pediococcus pentosaceus caused maximum ACE inhibition (IC50: 262.7 µg/mL protein equivalent), followed by camel milk (IC50: 290.9 µg/mL protein equivalent). Studies related to peptide identification and in silico analysis using HPEPDOCK score revealed presence of 11, 13, 9 and 9 peptides in fermented bovine, goat, sheep, and camel milk, respectively, with potent antihypertensive potential. The results obtained suggest that the goat and camel milk proteins demonstrated higher potential for generating antihypertensive peptides via fermentation when compared to bovine and sheep milk.
Collapse
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
| | - Mohd Affan Baig
- Food Science Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al-Ain 15551, United Arab Emirates
| | - Marwa Hamdi
- Food Science Department, 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.
| |
Collapse
|
100
|
Shu J, Li J, Wang S, Lin J, Wen L, Ye H, Zhou P. Systematic analysis and comparison of peptide specificity and selectivity between their cognate receptors and noncognate decoys. J Mol Recognit 2023; 36:e3006. [PMID: 36579779 DOI: 10.1002/jmr.3006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022]
Abstract
Protein-peptide interactions (PpIs) play an important role in cell signaling networks and have been exploited as new and attractive therapeutic targets. The affinity and specificity are two unity-of-opposite aspects of PpIs (and other biomolecular interactions); the former indicates the absolute binding strength between the peptide ligand and its cognate protein receptor in a PpI, while the latter represents the relative recognition selectivity of the peptide ligand for its cognate protein receptor in a PpI over those noncognate decoys that could be potentially encountered by the peptide in cell. Although the PpI binding affinity has been widely investigated over the past decades, the peptide recognition specificity (and selectivity) still remains largely unexplored to date. In this study, we classified PpI specificity into three types: (i) class-I specificity: peptide selectivity for its cognate wild-type protein receptor over the noncognate mutant decoys of this receptor, (ii) class-II specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are homologous with this receptor, and (iii) class-III specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are the cognate receptors of other peptides. We performed affinity and selectivity analysis for the three types of PpI specificity and revealed that the PpIs generally exhibit a moderate or modest specificity; peptide selectivity increases in the order: class-I < class-II < class-III. All the three types of PpI specificity were observed to have no statistically significant correlation with peptide length and hydrophobicity, but the class-I and class-II specificities can be influenced considerably by peptide secondary structures; the high specificity is preferentially associated with ordered structure types as compared to undefined structure types. In addition, the mutation distribution (for class-I specificity), sequence conservation (for class-II specificity), and structural similarity (for class-III specificity) seem also to address effects on peptide selectivity.
Collapse
Affiliation(s)
- Jianping Shu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Juelin Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shaozhou Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Haiyang Ye
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| |
Collapse
|