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Xia Y, Sun G, Xiao J, He X, Jiang H, Zhang Z, Zhang Q, Li K, Zhang S, Shi X, Wang Z, Liu L, Zhao Y, Yang Y, Duan K, Ye W, Wang Y, Dong S, Wang Y, Ma Z, Wang Y. AlphaFold-guided redesign of a plant pectin methylesterase inhibitor for broad-spectrum disease resistance. MOLECULAR PLANT 2024; 17:1344-1368. [PMID: 39030909 DOI: 10.1016/j.molp.2024.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/18/2024] [Accepted: 07/15/2024] [Indexed: 07/22/2024]
Abstract
Plant cell walls are a critical site where plants and pathogens continuously struggle for physiological dominance. Here we show that dynamic remodeling of pectin methylesterification of plant cell walls is a component of the physiological and co-evolutionary struggles between hosts and pathogens. A pectin methylesterase (PsPME1) secreted by Phytophthora sojae decreases the degree of pectin methylesterification, thus synergizing with an endo-polygalacturonase (PsPG1) to weaken plant cell walls. To counter PsPME1-mediated susceptibility, a plant-derived pectin methylesterase inhibitor protein, GmPMI1, protects pectin to maintain a high methylesterification status. GmPMI1 protects plant cell walls from enzymatic degradation by inhibiting both soybean and P. sojae pectin methylesterases during infection. However, constitutive expression of GmPMI1 disrupted the trade-off between host growth and defense responses. We therefore used AlphaFold structure tools to design a modified form of GmPMI1 (GmPMI1R) that specifically targets and inhibits pectin methylesterases secreted from pathogens but not from plants. Transient expression of GmPMI1R enhanced plant resistance to oomycete and fungal pathogens. In summary, our work highlights the biochemical modification of the cell wall as an important focal point in the physiological and co-evolutionary conflict between hosts and microbes, providing an important proof of concept that AI-driven structure-based tools can accelerate the development of new strategies for plant protection.
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Affiliation(s)
- Yeqiang Xia
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Guangzheng Sun
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Junhua Xiao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xinyi He
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Haibin Jiang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qi Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kainan Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Sicong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuechao Shi
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhaoyun Wang
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Agricultural University, Hefei 230036, China
| | - Lin Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yao Zhao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuheng Yang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Kaixuan Duan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yiming Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Zhenchuan Ma
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China; Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.
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Lackner A, Qiu Y, Armanus E, Nicholas A, Macapagal K, Leonidas L, Xu H, McNulty R. Measuring Interactions Between Proteins and Small Molecules or Nucleic Acids. Curr Protoc 2024; 4:e1105. [PMID: 39040024 PMCID: PMC11335060 DOI: 10.1002/cpz1.1105] [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] [Indexed: 07/24/2024]
Abstract
Interactions between proteins and small molecules or nucleic acids play a pivotal role in numerous biological processes critical for human health and are fundamental for advancing our understanding of biological systems. Proteins are the workhorses of the cell, executing various functions ranging from catalyzing biochemical reactions to transmitting signals within the body. Small molecules, including drugs and metabolites, can modulate protein activity, thereby impacting cellular processes and disease pathways. Similarly, nucleic acids, such as DNA and RNA, regulate protein synthesis and function through intricate interactions. Understanding these interactions is crucial for drug discovery and development and can shed light on gene regulation, transcriptional control, and RNA processing, providing insights into genetic diseases and developmental disorders. Moreover, studying protein-small molecule and protein-nucleic acid interactions enhances our comprehension of fundamental biological mechanisms. A wide array of methods to study these interactions range in cost, sensitivity, materials usage, throughput, and complexity. Notably in the last decade, new techniques have been developed that enhance our understanding of these interactions. In this review, we aim to summarize the new state-of-the-art methods for detecting interactions between proteins and small molecules or nucleic acids, as well as discuss older methods that still hold value today. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Angela Lackner
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Yanfei Qiu
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Emy Armanus
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Alijah Nicholas
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Kahea Macapagal
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Lemuel Leonidas
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Huilin Xu
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
| | - Reginald McNulty
- Laboratory of Macromolecular Structure, Department of Molecular Biology and Biochemistry, Charlie Dunlop School of Biological Sciences, University of California Irvine, Irvine, CA 92697 USA
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Kim S, Liu Y, Ziarnik M, Seo S, Cao Y, Zhang XF, Im W. Binding of human ACE2 and RBD of Omicron enhanced by unique interaction patterns among SARS-CoV-2 variants of concern. J Comput Chem 2023; 44:594-601. [PMID: 36398990 PMCID: PMC9825653 DOI: 10.1002/jcc.27025] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/11/2022] [Accepted: 10/11/2022] [Indexed: 11/20/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q498R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Among the Q493K and Q493R, we report that Q493R shows stronger binding to ACE2 than Q493K due to increased interactions. Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our results could help explain the Omicron variant's prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity.
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Affiliation(s)
- Seonghan Kim
- Department of Bioengineering, Daejeon 34141, Republic of Korea
| | - Yi Liu
- Department of Bioengineering, Daejeon 34141, Republic of Korea
| | - Matthew Ziarnik
- Department of Bioengineering, Daejeon 34141, Republic of Korea
| | - Sangjae Seo
- Korean Institute of Science and Technology Information, Daejeon 34141, Republic of Korea
| | - Yiwei Cao
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - X. Frank Zhang
- Department of Bioengineering, Daejeon 34141, Republic of Korea
- Current address: Department of Biomedical Engineering, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
| | - Wonpil Im
- Department of Bioengineering, Daejeon 34141, Republic of Korea
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
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Qiu X, Kong L, Chen H, Lin Y, Tu S, Wang L, Chen Z, Zeng M, Xiao J, Yuan P, Qiu M, Wang Y, Ye W, Duan K, Dong S, Wang Y. The Phytophthora sojae nuclear effector PsAvh110 targets a host transcriptional complex to modulate plant immunity. THE PLANT CELL 2023; 35:574-597. [PMID: 36222564 PMCID: PMC9806631 DOI: 10.1093/plcell/koac300] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/18/2022] [Indexed: 05/27/2023]
Abstract
Plants have evolved sophisticated immune networks to restrict pathogen colonization. In response, pathogens deploy numerous virulent effectors to circumvent plant immune responses. However, the molecular mechanisms by which pathogen-derived effectors suppress plant defenses remain elusive. Here, we report that the nucleus-localized RxLR effector PsAvh110 from the pathogen Phytophthora sojae, causing soybean (Glycine max) stem and root rot, modulates the activity of a transcriptional complex to suppress plant immunity. Soybean like-heterochromatin protein 1-2 (GmLHP1-2) and plant homeodomain finger protein 6 (GmPHD6) form a transcriptional complex with transcriptional activity that positively regulates plant immunity against Phytophthora infection. To suppress plant immunity, the nuclear effector PsAvh110 disrupts the assembly of the GmLHP1-2/GmPHD6 complex via specifically binding to GmLHP1-2, thus blocking its transcriptional activity. We further show that PsAvh110 represses the expression of a subset of immune-associated genes, including BRI1-associated receptor kinase 1-3 (GmBAK1-3) and pathogenesis-related protein 1 (GmPR1), via G-rich elements in gene promoters. Importantly, PsAvh110 is a conserved effector in different Phytophthora species, suggesting that the PsAvh110 regulatory mechanism might be widely utilized in the genus to manipulate plant immunity. Thus, our study reveals a regulatory mechanism by which pathogen effectors target a transcriptional complex to reprogram transcription.
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Affiliation(s)
- Xufang Qiu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Kong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Han Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yachun Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Siqun Tu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengzhu Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Junhua Xiao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiguo Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Min Qiu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaixuan Duan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
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Pawel GT, Ma Y, Wu Y, Lu Y, Peinetti AS. Binding Affinity Measurements Between DNA Aptamers and their Virus Targets Using ELONA and MST. Bio Protoc 2022; 12:e4548. [PMID: 36505027 PMCID: PMC9709635 DOI: 10.21769/bioprotoc.4548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/28/2022] [Accepted: 09/04/2022] [Indexed: 11/06/2022] Open
Abstract
Aptamers have been selected with strong affinity and high selectivity for a wide range of targets, as recently highlighted by the development of aptamer-based sensors that can differentiate infectious from non-infectious viruses, including human adenovirus and SARS-CoV-2. Accurate determination of the binding affinity between the DNA aptamers and their viral targets is the first step to understanding the molecular recognition of viral particles and the potential uses of aptamers in various diagnostics and therapeutic applications. Here, we describe protocols to obtain the binding curve of the DNA aptamers to SARS-CoV-2 using Enzyme-Linked Oligonucleotide Assay (ELONA) and MicroScale Thermophoresis (MST). These methods allow for the determination of the binding affinity of the aptamer to the infectious SARS-CoV-2 and the selectivity of this aptamer against the same SARS-CoV-2 that has been rendered non-infectious by UV inactivation, and other viruses. Compared to other techniques like Electrophoretic Mobility Shift Assay (EMSA), Surface Plasmon Resonance (SPR), and Isothermal Titration Calorimetry (ITC), these methods have advantages for working with larger particles like viruses and with samples that require biosafety level 2 facilities.
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Affiliation(s)
- Gregory T. Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
| | - Yuan Ma
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Yuting Wu
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
- Department of Chemistry, University of Texas at Austin, Austin, Texas, United States
| | - Ana Sol Peinetti
- INQUIMAE (CONICET), Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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Microscale Thermophoresis as a Tool to Study Protein Interactions and Their Implication in Human Diseases. Int J Mol Sci 2022; 23:ijms23147672. [PMID: 35887019 PMCID: PMC9315744 DOI: 10.3390/ijms23147672] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 02/06/2023] Open
Abstract
The review highlights how protein–protein interactions (PPIs) have determining roles in most life processes and how interactions between protein partners are involved in various human diseases. The study of PPIs and binding interactions as well as their understanding, quantification and pharmacological regulation are crucial for therapeutic purposes. Diverse computational and analytical methods, combined with high-throughput screening (HTS), have been extensively used to characterize multiple types of PPIs, but these procedures are generally laborious, long and expensive. Rapid, robust and efficient alternative methods are proposed, including the use of Microscale Thermophoresis (MST), which has emerged as the technology of choice in drug discovery programs in recent years. This review summarizes selected case studies pertaining to the use of MST to detect therapeutically pertinent proteins and highlights the biological importance of binding interactions, implicated in various human diseases. The benefits and limitations of MST to study PPIs and to identify regulators are discussed.
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8
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Ozaslan D, Byrd AK, Belachew B, Raney KD. Alignment of helicases on single-stranded DNA increases activity. Methods Enzymol 2022; 672:29-54. [PMID: 35934480 PMCID: PMC9421817 DOI: 10.1016/bs.mie.2022.03.066] [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] [Indexed: 11/29/2022]
Abstract
Helicases function in most biological processes that utilize RNA or DNA nucleic acids including replication, recombination, repair, transcription, splicing, and translation. They are motor proteins that bind ATP and then catalyze hydrolysis to release energy which is transduced for conformational changes. Different conformations correspond to different steps in a process that results in movement of the enzyme along the nucleic acid track in a unidirectional manner. Some helicases such as DEAD-box helicases do not translocate, but these enzymes transduce chemical energy from ATP hydrolysis to unwind secondary structure in DNA or RNA. Some helicases function as monomers while others assemble into defined structures, either dimers or higher order oligomers. Dda helicase from bacteriophage T4 and NS3 helicase domain from the hepatitis C virus are examples of monomeric helicases. These helicases can bind to single-stranded DNA in a manner that appears like train engines on a track. When monomeric helicases align on DNA, the activity of the enzymes increases. Helicase activity can include the rate of duplex unwinding and the total number of base pairs melted during a single binding event or processivity. Dda and NS3h are considered as having low processivity, unwinding fewer than 50 base pairs per binding event. Here, we report fusing two molecules of NS3h molecules together through genetically linking the C-terminus of one molecule to the N-terminus of a second NS3h molecule. We observed increased processivity relative to NS3h possibly arising from the increased probability that at least one of the helicases will completely unwind the DNA prior to dissociation. The dimeric enzyme also binds DNA more like the full-length NS3 helicase. Finally, the dimer can displace streptavidin from biotin-labeled oligonucleotide, whereas monomeric NS3h cannot.
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Affiliation(s)
- Deniz Ozaslan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Binyam Belachew
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
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9
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Kim S, Liu Y, Ziarnik M, Cao Y, Zhang XF, Im W. Binding of Human ACE2 and RBD of Omicron Enhanced by Unique Interaction Patterns Among SARS-CoV-2 Variants of Concern. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.01.24.477633. [PMID: 35118473 PMCID: PMC8811907 DOI: 10.1101/2022.01.24.477633] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 2019 coronavirus disease (COVID-19) pandemic has had devastating impacts on our global health. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has continued to mutate and spread worldwide despite global vaccination efforts. In particular, the Omicron variant, first identified in South Africa in late November 2021, has now overtaken the Delta variant and become the dominant strain worldwide. Compared to the original strain identified in Wuhan, Omicron features 50 genetic mutations, with 15 mutations in the receptor-binding domain (RBD) of the spike protein, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor for viral entry. However, it is not completely understood how these mutations alter the interaction and binding strength between the Omicron RBD and ACE2. In this study, we used a combined steered molecular dynamics (SMD) simulation and experimental microscale thermophoresis (MST) approach to quantify the interaction between Omicron RBD and ACE2. We report that the Omicron brings an enhanced RBD-ACE2 interface through N501Y, Q493K/R, and T478K mutations; the changes further lead to unique interaction patterns, reminiscing the features of previously dominated variants, Alpha (N501Y) and Delta (L452R and T478K). Our MST data confirmed that the Omicron mutations in RBD are associated with a five-fold higher binding affinity to ACE2 compared to the RBD of the original strain. In conclusion, our result could help explain the Omicron variant’s prevalence in human populations, as higher interaction forces or affinity for ACE2 likely promote greater viral binding and internalization, leading to increased infectivity. TOC GRAPHIC
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Affiliation(s)
- Seonghan Kim
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Matthew Ziarnik
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yiwei Cao
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - X. Frank Zhang
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
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10
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Kim S, Liu Y, Lei Z, Dicker J, Cao Y, Zhang XF, Im W. Differential Interactions between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern. J Chem Theory Comput 2021; 17:7972-7979. [PMID: 34856802 PMCID: PMC8672429 DOI: 10.1021/acs.jctc.1c00965] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. It is known that the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 interacts with the human angiotensin-converting enzyme 2 (ACE2) receptor, initiating the entry of SARS-CoV-2. Since its emergence, a number of SARS-CoV-2 variants have been reported, and the variants that show high infectivity are classified as variants of concern according to the United States Centers for Disease Control and Prevention. In this study, we performed both all-atom steered molecular dynamics (SMD) simulations and microscale thermophoresis (MST) experiments to characterize the binding interactions between ACE2 and RBD of all current variants of concern (Alpha, Beta, Gamma, and Delta) and two variants of interest (Epsilon and Kappa). We report that RBD of the Alpha (N501Y) variant requires the highest amount of force initially to be detached from ACE2 due to the N501Y mutation in addition to the role of N90-glycan, followed by Beta/Gamma (K417N/T, E484 K, and N501Y) or Delta (L452R and T478 K) variants. Among all variants investigated in this work, RBD of the Epsilon (L452R) variant is relatively easily detached from ACE2. Our results from both SMD simulations and MST experiments indicate what makes each variant more contagious in terms of RBD and ACE2 interactions. This study could shed light on developing new drugs to inhibit SARS-CoV-2 entry effectively.
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Affiliation(s)
- Seonghan Kim
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yi Liu
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Zewei Lei
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Jeffrey Dicker
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Yiwei Cao
- Department of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - X. Frank Zhang
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
- Department of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA
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11
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Mabonga L, Masamba P, Basson AK, Kappo AP. Microscale thermophoresis analysis of the molecular interaction between small nuclear ribonucleoprotein polypeptide G and the RING finger domain of RBBP6 towards anti-cancer drug discovery. Am J Transl Res 2021; 13:12775-12785. [PMID: 34956492 PMCID: PMC8661184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/16/2021] [Indexed: 06/14/2023]
Abstract
Regulatory core-splicing proteins are now becoming highly promising therapeutic targets for the development of anti-cancer drugs. SNRPG and RBBP6 are two good examples of regulatory core-splicing proteins involved in tumorigenesis and tumor development whose multi-functional role is primarily mediated by protein-protein interactions. Over the years, skepticism abutting from the two onco-proteins has been mounting. Suggestive evidence using yeast 2-hybrid technique observed possible involvement between SNRPG and the RING finger domain of RBBP6. However, the putative interaction remains elusive and yet to be characterized. In this study, we developed the first MST-based assay to confirm the interaction between SNRPG and the RING finger domain of RBBP6. The results demonstrated a strong binding affinity between SNRPG and the RING finger domain of RBBP6 with a KD in the low nanomolar concentration range of 3.1596 nM. The results are congruent with previous findings suggesting possible involvement between the two proteins in cancer-cell networks, thereby providing a new mechanistic insight into the interaction between SNRPG and the RING finger domain of RBBP6. The interaction is therapeutically relevant and represents a great milestone in the anti-cancer drug discovery space. Identification of small molecule inhibitors to modulate the binding affinity between the two proteins would therefore be a major breakthrough in the development of new PPI-focused anti-cancer drugs.
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Affiliation(s)
- Lloyd Mabonga
- Department of Biochemistry and Microbiology, University of ZululandKwaDlangezwa 3886, South Africa
| | - Priscilla Masamba
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Faculty of Science, University of Johannesburg, Kingsway CampusAuckland Park 2006, South Africa
| | - Albertus Kotze Basson
- Department of Biochemistry and Microbiology, University of ZululandKwaDlangezwa 3886, South Africa
| | - Abidemi Paul Kappo
- Molecular Biophysics and Structural Biology (MBSB) Group, Department of Biochemistry, Faculty of Science, University of Johannesburg, Kingsway CampusAuckland Park 2006, South Africa
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12
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Hein J, Cyert MS, Fordyce PM. MRBLE-pep Measurements Reveal Accurate Binding Affinities for B56, a PP2A Regulatory Subunit. ACS MEASUREMENT SCIENCE AU 2021; 1:56-64. [PMID: 35128539 PMCID: PMC8809670 DOI: 10.1021/acsmeasuresciau.1c00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Signal transduction pathways rely on dynamic interactions between protein globular domains and short linear motifs (SLiMs). The weak affinities of these interactions are essential to allow fast rewiring of signaling pathways and downstream responses but also pose technical challenges for interaction detection and measurement. We recently developed a technique (MRBLE-pep) that leverages spectrally encoded hydrogel beads to measure binding affinities between a single protein of interest and 48 different peptide sequences in a single small volume. In prior work, we applied it to map the binding specificity landscape between calcineurin and the PxIxIT SLiM (Nguyen, H. Q. et al. Elife 2019, 8). Here, using peptide sequences known to bind the PP2A regulatory subunit B56α, we systematically compare affinities measured by MRBLE-pep or isothermal calorimetry (ITC) and confirm that MRBLE-pep accurately quantifies relative affinity over a wide dynamic range while using a fraction of the material required for traditional methods such as ITC.
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Affiliation(s)
- Jamin
B. Hein
- Department
of Biology, Stanford University, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- The
Novo Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Martha S. Cyert
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Polly M. Fordyce
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg
Biohub, San Francisco, California 94110, United States
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13
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Yang Y, Yin Y, Wang S, Dong Y. Simultaneous determination of zearalenone and ochratoxin A based on microscale thermophoresis assay with a bifunctional aptamer. Anal Chim Acta 2021; 1155:338345. [PMID: 33766318 DOI: 10.1016/j.aca.2021.338345] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/14/2021] [Accepted: 02/17/2021] [Indexed: 11/29/2022]
Abstract
Nowadays, contamination of various mycotoxins in crops and their products exposes increasing risks to human health. Efficient determination methods are urgently needed. Herein, a bifunctional aptamer and a simple aptasensor based on microscale thermophoresis assay (MST) were constructed for the first time for simultaneous determination of two mycotoxins, i.e. zearalenone (ZEN) and ochratoxin A (OTA). The bifunctional aptamer was engineered by splicing a ZEN aptamer and an OTA aptamer with a linker according to the structure analysis of aptamers. The binding mechanism of the bifunctional aptamer to ZEN and OTA were revealed basing on the molecular docking studies. The MST assay proved that the bifunctional aptamer showed high affinity and specificity towards ZEN and OTA. Furthermore, a bifunctional aptamer-based MST-aptasensor was developed for simultaneous detection of ZEN and OTA in corn oil sample. The MST-aptasensor provided a limit of detection (LOD) of 0.12 nM, with satisfactory recoveries of 93.31-104.19% and excellent selectivity, indicating that the bifunctional aptamer and MST-aptasensor had great potential in practical applications.
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Affiliation(s)
- Yan Yang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Yingai Yin
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Sai Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, PR China.
| | - Yiyang Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
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14
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Tao H, Cheng L, Liu L, Wang H, Jiang Z, Qiang X, Xing L, Xu Y, Cai X, Yao J, Wang M, Qiu Z. A PD-1 peptide antagonist exhibits potent anti-tumor and immune regulatory activity. Cancer Lett 2020; 493:91-101. [PMID: 32805322 DOI: 10.1016/j.canlet.2020.08.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/30/2020] [Accepted: 08/09/2020] [Indexed: 01/12/2023]
Abstract
Antibodies blocking the PD-1/PD-L1 pathway have achieved great success. However, some disadvantages of antibodies have been found, which limit their clinical applications. Peptide antagonists are alternatives to antibodies in PD-1/PD-L1 blockage, but successful studies in this area are limited. A PD-1 targeting peptide, P-F4, was identified using phage display. P-F4 bound PD-1 with an affinity of 0.119 μM, inhibited PD-1/PD-L1 interaction at the cellular level and modulated T cell activity in vitro. We have overcome the poor solubility and rapid degradation problems of this peptide by packaging P-F4 in nanoparticles. In vivo experiments demonstrated that P-F4 nanoparticles could strongly inhibit tumor growth in a CT26 mouse model. Further research revealed that treatment of P-F4 nanoparticles increased CD8+T cells and reduced Tregs in the tumor microenvironment and tumor-draining lymph nodes. It was shown that treatment of P-F4 nanoparticles also increased lymphocytic activities, including proliferation, cytokine secretion and cytolytic activity. Moreover, computer modeling suggested that the P-F4 binding site to PD-1 overlaps with the PD-L1 binding surface. In this study, a peptide candidate for cancer immunotherapy was provided, and its working mechanisms were studied.
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Affiliation(s)
- Huimin Tao
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Lu Cheng
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Lihua Liu
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Hong Wang
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Zhijie Jiang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Pharmaceutics, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Xu Qiang
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Lijun Xing
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Yifeng Xu
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Xinying Cai
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Jing Yao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, Department of Pharmaceutics, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China
| | - Min Wang
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
| | - Zheng Qiu
- School of Life Science and Technology, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, 211198, China.
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15
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Lamut A, Gjorgjieva M, Naesens L, Liekens S, Lillsunde KE, Tammela P, Kikelj D, Tomašič T. Anti-influenza virus activity of benzo[d]thiazoles that target heat shock protein 90. Bioorg Chem 2020; 98:103733. [DOI: 10.1016/j.bioorg.2020.103733] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/12/2020] [Accepted: 03/06/2020] [Indexed: 12/21/2022]
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16
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Opoku F, Govender PP, Pooe OJ, Simelane MB. Evaluating Iso-Mukaadial Acetate and Ursolic Acid Acetate as Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase Inhibitors. Biomolecules 2019; 9:E861. [PMID: 31835879 PMCID: PMC6995562 DOI: 10.3390/biom9120861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/21/2022] Open
Abstract
To date, Plasmodium falciparum is one of the most lethal strains of the malaria parasite. P. falciparum lacks the required enzymes to create its own purines via the de novo pathway, thereby making Plasmodium falciparum hypoxanthine-guanine-xanthine phosphoribosyltransferase (PfHGXPT) a crucial enzyme in the malaria life cycle. Recently, studies have described iso-mukaadial acetate and ursolic acid acetate as promising antimalarials. However, the mode of action is still unknown, thus, the current study sought to investigate the selective inhibitory and binding actions of iso-mukaadial acetate and ursolic acid acetate against recombinant PfHGXPT using in-silico and experimental approaches. Recombinant PfHGXPT protein was expressed using E. coli BL21 cells and homogeneously purified by affinity chromatography. Experimentally, iso-mukaadial acetate and ursolic acid acetate, respectively, demonstrated direct inhibitory activity towards PfHGXPT in a dose-dependent manner. The binding affinity of iso-mukaadial acetate and ursolic acid acetate on the PfHGXPT dissociation constant (KD), where it was found that 0.0833 µM and 2.8396 µM, respectively, are indicative of strong binding. The mode of action for the observed antimalarial activity was further established by a molecular docking study. The molecular docking and dynamics simulations show specific interactions and high affinity within the binding pocket of Plasmodium falciparum and human hypoxanthine-guanine phosphoribosyl transferases. The predicted in silico absorption, distribution, metabolism and excretion/toxicity (ADME/T) properties predicted that the iso-mukaadial acetate ligand may follow the criteria for orally active drugs. The theoretical calculation derived from ADME, molecular docking and dynamics provide in-depth information into the structural basis, specific bonding and non-bonding interactions governing the inhibition of malarial. Taken together, these findings provide a basis for the recommendation of iso-mukaadial acetate and ursolic acid acetate as high-affinity ligands and drug candidates against PfHGXPT.
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Affiliation(s)
- Francis Opoku
- Department of Chemical Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg 2028, South Africa;
| | - Penny P. Govender
- Department of Chemical Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein Campus, Johannesburg 2028, South Africa;
| | - Ofentse J. Pooe
- Discipline of Biochemistry, School of Life Science, University of KwaZulu-Natal, Westville 4000, South Africa;
| | - Mthokozisi B.C. Simelane
- Department of Biochemistry, Faculty of Science, University of Johannesburg, Johannesburg 2006, South Africa
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17
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Michaeli A, Mezan S, Kühbacher A, Finkelmeier D, Elias M, Zatsepin M, Reed SG, Duthie MS, Rupp S, Lerner I, Burger-Kentischer A. Computationally Designed Bispecific MD2/CD14 Binding Peptides Show TLR4 Agonist Activity. THE JOURNAL OF IMMUNOLOGY 2018; 201:3383-3391. [PMID: 30348734 DOI: 10.4049/jimmunol.1800380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/20/2018] [Indexed: 12/28/2022]
Abstract
Toll-like receptor 4 plays an important role in the regulation of the innate and adaptive immune response. The majority of TLR4 activators currently in clinical use are derivatives of its prototypic ligand LPS. The discovery of innovative TLR4 activators has the potential of providing new therapeutic immunomodulators and adjuvants. We used computational design methods to predict and optimize a total of 53 cyclic and linear peptides targeting myeloid differentiation 2 (MD2) and cluster of differentiation 14 (CD14), both coreceptors of human TLR4. Activity of the designed peptides was first assessed using NF-κB reporter cell lines expressing either TLR4/MD2 or TLR4/CD14 receptors, then binding to CD14 and MD2 confirmed and quantified using MicroScale Thermophoresis. Finally, we incubated select peptides in human whole blood and observed their ability to induce cytokine production, either alone or in synergy with LPS. Our data demonstrate the advantage of computational design for the discovery of new TLR4 peptide activators with little structural resemblance to known ligands and indicate an efficient strategy with which to identify TLR4 targeting peptides that could be used as easy-to-produce alternatives to LPS-derived molecules in a variety of settings.
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Affiliation(s)
| | - Shaul Mezan
- Pepticom Ltd., Givat-Ram, 9139002 Jerusalem, Israel
| | - Andreas Kühbacher
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Doris Finkelmeier
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany
| | - Maayan Elias
- Pepticom Ltd., Givat-Ram, 9139002 Jerusalem, Israel
| | | | - Steven G Reed
- Infectious Disease Research Institute, Seattle, WA 98102; and
| | | | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany; .,Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, 70569 Stuttgart, Germany
| | | | - Anke Burger-Kentischer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, 70569 Stuttgart, Germany; .,Institute of Interfacial Process Engineering and Plasma Technology, University of Stuttgart, 70569 Stuttgart, Germany
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