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Next-generation sequencing-based HLA typing reveals the association of HLA-B*46:01:01 and HLA-DRB1*09:01:02 alleles with carbamazepine-induced hypersensitivity reactions in Vietnamese patients with epilepsy. Hum Immunol 2023; 84:186-195. [PMID: 36725456 DOI: 10.1016/j.humimm.2023.01.005] [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: 06/15/2022] [Revised: 11/03/2022] [Accepted: 01/17/2023] [Indexed: 02/02/2023]
Abstract
Several studies have reported an association between certain human leukocyte antigen (HLA) alleles and carbamazepine (CBZ)-induced hypersensitivity reactions in patients with epilepsy. Here, the relationship between the clinical spectrum and the HLA allele profiles in patients with CBZ-induced hypersensitivity reactions was investigated using next-generation sequence (NGS) data obtained from 65 Vietnamese patients with epilepsy, including 33 with CBZ-tolerance and 32 patients with CBZ-hypersensitivity, in which only 8 with severe cutaneous adverse drug reactions and 24 were mild-hypersensitive patients. Three loci of HLA class I (HLA-A, -B, and -C) and two loci of HLA class II (HLA-DQA1 and -DRB1) were included in our analysis. We observed a higher prevalence of three alleles, HLA-B*46:01:01, HLA-DQA1*03:02:01, and HLA-DRB1*09:01:02, in the CBZ hypersensitivity group compared to that in the CBZ tolerant group. Notably, all hypersensitive patients with HLA-DQA1*03:02:01 also harbored HLA-DRB1*09:01:02. We also used molecular modeling to gain mechanistic insight into the interactions of HLA-B*46:01 and HLA-DRB1*09:01 with CBZ. Our findings proposed the direct interaction of CBZ with peptide-binding pockets of these HLA proteins. The sensitivity and specificity of HLA-B*46:01:01 in considering with the appearance of HLA-DRB1*09:01:02 were 46.88% and 84.85%, respectively. Our data suggest that the presence of HLA-B*46:01:01/HLA-DRB1*09:01:02 is a potential marker of CBZ-induced hypersensitivity reactions in Vietnamese patients.
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Copaescu AM, Ben-Shoshan M, Trubiano JA. Tools to improve the diagnosis and management of T-cell mediated adverse drug reactions. Front Med (Lausanne) 2022; 9:923991. [PMID: 36313986 PMCID: PMC9606226 DOI: 10.3389/fmed.2022.923991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Delayed drug T-cell immune-mediated hypersensitivity reactions have a large clinical heterogeneity varying from mild maculopapular exanthema (MPE) to severe cutaneous adverse reactions (SCARs) such as acute generalized exanthematous pustulosis (AGEP), drug reaction with eosinophilia and systemic symptoms (DRESS) and severe skin necrosis and blistering as seen in Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). Given the knowledge gaps related to the immunopathogenesis of these conditions, the absence of validated diagnostic tools and the significant associated morbidity and mortality, patients with SCARs often have limited drug choices. We performed a comprehensive review aiming to evaluate in vivo diagnostic tools such as delayed intradermal skin and patch testing and ex vivo/in vitro research assays such as the lymphocyte transformation test (LTT) and the enzyme-linked ImmunoSpot (ELISpot) assay. We searched through PubMed using the terms “drug allergy,” “in vivo” and “ex vivo” for original papers in the last 10 years. A detailed meticulous approach adapted to the various clinical phenotypes is recommended for the diagnostic and management of delayed drug hypersensitivity reactions. This review highlights the current diagnostic tools for the delayed drug hypersensitivity phenotypes.
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Affiliation(s)
- Ana Maria Copaescu
- Department of Infectious Diseases, Centre for Antibiotic Allergy and Research, Austin Health, Heidelberg, VIC, Australia,Division of Allergy and Clinical Immunology, Department of Medicine, McGill University Health Centre (MUHC), Montreal, QC, Canada,The Research Institute of the McGill University Health Centre, McGill University Health Centre (MUHC), Montreal, QC, Canada,*Correspondence: Ana Maria Copaescu,
| | - Moshe Ben-Shoshan
- The Research Institute of the McGill University Health Centre, McGill University Health Centre (MUHC), Montreal, QC, Canada,Division of Allergy, Immunology and Dermatology, Montreal Children’s Hospital, McGill University Health Centre (MUHC), Montreal, QC, Canada
| | - Jason A. Trubiano
- Department of Infectious Diseases, Centre for Antibiotic Allergy and Research, Austin Health, Heidelberg, VIC, Australia,Department of Oncology, Sir Peter MacCallum Cancer Centre, The University of Melbourne, Parkville, VIC, Australia,Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, Australia,The National Centre for Infections in Cancer, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
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3
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Functional and structural characteristics of HLA-B*13:01-mediated specific T cells reaction in dapsone-induced drug hypersensitivity. J Biomed Sci 2022; 29:58. [PMID: 35964029 PMCID: PMC9375929 DOI: 10.1186/s12929-022-00845-8] [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: 05/31/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Severe cutaneous adverse drug reactions (SCARs) are a group of serious clinical conditions caused by immune reaction to certain drugs. The allelic variance of human leukocyte antigens of HLA-B*13:01 has been strongly associated with hypersensitivities induced by dapsone (DDS). T-cell receptor mediated activation of cytotoxic T lymphocytes (CTLs) has also been suggested to play an essential role in pathogenesis of SCARs. However, HLA-B*13:01-DDS-TCR immune synapse that plays role in drug-induced hypersensitivity syndrome (DIHS) associated T cells activation remains uncharacterized. METHODS To investigate the molecular mechanisms for HLA-B*13:01 in the pathogenesis of Dapsone-induced drug hypersensitivity (DDS-DIHS), we performed crystallization and expanded drug-specific CTLs to analyze the pathological role of DDS-DIHS. RESULTS Results showed the crystal structure of HLA-B*13:01-beta-2-microglobulin (β2M) complex at 1.5 Å resolution and performed mutation assays demonstrating that I118 or I119, and R121 of HLA-B*13:01 were the key residues that mediate the binding of DDS. Subsequent single-cell TCR and RNA sequencing indicated that TCRs composed of paired TRAV12-3/TRBV28 clonotype with shared CDR3 region specifically recognize HLA-B*13:01-DDS complex to trigger inflammatory cytokines associated with DDS-DIHS. CONCLUSION Our study identified the novel p-i-HLA/TCR as the model of interaction between HLA-B*13:01, DDS and the clonotype-specific TCR in DDS-DIHS.
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Pichler WJ, Watkins S, Yerly D. Risk Assessment in Drug Hypersensitivity: Detecting Small Molecules Which Outsmart the Immune System. FRONTIERS IN ALLERGY 2022; 3:827893. [PMID: 35386664 PMCID: PMC8974731 DOI: 10.3389/falgy.2022.827893] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/26/2022] [Indexed: 12/19/2022] Open
Abstract
Drug hypersensitivity (DH) reactions are clinically unusual because the underlying immune stimulations are not antigen-driven, but due to non-covalent drug-protein binding. The drugs may bind to immune receptors like HLA or TCR which elicits a strong T cell reaction (p-i concept), the binding may enhance the affinity of antibodies (enhanced affinity model), or drug binding may occur on soluble proteins which imitate a true antigen (fake antigen model). These novel models of DH could have a major impact on how to perform risk assessments in drug development. Herein, we discuss the difficulties of detecting such non-covalent, labile and reversible, but immunologically relevant drug-protein interactions early on in drug development. The enormous diversity of the immune system, varying interactions, and heterogeneous functional consequences make it to a challenging task. We propose that a realistic approach to detect clinically relevant non-covalent drug interactions for a new drug could be based on a combination of in vitro cell culture assays (using a panel of HLA typed donor cells) and functional analyses, supplemented by structural analysis (computational data) of the reactive cells/molecules. When drug-reactive cells/molecules with functional impact are detected in these risk assessments, a close clinical monitoring of the drug may reveal the true incidence of DH, as suppressing but also enhancing factors occurring in vivo can influence the clinical manifestation of a DH.
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Pichler WJ. The important role of non-covalent drug-protein interactions in drug hypersensitivity reactions. Allergy 2022; 77:404-415. [PMID: 34037262 PMCID: PMC9291849 DOI: 10.1111/all.14962] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Drug hypersensitivity reactions (DHR) are heterogeneous and unusual immune reactions with rather unique clinical presentations. Accumulating evidence indicates that certain non-covalent drug-protein interactions are able to elicit exclusively effector functions of antibody reactions or complete T-cell reactions which contribute substantially to DHR. Here, we discuss three key interactions; (a) mimicry: whereby soluble, non-covalent drug-protein complexes ("fake antigens") mimic covalent drug-protein adducts; (b) increased antibody affinity: for example, in quinine-type immune thrombocytopenia where the drug gets trapped between antibody and membrane-bound glycoprotein; and (c) p-i-stimulation: where naïve and memory T cells are activated by direct binding of drugs to the human leukocyte antigen and/or T-cell receptors. This transient drug-immune receptor interaction initiates a polyclonal T-cell response with mild-to-severe DHR symptoms. Notable complications arising from p-i DHR can include viral reactivations, autoimmunity, and multiple drug hypersensitivity. In conclusion, DHR is characterized by abnormal immune stimulation driven by non-covalent drug-protein interactions. This contrasts DHR from "normal" immunity, which relies on antigen-formation by covalent hapten-protein adducts and predominantly results in asymptomatic immunity.
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Kloypan C, Koomdee N, Satapornpong P, Tempark T, Biswas M, Sukasem C. A Comprehensive Review of HLA and Severe Cutaneous Adverse Drug Reactions: Implication for Clinical Pharmacogenomics and Precision Medicine. Pharmaceuticals (Basel) 2021; 14:1077. [PMID: 34832859 PMCID: PMC8622011 DOI: 10.3390/ph14111077] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022] Open
Abstract
Human leukocyte antigen (HLA) encoded by the HLA gene is an important modulator for immune responses and drug hypersensitivity reactions as well. Genetic polymorphisms of HLA vary widely at population level and are responsible for developing severe cutaneous adverse drug reactions (SCARs) such as Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), drug reaction with eosinophilia and systemic symptoms (DRESS), maculopapular exanthema (MPE). The associations of different HLA alleles with the risk of drug induced SJS/TEN, DRESS and MPE are strongly supportive for clinical considerations. Prescribing guidelines generated by different national and international working groups for translation of HLA pharmacogenetics into clinical practice are underway and functional in many countries, including Thailand. Cutting edge genomic technologies may accelerate wider adoption of HLA screening in routine clinical settings. There are great opportunities and several challenges as well for effective implementation of HLA genotyping globally in routine clinical practice for the prevention of drug induced SCARs substantially, enforcing precision medicine initiatives.
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Affiliation(s)
- Chiraphat Kloypan
- Unit of Excellence in Integrative Molecular Biomedicine, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand;
- Division of Clinical Immunology and Transfusion Science, Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao 56000, Thailand
| | - Napatrupron Koomdee
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
| | - Patompong Satapornpong
- Division of General Pharmacy Practice, Department of Pharmaceutical Care, College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand;
- Excellence Pharmacogenomics and Precision Medicine Centre, College of Pharmacy, Rangsit University, Pathum Thani 12000, Thailand
| | - Therdpong Tempark
- Division of Dermatology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Mohitosh Biswas
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
- Department of Pharmacy, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Chonlaphat Sukasem
- Division of Pharmacogenomics and Personalized Medicine, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.K.); (M.B.)
- Laboratory for Pharmacogenomics, Ramathibodi Hospital, Somdech Phra Debaratana Medical Center SDMC, Bangkok 10400, Thailand
- The Thai Severe Cutaneous Adverse Drug Reaction THAI-SCAR Research-Genomics Thailand, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- The Preventive Genomics & Family Check-Up Services Center, Bumrungrad International Hospital, Pharmacogenomics and Precision Medicine Clinic, Bangkok 10110, Thailand
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3GL, UK
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7
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Zhang D, Tang W, Weng S, Zhang N, Luo T, Shen X, Dong L. Integrated in silico‐in vitro analysis of systematic kinase gatekeeper mutation effects on pan‐kinase inhibitors in targeted liver cancer therapy. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202000241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Danying Zhang
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
| | - Wenqing Tang
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
| | - Shuqiang Weng
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
| | - Ningping Zhang
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
| | - Tiancheng Luo
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
| | - Xizhong Shen
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
| | - Ling Dong
- Department of Gastroenterology Zhongshan Hospital of Fudan University Shanghai China
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8
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Goh SJR, Tuomisto JEE, Purcell AW, Mifsud NA, Illing PT. The complexity of T cell-mediated penicillin hypersensitivity reactions. Allergy 2021; 76:150-167. [PMID: 32383256 DOI: 10.1111/all.14355] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/16/2020] [Accepted: 04/30/2020] [Indexed: 12/20/2022]
Abstract
Penicillin refers to a group of beta-lactam antibiotics that are the first-line treatment for a range of infections. However, they also possess the ability to form novel antigens, or neoantigens, through haptenation of proteins and can stimulate a range of immune-mediated adverse reactions-collectively known as drug hypersensitivity reactions (DHRs). IgE-mediated reactions towards these neoantigens are well studied; however, IgE-independent reactions are less well understood. These reactions usually manifest in a delayed manner as different forms of cutaneous eruptions or liver injury consistent with priming of an immune response. Ex vivo studies have confirmed the infiltration of T cells into the site of inflammation, and the subsets of T cells involved appear dependent on the nature of the reaction. Here, we review the evidence that has led to our current understanding of these immune-mediated reactions, discussing the nature of the lesional T cells, the characterization of drug-responsive T cells isolated from patient blood, and the potential mechanisms by which penicillins enter the antigen processing and presentation pathway to stimulate these deleterious responses. Thus, we highlight the need for a more comprehensive understanding of the underlying genetic and molecular basis of penicillin-induced DHRs.
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Affiliation(s)
- Shawn J. R. Goh
- Infection and Immunity Program Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
| | - Johanna E. E. Tuomisto
- Infection and Immunity Program Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
| | - Anthony W. Purcell
- Infection and Immunity Program Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
| | - Nicole A. Mifsud
- Infection and Immunity Program Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
| | - Patricia T. Illing
- Infection and Immunity Program Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology Monash University Clayton Vic. Australia
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9
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Structure-Based Optimization of Therapeutic Peptide Selectivity Between Cerebrovascular Rho-1 and Rho-2 Kinase Isoforms. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10032-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Zhou P, Wang H, Chen Z, Liu Q. Context contribution to the intermolecular recognition of human ACE2-derived peptides by SARS-CoV-2 spike protein: implications for improving the peptide affinity but not altering the peptide specificity by optimizing indirect readout. Mol Omics 2020; 17:86-94. [PMID: 33174576 DOI: 10.1039/d0mo00103a] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an etiological agent of the current rapidly growing outbreak of coronavirus disease (COVID-19), which is straining health systems around the world. Disrupting the intermolecular association of SARS-CoV-2 spike glycoprotein (S protein) with its cell surface receptor human angiotensin-converting enzyme 2 (hACE2) has been recognized as a promising therapeutic strategy against COVID-19. The association is a typical peptide-mediated interaction, where the hACE adopts an α1-helix, which can form a two-helix bundle with the α2-helix, to pack against a flat pocket on the S protein surface. Here, we demonstrate that the protein context of full-length hACE plays an essential role in supporting the hACE2 α1-helix recognition by viral S protein. Energetic analysis reveals that the α1-helical peptide (αHP) and also the two-helix bundle peptide (tBP) cannot bind effectively to S protein when they are split from the hACE protein. The context contributes moderately and considerably to the direct readout (DR) and indirect readout (IR) of peptide recognition, respectively. Dynamics simulation suggests that the two free peptides exhibit a large intrinsic disorder without the support of protein context, which would incur a considerable entropy penalty upon binding to S protein. To restore the IR effect lost by splitting peptides from hACE, we herein propose employing hydrocarbon stapling and cyclization strategies to constrain the free αHP and tBP peptides into their native ordered conformations, respectively. The stapling and cyclization are carefully designed in order to avoid influencing the peptide DR effect, which has been demonstrated to improve the peptide binding affinity (but not specificity) to S protein. The stapling/cyclization-imposed conformational constraint can effectively minimize the unfavorable IR effect (i) by reducing the peptide flexibility and entropy cost upon their binding to S protein, and (ii) by helping peptide pre-folding into their native state to facilitate the conformational selection by S protein.
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Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, No. 2006 Xiyuan Ave West Hi-Tech Zone, Chengdu 611731, China.
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11
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Chen X, Wang H, Yang S, Zheng J, Liu X, Mao G. Structure-based discovery and redesign of TGF-β1 Elbow epitope recognition by its type-II receptor in hypertrophic scarring biotherapy. J Mol Recognit 2020; 34:e2881. [PMID: 33137847 DOI: 10.1002/jmr.2881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/05/2020] [Accepted: 10/20/2020] [Indexed: 11/06/2022]
Abstract
Transforming growth factor-β1 (TGF-β1) signaling pathway has been implicated in the fibroblast activation of hypertrophic scarring (HS). Previously, we proposed a new biotherapeutic strategy to combat HS by disrupting the intermolecular interaction of TGF-β1 with its cognate type-II receptor (TβR-II). Here, we further demonstrate that the binding site of TGF-β1 to TβR-II is not overlapped with the conformational wrist epitope and linear knuckle epitope that are traditionally recognized as the functional binding sites of bone morphogenetic protein-2 (BMP-2) to its type-II receptor (BMPR-II), which can thus be regarded as a new functional site we called elbow epitope. Structural, energetic, and dynamic investigations reveal that the elbow epitope consists of two sequentially discontinuous, spatially vicinal segments Loop30-34 and Turn90-95 ; they cannot work effectively to independently interact with TβR-II. Rational redesign of the epitope is performed using an integrated in silio-in vitro method based on crystal and modeled structure data. In the procedure, the two epitope segments are split from the interface of TGF-β1-TβR-II complex and then connected with each other in a head-to-tail manner by adding a flexible poly-(Gly)n linker between them, thus resulting in a series of combined peptides. We found that the peptide affinity reaches maximum at n = 2, which shares a consistent binding mode with the elbow epitope at native complex interface. The linker of either too long (n > 2) or too short (n < 2) cannot properly place the gap space between the two segments, thus impairing the binding compatibility of designed peptides with TβR-II active site.
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Affiliation(s)
- Xiaoting Chen
- Department of Plastic Surgery, Inner Mongolia Baogang Hospital, Baotou, China
| | - Huixiong Wang
- Department of Hepatobiliary Surgery, Inner Mongolia Baogang Hospital, Baotou, China
| | - Songlin Yang
- Department of Plastic Surgery, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jianghong Zheng
- Department of Plastic Surgery, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiangdong Liu
- Department of Plastic Surgery, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Guangyu Mao
- Department of Plastic Surgery, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai, China
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12
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Wu Y, Jia G, Chi H, Jiao Z, Sun Y. Integrated In Silico-In Vitro Identification and Optimization of Bone Morphogenic Protein-2 Armpit Epitope as Its Antagonist Binding Site. Protein J 2020; 39:703-710. [PMID: 33130958 DOI: 10.1007/s10930-020-09937-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2020] [Indexed: 11/28/2022]
Abstract
Bone morphogenic protein-2 (BMP-2) is the most documented member of BMP family and plays a crucial role in bone formation and growth. In this study, we systematically analyze and compare the complex crystal structures and interaction properties of BMP-2 with its cognate receptors BMPR-I/BMPR-II and with its natural antagonist crossveinless-2 (CV-2) using an integrated in silico-in vitro strategy. It is found that the antagonist-binding site is not fully overlapped with the two receptor-binding sites on BMP-2 surface; the antagonist can competitively disrupt BMP-2-BMPR-II interaction using a blocking-out-of-site manner, but has no substantial influence on BMP-2-BMPR-I interaction. Here, the antagonist-binding site is assigned as a new functional epitope armpit to differ from the traditional conformational epitope wrist and linear epitope knuckle at receptor-binding sites. Structural analysis reveals that the armpit comprises three sequentially discontinuous, structurally vicinal peptide segments, separately corresponding to a loop region and two β-strands crawling on the protein surface. The three segments cannot work independently when splitting from the protein context, but can restore binding capability to CV-2 if they are connected to a single peptide. A systematic combination of different-length polyglycine linkers between these segments obtains a series of designed single peptides, from which several peptides that can potently interact with the armpit-recognition site of CV-2 with high affinity and specificity are identified using energetic analysis and fluorescence assay; they are expected to target BMP-2-CV-2 interaction in a self-inhibitory manner.
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Affiliation(s)
- Yanping Wu
- Department of Joint and Traumatic Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Guanghong Jia
- Department of Pediatrics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Haiyan Chi
- Department of Pediatrics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Zhaode Jiao
- Department of Joint and Traumatic Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Yinghua Sun
- Department of Joint and Traumatic Orthopedics, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China.
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13
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Zhang D, He D, Pan X, Liu L. Rational Design and Intramolecular Cyclization of Hotspot Peptide Segments at YAP–TEAD4 Complex Interface. Protein Pept Lett 2020; 27:999-1006. [DOI: 10.2174/0929866527666200414160723] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 11/22/2022]
Abstract
Background:
The Yes-Associated Protein (YAP) is a central regulator of Hippo pathway
involved in carcinogenesis, which functions through interaction with TEA Domain (TEAD)
transcription factors. Pharmacological disruption of YAP–TEAD4 complexes has been recognized
as a potential therapeutic strategy against diverse cancers by suppressing the oncogenic activity of
YAP.
Objective:
Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein.
Dynamics simulations, energetics analyses and fluorescence polarizations are employed to
characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to
TEAD4 protein.
Methods:
Two peptides, termed PS-1 and PS-2 are split from the interfacial context of YAP protein.
Dynamics simulations, energetics analyses and fluorescence polarizations are employed to
characterize the intrinsic disorder as well as binding energy/affinity of the two YAP peptides to
TEAD4 protein.
Result:
The native conformation of PS-2 peptide is a cyclic loop, which is supposed to be constrained
by adding a disulfide bond across the spatially vicinal residue pair Arg87-Phe96 or Met86-
Phe95 at the peptide’s two ends, consequently resulting in two intramolecular cyclized counterparts
of linear PS-2 peptide, namely PS-2(cyc87,96) and PS-2(cyc86,95). The linear PS-2 peptide
is determined as a weak binder of TEAD4 (Kd = 190 μM), while the two cyclic PS-2(cyc87,96) and
PS-2(cyc86,95) peptides are measured to have moderate or high affinity towards TEAD4 (Kd = 21
and 45 μM, respectively).
Conclusion:
PS-1 and PS-2 peptides are highly flexible and cannot maintain in native active conformation
when splitting from the interfacial context, and thus would incur a considerable entropy
penalty upon rebinding to the interface. Cyclization does not influence the direct interaction between
PS-2 peptide and TEAD4 protein, but can largely reduce the intrinsic disorder of PS-2 peptide
in free state and considerably minimize indirect entropy effect upon the peptide binding.
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Affiliation(s)
- Dingwa Zhang
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Deyong He
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Xiaoliang Pan
- School of Mechanical and Electrical Engineering, Jinggangshan University, Ji’an 343009, China
| | - Lijun Liu
- School of Chemistry and Chemical Engineering, Jinggangshan University, Ji’an 343009, China
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14
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Wang H, Yang Z, Liu Y. Systematic characterization of
adenosine triphosphate
response to lung cancer epidermal growth factor receptor missense mutations: A molecular insight into “generic” drug resistance mutations. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.201900435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hui Wang
- Department of Respiratory Medicine Zhucheng People's Hospital Affiliated to Weifang Medical University Zhucheng China
| | - Zengjian Yang
- Department of Respiratory Medicine Zhucheng People's Hospital Affiliated to Weifang Medical University Zhucheng China
| | - Yanliang Liu
- Department of Respiratory Medicine Zhucheng People's Hospital Affiliated to Weifang Medical University Zhucheng China
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15
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Gao S, Wang Y, Ji L. Rational design and chemical modification of TEAD coactivator peptides to target hippo signaling pathway against gastrointestinal cancers. J Recept Signal Transduct Res 2020; 41:408-415. [PMID: 32912021 DOI: 10.1080/10799893.2020.1818093] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human Hippo signaling pathway has been recognized as a new and promising therapeutic target of gastrointestinal cancers, which is regulated by the intermolecular recognition between the TEA domain (TEAD) transcription factor and its prime coactivators. The coactivator proteins adopt two hotspot sites, namely α-helix and Ω-loop, to interact with TEAD. Here, we demonstrate that both the α-helix and Ω-loop peptides cannot maintain in structured state when splitting from the full-length coactivator proteins; they exhibit a large intrinsic disorder in free state that prevents the coactivator peptide recognition by TEAD. Rational design is used to optimize the interfacial residues of coactivator α-helix peptides, which can effectively improve the favorable direct readout effect upon the peptide binding to TEAD. Chemical modification is employed to constrain the free α-helix peptide into native ordered conformation. The method introduces an all-hydrocarbon bridge across i and i + 4 residues to stabilize the helical structure of a free coactivator peptide, which can considerably reduce the unfavorable indirect readout effect upon the peptide binding to TEAD. The all-hydrocarbon bridge is designed to point out of the TEAD-peptide complex interface, which would not disrupt the direct intermolecular interaction between the TEAD and peptide. Therefore, the stapling only improves peptide affinity, but does not alter peptide specificity, to TEAD. Affinity assay confirms that the binding potency of coactivator α-helix peptides is improved substantially by >5-fold upon the rational design and chemical modification. Structural analysis reveals that the optimized/stapled peptides can form diverse nonbonded interactions such as hydrogen bonds and hydrophobic contacts with TEAD, thus conferring stability and specificity to the TEAD-peptide complex systems.
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Affiliation(s)
- Shuxia Gao
- Department of Gastroenterology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Yingchao Wang
- Department of Gastroenterology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
| | - Lijuan Ji
- Department of Gastroenterology, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, China
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16
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Liu Q, Zhou J, Gao J, Ma W, Wang S, Xing L. Rational design of EGFR dimerization-disrupting peptides: A new strategy to combat drug resistance in targeted lung cancer therapy. Biochimie 2020; 176:128-137. [DOI: 10.1016/j.biochi.2020.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/13/2020] [Accepted: 07/18/2020] [Indexed: 12/24/2022]
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17
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Kuijper E, French L, Tensen C, Vermeer M, Bouwes Bavinck J. Clinical and pathogenic aspects of the severe cutaneous adverse reaction epidermal necrolysis (EN). J Eur Acad Dermatol Venereol 2020; 34:1957-1971. [PMID: 32415695 PMCID: PMC7496676 DOI: 10.1111/jdv.16339] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/25/2020] [Indexed: 12/12/2022]
Abstract
The severe cutaneous adverse reaction epidermal necrolysis (EN) which includes toxic epidermal necrolysis and the milder Stevens-Johnson syndrome is characterized by epidermal loss due to massive keratinocyte apoptosis and/or necroptosis. EN is often caused by a drug mediating a specific TCR-HLA interaction via the (pro)hapten, pharmacological interaction or altered peptide loading mechanism involving a self-peptide presented by keratinocytes. (Memory) CD8 + T cells are activated and exhibit cytotoxicity against keratinocytes via the perforin/granzyme B and granulysin pathway and Fas/FasL interaction. Alternatively drug-induced annexin release by CD14 + monocytes can induce formyl peptide receptor 1 death of keratinocytes by necroptosis. Subsequent keratinocyte death stimulates local inflammation, activating other immune cells producing pro-inflammatory molecules and downregulating regulatory T cells. Widespread epidermal necrolysis and inflammation can induce life-threatening systemic effects, leading to high mortality rates. Research into genetic susceptibility aims to identify risk factors for eventual prevention of EN. Specific HLA class I alleles show the strongest association with EN, but risk variants have also been identified in genes involved in drug metabolism, cellular drug uptake, peptide presentation and function of CD8 + T cells and other immune cells involved in cytotoxic responses. After the acute phase of EN, long-term symptoms can remain or arise mainly affecting the skin and eyes. Mucosal sequelae are characterized by occlusions and strictures due to adherence of denuded surfaces and fibrosis following mucosal inflammation. In addition, systemic pathology can cause acute and chronic hepatic and renal symptoms. EN has a large psychological impact and strongly affects health-related quality of life among EN survivors.
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Affiliation(s)
- E.C. Kuijper
- Department of DermatologyLeiden University Medical CentreLeidenThe Netherlands
| | - L.E. French
- Department of Dermatology and AllergyUniversity HospitalLMU MunichMunichGermany
| | - C.P. Tensen
- Department of DermatologyLeiden University Medical CentreLeidenThe Netherlands
| | - M.H. Vermeer
- Department of DermatologyLeiden University Medical CentreLeidenThe Netherlands
| | - J.N. Bouwes Bavinck
- Department of DermatologyLeiden University Medical CentreLeidenThe Netherlands
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18
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Zhou W, Yang H, Wang H. Inverse in silico-in vitro fishing of unexpected paroxetine kinase targets from tumor druggable kinome. J Mol Model 2020; 26:197. [PMID: 32623519 DOI: 10.1007/s00894-020-04444-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 06/15/2020] [Indexed: 12/11/2022]
Abstract
The serotonin selective reuptake inhibitor paroxetine has been clinically observed to reposition a significant suppressing potency on human tumors by unexpectedly targeting diverse kinase pathways involved in tumorigenesis. Here, we describe an inverse in silico-in vitro strategy to fish potential kinase targets using the paroxetine as bait. This is different (inverse) to the traditional drug discovery process that commonly screens small-molecule inhibitors for a specific kinase target. In the procedure, cell viability assays demonstrate that paroxetine has strong cytotoxicity on human tumor cell lines. Various protooncogene protein kinases are ontologically/manually enriched to define a druggable kinome, and a systematic interaction profile of paroxetine with the kinome is created, which indicates that paroxetine can potentially bind to some known targets or key regulators of human tumors. Kinase assays determine that paroxetine can effectively inhibit c-Src family kinases at nanomolar or micromolar levels. It is observed that the paroxetine ligand forms a tightly packed interface against the active site of these unexpected kinase targets to constitute several specific hydrogen bonds/π-π/cation-π stackings and a number of nonspecific hydrophobic/vdW contacts, while exposing a portion of molecular surface to solvent. More significantly, the ligand adopts two distinct binding modes (i.e., class I and class II) to interact with different kinases; the class-I mode has a higher stability and inhibitory activity than class-II mode. Steric clash seems to cause the ligand flipping from class I to class II. Graphical abstract.
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Affiliation(s)
- Weiyan Zhou
- Department of Gynaecology, The Affiliated Huai'an Hospital of Xuzhou Medical University and the Second People's Hospital of Huai'an, Huai'an, 223002, China
| | - Hongbo Yang
- Department of Gynaecology, Huai'an Maternal and Child Health Care Center, The Affiliated Hospital of Yangzhou University Medical College, Huai'an, 223000, China
| | - Haifeng Wang
- Department of Gynaecology, Huai'an Maternal and Child Health Care Center, The Affiliated Hospital of Yangzhou University Medical College, Huai'an, 223000, China.
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19
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Tang W, Wang C, Zhou Y, Luo J, Ye T, Yang B. Hydrocarbon-stapling stabilization of the reduced homodimerization interaction of hepatic cancer DAP12 transmembrane domain in water phase. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-019-01016-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Yu X, Zhang A, Sun G, Li X. Molecular selectivity design of mitogen-inducible gene-derived phosphopeptides between oncogenic HER kinases. J Mol Graph Model 2020; 99:107661. [PMID: 32574989 DOI: 10.1016/j.jmgm.2020.107661] [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: 03/10/2020] [Revised: 05/23/2020] [Accepted: 05/29/2020] [Indexed: 11/28/2022]
Abstract
Mitogen-inducible gene (MIG) is a natural negative regulator of the oncogenic HER kinase signaling by binding at the activation interface of kinase domain to disrupt the kinase dimerization. In this study, we systematically examine the binding structures, dynamics and energetics of MIG region 2 to four HER kinases based on their crystal or modeled complex structures, and identify an 8-mer phosphopeptide segment pYpY from the core strand sequence of MIG region 2 as the binding hotspot of MIG protein to HER kinases. We demonstrate that the small pYpY phosphopeptide can partially restore the binding affinity of full-length MIG protein, but exhibit a moderate selectivity over different HER kinases (S = 2.3-fold). In addition, the two phosphotyrosine residues pTyr394 and pTyr395 play an essential role in MIG-HER binding; dephosphorylation of them would fully eliminate the binding capability. A machine evolution algorithm is used to optimize the wild-type pYpY phosphopeptide, aiming to simultaneously improve affinity for these kinases and to maximize the affinity gap between different kinases. Consequently, a population is computationally evolved as selective phosphopeptide candidates; the dissociation constants of four representatives with HER kinases are systematically determined using binding affinity analysis, from which their selectivity is derived. The designed pYpYp3 phosphopeptide possesses a high selectivity over different HER kinases (S = 4.8-fold) and satisfactory affinity profile to these kinase (KD = 140-1000 μM). Structural analysis observes that the global binding modes of pYpYp3 to different kinases are roughly consistent, but its local conformation may vary considerably, thus conferring specificity to the phosphopeptide.
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Affiliation(s)
- Xiuli Yu
- Department of Radiotherapy, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Aiying Zhang
- Orthopaedic Trauma, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Guoyu Sun
- Intensive Care Unit, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China
| | - Xuebo Li
- Department of Radiotherapy, Yidu Central Hospital Affiliated to Weifang Medical University, Weifang, 262500, China.
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21
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Song L, Zhu C, Zheng W, Lu D, Jiao H, Zhao R, Bao Z. Computational systematic selectivity of the Fasalog inhibitors between ROCK-I and ROCK-II kinase isoforms in Alzheimer's disease. Comput Biol Chem 2020; 87:107314. [PMID: 32619776 DOI: 10.1016/j.compbiolchem.2020.107314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/31/2022]
Abstract
Human Rho-associated coiled-coil forming kinase (ROCK) is a class of essential neurokinases that consists of two structurally conserved isoforms ROCK-I and ROCK-II; they have been revealed to play distinct roles in the pathogenesis of Alzheimer's disease (AD) and other neurological disorders. Selective targeting of the two kinase isoforms with small-molecule inhibitors is a great challenge due to the surprisingly high homology in kinase domain (92 %) and the full identity in kinase active site (100 %). Here, we describe a computational protocol to systematically profile the selectivity of Fasudil and its 25 analogs (termed as Fasalogs) between the two kinase isoforms. It is suggested that the substitution of Fasudil's 1,4-diazepane moiety with rigid ring such as Ripasudil and Dimehtylfasudil would render the resulting inhibitors of ROCK-II over ROCK-I (II-o-I) selectivity, while the substitution with long, flexible group such as H-89 and BDBM92607 tends to have I-o-II selectivity. Structural analysis reveals that the inhibitor affinity is not only determined by the identical active site, but also contributed from the non-identical first and second shells of the site as well as other non-conserved kinase regions, which can indirectly influence the active site and inhibitor binding through allosteric effect. A further kinase assay basically confirms the computational findings, which also exhibits a good consistence with theoretical selectivity over 10 tested samples (Rp = 0.89). In particular, the Fasalog compounds Dimehtylfasudil and H-89 are identified as II-o-I and I-o-II selective inhibitors. They can be considered as promising lead molecular entities to develop new specific ROCK isoform-selective Fasalog inhibitors.
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Affiliation(s)
- Laijun Song
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Chunyu Zhu
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Wenxin Zheng
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Dan Lu
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China
| | - Hong Jiao
- Department of Neurology, Second Affiliated Hospital, Harbin Medical University, Harbin, 150086, China
| | - Rongbing Zhao
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China.
| | - Zhonglei Bao
- Department of Neurology, Daqing Oil Field General Hospital, Daqing, 163001, China.
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22
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Studying Calcium Ion-Dependent Effect on the Inter-subunit Interaction Between the cTnC N-terminal Domain and cTnI C-terminal Switch Peptide of Human Cardiac Troponin via Chou’s 5-Steps Rule. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09875-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Wu D, Luo L, Yang Z, Chen Y, Quan Y, Min Z. Targeting Human Hippo TEAD Binding Interface with YAP/TAZ-Derived, Flexibility-Reduced Peptides in Gastric Cancer. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10069-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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24
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Xiao D, Fan Z, Jiaqi W, Liu H, Shen L, He B, Zhang M. Rational molecular targeting of the inter-subunit interaction between human cardiac troponin hcTnC and hcTnI using switch peptide-competitive biogenic medicines. Comput Biol Chem 2020; 87:107272. [PMID: 32438115 DOI: 10.1016/j.compbiolchem.2020.107272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 01/19/2023]
Abstract
The human cardiac troponin (hcTn) has been implicated in diverse cardiovascular diseases (CDs). The protein function is regulated by the inter-subunit interaction between the N-terminal domain of hcTnC and the C-terminal switch peptide of hcTnI; disruption of the interaction has been recognized as a potential therapeutic strategy for CDs. Here, we report use of biogenic medicines as small-molecule competitors to directly disrupt the protein-protein interaction by competitively targeting the core binding site (CBS) of hcTnC NTD domain. A multistep virtual screening protocol is performed against a biogenic compound library to identify competitor candidates and competition assay is employed to verify the screening results. Consequently, two compounds Collismycin and Compound e are identified as strong competitors (CC50 < 10 μM) with hcTnI for hcTnC CBS site, while other tested compounds are found to have moderate (CC50 = 10-100 μM), low (CC50 > 100 μM) or no (CC50 = N.D.) potency. The competitor ligands are anchored at the core groove of hcTnC CBS site through aromatic and hydrophobic interactions, while few peripheral hydrogen bonds are formed to further confer specificity for domain-compound recognition. These molecular-level findings would benefit from further in vitro and in vivo studies at cellular and animal levels, which can help to practice the ultimate therapeutic purpose.
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Affiliation(s)
- Danrui Xiao
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Zixun Fan
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Wu Jiaqi
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Hua Liu
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Linghong Shen
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Ben He
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Min Zhang
- Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China.
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25
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Zhang W, Liu J, Shan H, Yin F, Zhong B, Zhang C, Yu X. Machine learning-guided evolution of BMP-2 knuckle Epitope-Derived osteogenic peptides to target BMP receptor II. J Drug Target 2020; 28:802-810. [PMID: 32354236 DOI: 10.1080/1061186x.2020.1757100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wei Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jiazhi Liu
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Haojie Shan
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Fuli Yin
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Biao Zhong
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chi Zhang
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiaowei Yu
- Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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26
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Ding X, Tong C, Chen R, Wang X, Gao D, Zhu L. Systematic molecular profiling of inhibitor response to the clinical missense mutations of ErbB family kinases in human gastric cancer. J Mol Graph Model 2020; 96:107526. [DOI: 10.1016/j.jmgm.2019.107526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/14/2019] [Accepted: 12/24/2019] [Indexed: 01/20/2023]
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27
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Rational Derivation of Osteogenic Peptides from Bone
Morphogenetic Protein-2 Knuckle Epitope by Integrating In
Silico Analysis and In Vitro Assay. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10058-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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28
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He Y. Systematic response of staurosporine scaffold-based inhibitors to drug-resistant cancer kinase mutations. Arch Pharm (Weinheim) 2020; 353:e1900320. [PMID: 32285482 DOI: 10.1002/ardp.201900320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/25/2020] [Accepted: 03/24/2020] [Indexed: 11/10/2022]
Abstract
Human protein kinases have been established as promising druggable targets in cancer therapy. However, a large number of acquired drug-resistant kinase mutations are observed after first- and second-line kinase inhibitor treatments, largely limiting the application of small-molecule inhibitors in the targeted cancer therapy. Previously, the pan-kinase inhibitor staurosporine and its derivatives have been reported to selectively inhibit gatekeeper mutants over wild-type kinases, suggesting that the staurosporine scaffold is potentially helpful in developing wild-type-sparing inhibitors of drug-resistant kinase mutants. Here, a systematic response profile of 32 staurosporine scaffold-based inhibitors (SSBIs) for 61 ontology-enriched drug-resistant cancer kinase mutations is created using a combination of in silico analysis and in vitro assay, from which it is possible to identify those mutations that have the potential to cause resistance or confer sensitivity to SSBIs. The profile reveals that SSBIs exhibit distinct responses to kinase gatekeeper and nongatekeeper mutations, and SSBIs bearing p7 substituents can considerably influence their response to kinase gatekeeper mutations, particularly for the mutations of the Ile residue, which possesses a Cβ methyl group that tends to cause steric clash with bound SSBIs. Nongatekeeper mutations generally have a moderate and unfavorable effect on SSBI activity, as most of them are outside the kinase active site and do not directly contact inhibitor ligands. In addition, it is found that resistance is commonly caused by mutation-induced hindrance effects, whereas sensitivity is primarily conferred by mutation-established additional interactions.
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Affiliation(s)
- Yongkang He
- Department of Infectious Diseases, Taixing People's Hospital, Yangzhou University, Taixing, China
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29
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Lian F, Wang Z, Zhou Z, Xu G. Identification, characterization, and comparison of n-alkanols and anesthetics binding to the C1b subdomain of protein kinase cα: similar function with different binding sites. J Recept Signal Transduct Res 2020; 40:109-116. [PMID: 32054382 DOI: 10.1080/10799893.2020.1726950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Protein kinase C (PKC) is a family of lipid-activated enzymes involved in anesthetic preconditioning signaling pathways. Previously, n-alkanols and general anesthetics have been found to activate PKC by binding to the kinase C1B subdomain. In the present study, we attempt to ascertain the molecular mechanism and interaction mode of human PKCα C1B subdomain with a variety of exogenous n-alkanols and volatile general anesthetics as well as endogenous activator phorbol ester (PE) and co-activator diacylglycerol (DG). Systematic bioinformatics analysis identifies three spatially vicinal sites on the subdomain surface to potentially accommodate small-molecule ligands, where the site 1 is a narrow, amphipathic pocket, the site 2 is a wide, flat and hydrophobic pocket, and the site 3 is a rugged, polar pocket. Further interaction modeling reveals that site 1 is the cognate binding region of natural PE activator, which can moderately simulate the kinase activity in an independent manner. The short-chain n-alkanols are speculated to also bind at the site to competitively inhibit PE-induced kinase activation. The long-chain n-alkanols and co-activator DG are found to target site 2 in a nonspecific manner, while the volatile anesthetics prefer to interact with site 3 in a specific manner. Since the site 1 is composed of two protein loops that are also shared by sites 2 and 3, binding of n-alkanols, DG and anesthetics to sites 2 and 3 can trigger a conformational displacement on the two loops, which enlarges the pocket size and changes the pocket configuration of site 1 through an allosteric mechanism, consequently enhancing kinase activation by improving PE affinity to the site.
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Affiliation(s)
- Fang Lian
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhong Wang
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhidong Zhou
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Guohai Xu
- Department of Anesthesiology, the Second Affiliated Hospital of Nanchang University, Nanchang, China
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30
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Systematic profiling of staralog response to acquired drug resistant kinase gatekeeper mutations in targeted cancer therapy. Amino Acids 2020; 52:511-521. [PMID: 32206932 DOI: 10.1007/s00726-020-02832-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/19/2020] [Indexed: 12/14/2022]
Abstract
Kinase-targeted therapy has been widely used as a lifesaving strategy for cancer patients. However, many patients treated with targeted cancer drugs are clinically observed to rapidly develop acquired resistance. Kinase gatekeeper mutation is one of the most chief factors contributing to the resistance, which modulates the accessibility of kinase's ATP-binding pocket. Previously, the pan-kinase inhibitor Staurosporine and its analogs (termed as Staralogs) have been reported to exhibit wild-type sparing selectivity for some kinase gatekeeper mutants, such as EGFR T790M, Her2 T798M and cSrc T338M. Here, we describe an integrative approach to systematically profile the molecular response of 15 representative Staralogs to 17 kinase gatekeeper mutations in targeted cancer therapy. With the profile we are able to divide gatekeeper mutations into three classes (i.e. classes I, II and III) and to divide Staralogs into two groups (i.e. groups 1 and 2) using heuristic clustering. The class I and II mutations confer consistent sensitivity and resistance for all Staralogs, respectively, while the class III mutations address divergent effects on different Staralogs. The mutations to Ile residue can generally reduce Staralog affinity by inducing unfavorable steric hindrance, whereas the mutations to Met and Leu residues would improve Staralog affinity by establishing favorable S···π interaction, van der Waals packing and/or hydrophobic contact. The group 1 and 2 Staralogs are primarily determined by carbonyl or hydroxyl substitution state at the position 7 of Staralog core, where points to kinase gatekeeper residue and can thus be directly influenced by gatekeeper mutation.
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31
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Li Y, Wei X, Wang Q, Li W, Yang T. Inverse screening of Simvastatin kinase targets from glioblastoma druggable kinome. Comput Biol Chem 2020; 86:107243. [PMID: 32172201 DOI: 10.1016/j.compbiolchem.2020.107243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/04/2020] [Accepted: 03/01/2020] [Indexed: 12/16/2022]
Abstract
The statin drug Simvastatin is a HMG-CoA reductase inhibitor that has been widely used to lower blood lipid. However, the drug is clinically observed to reposition a significant suppressing potency on glioblastoma (GBM) by unexpectedly targeting diverse kinase pathways involved in GBM tumorigensis. Here, an inverse screening strategy is described to discover potential kinase targets of Simvastatin. Various human protein kinases implicated in GBM are enriched to define a druggable kinome; the binding behavior of Simvastatin to the kinome is profiled systematically via an integrative computational approach, from which most kinases have only low or moderate binding potency to Simvastatin, while only few are identified as promising kinase hits. It is revealed that Simvastatin can potentially interact with certain known targets or key regulators of GBM such as ErbB, c-Src and FGFR signaling pathways, but exhibit low affinity to the well-established GBM target of PI3K/Akt/mTOR pathway. Further assays determine that Simvastatin can inhibit kinase hits EGFR, MET, SRC and HER2 at nanomolar level, which are comparable with those of cognate kinase inhibitors. Structural analyses reveal that the sophisticated T790 M gatekeeper mutation can considerably reduce Simvastatin sensitivity to EGFR by inducing the ligand change between different binding modes.
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Affiliation(s)
- Yi Li
- Department of Neurosurgery, Second Affiliated Hospital, Zunyi Medical University, Zunyi 563006, China
| | - Xu Wei
- Department of Neurosurgery, Second Affiliated Hospital, Zunyi Medical University, Zunyi 563006, China
| | - Qiuhong Wang
- Department of Neurosurgery, Second Affiliated Hospital, Zunyi Medical University, Zunyi 563006, China
| | - Wei Li
- Department of Neurosurgery, Second Affiliated Hospital, Zunyi Medical University, Zunyi 563006, China
| | - Tao Yang
- Department of Neurosurgery, Second Affiliated Hospital, Zunyi Medical University, Zunyi 563006, China.
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Ge C, Zhang W, He R, Cai H. Systematic Identification and Comparative Analysis of Human Cartilage-Derived Self-peptides Presented Differently by Ankylosing Spondylitis (AS)-Associated HLA-B*27:05 and Non-AS-associated HLA-B*27:09. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09857-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gu Z, Yan T, Yan F. Rational design and improvement of the dimerization-disrupting peptide selectivity between ROCK-I and ROCK-II kinase isoforms in cerebrovascular diseases. J Mol Recognit 2020; 33:e2835. [PMID: 31995258 DOI: 10.1002/jmr.2835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/17/2019] [Accepted: 12/25/2019] [Indexed: 02/05/2023]
Abstract
Human rho-associated coiled-coil forming kinases (ROCKs) ROCK-I and ROCK-II have been documented as attractive therapeutic targets for cerebrovascular diseases. Although ROCK-I and ROCK-II share a high degree of structural conservation and are both present in classic rho/ROCK signaling pathway, their downstream substrates and pathological functions may be quite different. Selective targeting of the two kinase isoforms with traditional small-molecule inhibitors is a great challenge due to their surprisingly high homology in kinase domain (~90%) and the full identity in kinase active site (100%). Here, instead of developing small-molecule drugs to selectively target the adenosine triphosphate (ATP) site of two isoforms, we attempt to design peptide agents to selectively disrupt the homo-dimerization event of ROCK kinases through their dimerization domains which have a relatively low conservation (~60%). Three helical peptides H1, H2, and H3 are split from the kinase dimerization domain, from which the isolated H2 peptide is found to have the best capability to rebind at the dimerization interface. A simulated annealing (SA) iteration method is used to improve the H2 peptide selectivity between ROCK-I and ROCK-II. The method accepts moderate degradation in peptide affinity in order to maximize the affinity difference between peptide binding to the two isoforms. Consequently, hundreds of parallel SA runs yielded six promising peptide candidates with ROCK-I over ROCK-II (I over II [IoII]) calculated selectivity and four promising peptide candidates with ROCK-II over ROCK-I (II over I [IIoI]) calculated selectivity. Subsequent anisotropy assays confirm that the selectivity values range between 13.2-fold and 83.9-fold for IoII peptides, and between 5.8-fold and 21.2-fold for IIoI peptides, which are considerably increased relative to wild-type H2 peptide (2.6-fold for IoII and 2.0-fold for IIoI). The molecular origin of the designed peptide selectivity is also analyzed at structural level; it is revealed that the peptide residues can be classified into conserved, non-conserved, and others, in which the non-conserved residues play a crucial role in defining peptide selectivity, while conserved residues confer stability to kinase-peptide binding.
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Affiliation(s)
- Zhengtian Gu
- Department of Neurology, Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
| | - Tingting Yan
- Department of Pediatrics, Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Fuling Yan
- Department of Neurology, Affiliated Zhongda Hospital, School of Medicine, Southeast University, Nanjing, China
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Zhou P, Yan F, Miao Q, Chen Z, Wang H. Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode? J Biomol Struct Dyn 2020; 39:310-318. [DOI: 10.1080/07391102.2019.1709547] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
- Center for Information in BioMedicine, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
| | - Fugang Yan
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Qingqing Miao
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Zheng Chen
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
| | - Heyi Wang
- Center for Informational Biology, University of Electronic Science and Technology of China (UESTC) at Qingshuihe Campus, Chengdu, China
- School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC) at Shahe Campus, Chengdu, China
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Xu L, Chen Z, Shao K, Wang Y, Cui L, Guo N. Rational discovery of novel type-III FTF antagonists to competitively suppress TIF-2 coactivation in liver cancer. J Recept Signal Transduct Res 2019; 39:304-311. [PMID: 31755335 DOI: 10.1080/10799893.2019.1690513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Linlin Xu
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Zhongming Chen
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Keke Shao
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Yungang Wang
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Leilei Cui
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
| | - Naizhou Guo
- Department of Laboratory Medicine, The First People’s Hospital of Yancheng City, the Fourth Affiliated Hospital of Nantong University, Yancheng, China
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Chen Z, Yu X, Zhang A, Wang F, Xing Y. De Novo Hydrocarbon-Stapling Design of Single-Turn α-Helical Antimicrobial Peptides. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09964-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Rational design of type-IA receptor-derived cyclic peptides to target human bone morphogenic protein 2. J Biosci 2019. [DOI: 10.1007/s12038-019-9945-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Zhu J, Wei S, Huang L, Zhao Q, Zhu H, Zhang A. Molecular modeling and rational design of hydrocarbon-stapled/halogenated helical peptides targeting CETP self-binding site: Therapeutic implication for atherosclerosis. J Mol Graph Model 2019; 94:107455. [PMID: 31586754 DOI: 10.1016/j.jmgm.2019.107455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/04/2019] [Accepted: 09/24/2019] [Indexed: 11/28/2022]
Abstract
The human plasma cholesteryl ester transfer protein (CETP) collects triglycerides from very-/low-density lipoproteins (V/LDL) and exchanges them for cholesteryl esters from high-density lipoproteins (HDL), which has recognized as an important therapeutic target for atherosclerosis. The protein has a C-terminal amphipathic α-helix that serves as self-binding peptide to fulfill biological function by dynamically binding to/unbinding from its cognate site (termed self-binding site) in the same protein. Previously, we successfully derived and halogenated the helical peptide to competitively disrupt the self-binding behavior of CETP C-terminal tail. However, the halogenated peptides have only a limited affinity increase as compared to native helical peptide (∼3-fold), thus exhibiting only a moderate competitive potency. Here, instead of optimizing the direct intermolecular interaction of peptide with CETP self-binding site we attempt to further improve the peptide competitive potency by reducing its conformational flexibility with hydrocarbon-stapling technique. Computational analysis reveals that the helical peptide has large intrinsic disorder in unbound free state, which would incur a considerable entropy penalty upon rebinding to the self-binding site. All-hydrocarbon bridge is designed and optimized on native and halogenated peptides in terms of the helical pattern and binding mode of self-binding peptide. Dynamics simulation and circular dichroism indicate that the stapling can considerably reduce peptide disorder in free state. Energetics calculation and fluorescence assay conform that the binding affinity of stapled/halogenated peptides is improved substantially (by > 5-fold), thus exhibiting an effective competition potency with native peptide for the self-binding site. Structural examination suggests that the binding modes and nonbonded interactions of native and halogenated peptides are not influenced essentially due to the stapling.
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Affiliation(s)
- Jian Zhu
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Sen Wei
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China.
| | - Linchen Huang
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Qi Zhao
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Haichao Zhu
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
| | - Anwei Zhang
- Department of Vascular Surgery, The Affiliated Hospital of Jiangsu University (Kunshan 1st People's Hospital), Kunshan, 215300, China
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Zhou K, Lu J, Yin X, Xu H, Li L, Ma B. Structure-based derivation and intramolecular cyclization of peptide inhibitors from PD-1/PD-L1 complex interface as immune checkpoint blockade for breast cancer immunotherapy. Biophys Chem 2019; 253:106213. [DOI: 10.1016/j.bpc.2019.106213] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/16/2022]
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Bo G, Cao F, Li M, Xing J, Su X, Zhu Y, Wu D. Exploring calcium ion-dependent effect on the intermolecular interaction between human secreted phospholipase A2 and its peptide inhibitors in coronary artery disease. J Mol Graph Model 2019; 93:107449. [PMID: 31536875 DOI: 10.1016/j.jmgm.2019.107449] [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: 06/08/2019] [Revised: 08/31/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022]
Abstract
Human secreted phospholipase A2 (hsPLA2) is a small calcium ion (Ca2+)-regulatory protein secreting from platelets, eosinophils and T-lymphocytes, which has been established as an important biomarker and potential target for the diagnosis and therapy of coronary artery disease. Short peptide inhibitors are used to competitively suppress the enzymatic activity of hsPLA2. Here, Ca2+ effect on the intermolecular recognition and interaction between hsPLA2 and its peptide inhibitors is investigated systematically by using molecular modeling and bioinformatics analysis. Dynamics simulations reveal that the hsPLA2 structure bound with Ca2+ is rather stable and has low thermal motion; removal of Ca2+ considerably increases structural flexibility and intrinsic disorder of the protein. Energetics calculations suggest that presence of Ca2+ can effectively promote the interaction of hsPLA2 with peptide inhibitors. In particular, the local substructures of hsPLA2 such as helix H1, loop L2 and double-stranded β-sheet DS that participate in peptide recognition are involved in or nearby Ca2+-coordinating site and can be directly stabilized by the Ca2+. In addition, a significant concentration-dependent effect of Ca2+ on peptide-hsPLA2 binding is observed in vitro, that is, a little of Ca2+ can largely improve peptide binding affinity, but high Ca2+ concentration does not increase the affinity substantially. The correlation between calculated free energy and experimental binding affinity over different peptide inhibitors is improved considerably by adding Ca2+ to hsPLA2. Specifically, the FLSYK peptide can generally bind to Ca2+-bound hsPLA2 with a moderate or high affinity (Kd ranges between 56 and 210 μM), but have only a modest affinity or even nonbinding to Ca2+-free hsPLA2 (Kd > 400 μM or = n.d.).
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Affiliation(s)
- Guanggan Bo
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China.
| | - Fang Cao
- Department of Respiration, Anhui Provincial Children's Hospital, Hefei, 230051, China
| | - Min Li
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Junwu Xing
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Xiaoye Su
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Yunxian Zhu
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
| | - Dingkun Wu
- Department of Cardiology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Nanjing, 210014, China
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41
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Tang W, Zhao Z, Wang C, Ye T, Yang B. Molecular design and optimization of hepatic cancer SLP76-derived PLCγ1 SH3-binding peptide with the systematic N-substitution of peptide PXXP motif. J Mol Recognit 2019; 32:e2806. [PMID: 31397025 DOI: 10.1002/jmr.2806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/23/2022]
Abstract
The phospholipase Cγ1 (PLCγ1) is essential for T-cell signaling and activation in hepatic cancer immune response, which has a regulatory Src homology 3 (SH3) domain that can specifically recognize and interact with the PXXP-containing decapeptide segment (185 QPPVPPQRPM194 , termed as SLP76185-194 peptide) of adaptor protein SLP76 following T-cell receptor ligation. The isolated peptide can only bind to the PLCγ1 SH3 domain with a moderate affinity due to lack of protein context support. Instead of the traditional natural residue mutagenesis that is limited by low structural diversity and shifted target specificity, we herein attempt to improve the peptide affinity by replacing the two key proline residues Pro187 and Pro190 of SLP76185-194 PXXP motif with nonnatural N-substituted amino acids, as the proline is the only endogenous N-substituted amino acid. The replacement would increase peptide flexibility but can restore peptide activity by establishing additional interactions with the domain. Structural analysis reveals that the domain pocket can be divided into a large amphipathic region and a small negatively charged region; they accommodate hydrophobic, aromatic, polar, and moderate-sized N-substituted amino acid types. A systematic replacement combination profile between the peptide residues Pro187 and Pro190 is created by structural modeling, dynamics simulation, and energetics analysis, from which six improved and two reduced N-substituted peptides as well as native SLP76185-194 peptide are identified and tested for their binding affinity to the recombinant protein of the human PLCγ1 SH3 domain using fluorescence-based assays. Two N-substituted peptides, SLP76185-194 (N-Leu187/N-Gln190) and SLP76185-194 (N-Thr187/N-Gln190), are designed to have high potency (Kd = 0.67 ± 0.18 and 1.7 ± 0.3 μM, respectively), with affinity improvement by, respectively, 8.5-fold and 3.4-fold relative to native peptide (Kd = 5.7 ± 1.2 μM).
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Affiliation(s)
- Wenqing Tang
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhiying Zhao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Wang
- Department of Oncology, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Ye
- Department of Oncology, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Biwei Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
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42
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Liu H, Xu L, Huang H, Zhao P, Yang R, Zhou Q, Liu G. Systematic profiling of clinical missence mutation effects on the intermolecular interaction between human growth hormone and its receptor in isolated growth hormone deficiency. J Mol Graph Model 2019; 92:1-7. [PMID: 31279174 DOI: 10.1016/j.jmgm.2019.06.018] [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: 05/28/2019] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 11/17/2022]
Abstract
Isolated growth hormone deficiency (IGHD) is the most common pituitary hormone deficiency and can result from congenital or acquired causes. Among the known factors, genetic mutations in human growth hormone (hGH) remain the most frequent cause of IGHD, which influence the binding of hGH to its cognate receptor (hGHbp). Although previous studies have systematically investigated the residue importance at hGH-hGHbp complex interface, the molecular role of IGHD-associated residue mutations in the complex function still remains largely unexplored. Here, a total of 21 known hGH naturally-occurring missence mutations that have been clinically observed to be involved in IGHD disorder are collected and confirmed by original literature; they effects on the conformation, energetics and dynamics of hGH-hGHbp recognition and interaction are dissected at molecular level by using atomistic dynamics simulations, binding energy calculations and fluorescence spectroscopy assays. A systematic profile of hGH-hGHbp binding response to these clinical missence mutations is created, based on which it is revealed that (i) most mutations have appreciably unfavorable effect on the binding, which potentially destabilize the complex interaction, while only very few are predicted as moderate stabilizers for the complex system, and (ii) these disease-related mutations can locate either at complex interface or in hGH protein interior far away from the interface; both can influence the complex binding through either direct interaction or indirect allostericity. Two mutations, E100K (non-interface) and G146R (interface), are identified to address potent destabilization effect on hGH-hGHbp complex system; they can reduce the complex binding affinity by 8-fold (Kd changes from 0.76 to 5.9 nM) and 46-fold (Kd changes from 0.76 to 34.7 nM), respectively.
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Affiliation(s)
- Hui Liu
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Peiran Zhao
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Rongrong Yang
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Qing Zhou
- Department of Endocrinology, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China
| | - Guanghua Liu
- Department of Pediatrics, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, 350001, China.
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43
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Bai X, Chen X. Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia. J Theor Biol 2019; 473:44-51. [DOI: 10.1016/j.jtbi.2019.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/17/2019] [Accepted: 03/23/2019] [Indexed: 10/27/2022]
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44
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Fu Y, He P, Zhou Y, Huang S, Liang L, Liu S. Exploring the systematic effect of
N
‐substituted PxxP motifs on peptoid affinity to ARHGEF5/TIM SH3 domain and its relationship with ARHGEF5/TIM activation. Proteins 2019; 87:979-991. [PMID: 31197859 DOI: 10.1002/prot.25760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/04/2019] [Accepted: 06/07/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Yong Fu
- Department of Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical University Chongqing China
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of Chongqing Chongqing China
| | - Ping He
- Department of Cardiac SurgerySouthwest Hospital, Third Army Medical University Chongqing China
| | - Yu Zhou
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of Chongqing Chongqing China
| | - Shengyuan Huang
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of Chongqing Chongqing China
| | - Lin Liang
- Department of Cardiothoracic SurgeryDianjiang People's Hospital of Chongqing Chongqing China
| | - Shengchun Liu
- Department of Endocrine and Breast SurgeryThe First Affiliated Hospital of Chongqing Medical University Chongqing China
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45
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Han M, Sun D. Rational creation and systematic analysis of cervical cancer kinase–inhibitor binding profile. J Comput Aided Mol Des 2019; 33:689-698. [DOI: 10.1007/s10822-019-00211-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/08/2019] [Indexed: 10/26/2022]
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46
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Zhu LX, Liu Q, Hua YF, Yang N, Zhang XG, Ding X. Systematic Profiling and Evaluation of Structure-based Kinase–Inhibitor Interactome in Cervical Cancer by Integrating In Silico Analyses and In Vitro Assays at Molecular and Cellular Levels. Comput Biol Chem 2019; 80:324-332. [DOI: 10.1016/j.compbiolchem.2019.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/08/2019] [Accepted: 04/30/2019] [Indexed: 12/16/2022]
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47
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Ning L, He B, Zhou P, Derda R, Huang J. Molecular Design of Peptide-Fc Fusion Drugs. Curr Drug Metab 2019; 20:203-208. [DOI: 10.2174/1389200219666180821095355] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 01/18/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
Background:Peptide-Fc fusion drugs, also known as peptibodies, are a category of biological therapeutics in which the Fc region of an antibody is genetically fused to a peptide of interest. However, to develop such kind of drugs is laborious and expensive. Rational design is urgently needed.Methods:We summarized the key steps in peptide-Fc fusion technology and stressed the main computational resources, tools, and methods that had been used in the rational design of peptide-Fc fusion drugs. We also raised open questions about the computer-aided molecular design of peptide-Fc.Results:The design of peptibody consists of four steps. First, identify peptide leads from native ligands, biopanning, and computational design or prediction. Second, select the proper Fc region from different classes or subclasses of immunoglobulin. Third, fuse the peptide leads and Fc together properly. At last, evaluate the immunogenicity of the constructs. At each step, there are quite a few useful resources and computational tools.Conclusion:Reviewing the molecular design of peptibody will certainly help make the transition from peptide leads to drugs on the market quicker and cheaper.
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Affiliation(s)
- Lin Ning
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Bifang He
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ratmir Derda
- Department of Chemistry, University of Alberta, Alberta, Canada
| | - Jian Huang
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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48
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Wang X, Chang C, Wang D, Hong S. Systematic profiling of SH3-mediated Tau-Partner interaction network in Alzheimer's disease by integrating in silico analysis and in vitro assay. J Mol Graph Model 2019; 90:265-272. [PMID: 31112821 DOI: 10.1016/j.jmgm.2019.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/20/2019] [Accepted: 05/07/2019] [Indexed: 11/24/2022]
Abstract
The aberrant assembly of microtubule-associated protein Tau (τ) into insoluble aggregates is closely related to Alzheimer's disease (AD), which is elicited from Tau phosphorylation events and regulated by the specific intermolecular recognition between the proline-rich PxxP motifs of Tau and the SH3 domains of its diverse partner proteins/kinases. Here, we attempt to create a systematic interaction profile for the 10 SH3 domains of previously reported Tau partners across all the 18 Tau PxxP peptides. A number of biologically functional SH3-PxxP interaction events are identified from the profile and then tested using fluorescence spectroscopy. It is revealed that (i) the region (residues 520-560) precedent to the tubulin-binding partial repeats of Tau protein is an important target of SH3 domains, where contains the three PxxP peptides τp527-536, τp530-539 and τp547-556 that exhibit different binding profiles towards the investigated SH3 domains, (ii) as compared to τp527-536 and τp547-556, the τp530-539 peptide located between them has only a modest binding potency to most SH3 domains, suggesting that the three peptides contribute unevenly to Tau-SH3 interactions, and (iii) some other Tau PxxP peptides, particularly those within the residue range 490-510 that is neighboring to the region 520-560, can also interact effectively with several SH3 domains. The SH3 domain of the well known Tau partner kinase Fyn is determined to have high or moderate affinity for an array of Tau PxxP peptides, including τp137-146, τp493-502, τp527-536 and τp547-556 (Kd ranges 15.7-85.6 μM).
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Affiliation(s)
- Xiaoming Wang
- Department of Neurology, Wuxi People's Hospital, Nanjing Medical University, Wuxi, 214023, China
| | - Chunyan Chang
- Center of Clinical Research, Wuxi People's Hospital, Nanjing Medical University, Wuxi, 214023, China
| | - Dongxue Wang
- Department of Cardiology, Wuxi People's Hospital, Nanjing Medical University, Wuxi, 214023, China
| | - Shanchao Hong
- Department of Medical Clinical Laboratory, Wuxi People's Hospital, Nanjing Medical University, Wuxi, 214023, China.
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Structural Dissection and Optimization of a Cation–π–π Stacking System in Human Pregnancy-Related Serine Protease–Peptide Complex. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09866-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Qian H, He P, Lv F, Wu W. Genome-wide analysis of LXXLL-mediated DAX1/SHP–nuclear receptor interaction network and rational design of stapled LXXLL-based peptides to target the specific network profile. Int J Biol Macromol 2019; 129:13-22. [DOI: 10.1016/j.ijbiomac.2019.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 02/02/2019] [Accepted: 02/02/2019] [Indexed: 01/22/2023]
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