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Cimini M, Hansmann UHE, Gonzalez C, Chesney AD, Truongcao MM, Gao E, Wang T, Roy R, Forte E, Mallaredy V, Thej C, Magadum A, Joladarashi D, Benedict C, Koch WJ, Tükel Ç, Kishore R. Podoplanin Positive Cell-derived Extracellular Vesicles Contribute to Cardiac Amyloidosis After Myocardial Infarction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601297. [PMID: 39005419 PMCID: PMC11244852 DOI: 10.1101/2024.06.28.601297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background Amyloidosis is a major long-term complication of chronic disease; however, whether it represents one of the complications of post-myocardial infarction (MI) is yet to be fully understood. Methods Using wild-type and knocked-out MI mouse models and characterizing in vitro the exosomal communication between bone marrow-derived macrophages and activated mesenchymal stromal cells (MSC) isolated after MI, we investigated the mechanism behind Serum Amyloid A 3 (SAA3) protein overproduction in injured hearts. Results Here, we show that amyloidosis occurs after MI and that amyloid fibers are composed of macrophage-derived SAA3 monomers. SAA3 overproduction in macrophages is triggered by exosomal communication from a subset of activated MSC, which, in response to MI, acquire the expression of a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin (PDPN). Cardiac MSC PDPN+ communicate with and activate macrophages through their extracellular vesicles or exosomes. Specifically, MSC PDPN+ derived exosomes (MSC PDPN+ Exosomes) are enriched in SAA3 and exosomal SAA3 protein engages with Toll-like receptor 2 (TRL2) on macrophages, triggering an overproduction and impaired clearance of SAA3 proteins, resulting in aggregation of SAA3 monomers as rigid amyloid deposits in the extracellular space. The onset of amyloid fibers deposition alongside extra-cellular-matrix (ECM) proteins in the ischemic heart exacerbates the rigidity and stiffness of the scar, hindering the contractility of viable myocardium and overall impairing organ function. Using SAA3 and TLR2 deficient mouse models, we show that SAA3 delivered by MSC PDPN+ exosomes promotes post-MI amyloidosis. Inhibition of SAA3 aggregation via administration of a retro-inverso D-peptide, specifically designed to bind SAA3 monomers, prevents the deposition of SAA3 amyloid fibrils, positively modulates the scar formation, and improves heart function post-MI. Conclusion Overall, our findings provide mechanistic insights into post-MI amyloidosis and suggest that SAA3 may be an attractive target for effective scar reversal after ischemic injury and a potential target in multiple diseases characterized by a similar pattern of inflammation and amyloid deposition. NOVELTY AND SIGNIFICANCE What is known? Accumulation of rigid amyloid structures in the left ventricular wall impairs ventricle contractility.After myocardial infarction cardiac Mesenchymal Stromal Cells (MSC) acquire Podoplanin (PDPN) to better interact with immune cells.Amyloid structures can accumulate in the heart after chronic inflammatory conditions. What information does this article contribute? Whether accumulation of cumbersome amyloid structures in the ischemic scar impairs left ventricle contractility, and scar reversal after myocardial infarction (MI) has never been investigated.The pathophysiological relevance of PDPN acquirement by MSC and the functional role of their secreted exosomes in the context of post-MI cardiac remodeling has not been investigated.Amyloid structures are present in the scar after ischemia and are composed of macrophage-derived Serum Amyloid A (SAA) 3 monomers, although mechanisms of SAA3 overproduction is not established. SUMMARY OF NOVELTY AND SIGNIFICANCE Here, we report that amyloidosis, a secondary phenomenon of an already preexisting and prolonged chronic inflammatory condition, occurs after MI and that amyloid structures are composed of macrophage-derived SAA3 monomers. Frequently studied cardiac amyloidosis are caused by aggregation of immunoglobulin light chains, transthyretin, fibrinogen, and apolipoprotein in a healthy heart as a consequence of systemic chronic inflammation leading to congestive heart failure with various types of arrhythmias and tissue stiffness. Although chronic MI is considered a systemic inflammatory condition, studies regarding the possible accumulation of amyloidogenic proteins after MI and the mechanisms involved in that process are yet to be reported. Here, we show that SAA3 overproduction in macrophages is triggered in a Toll-like Receptor 2 (TLR2)-p38MAP Kinase-dependent manner by exosomal communication from a subset of activated MSC, which, in response to MI, express a platelet aggregation-inducing type I transmembrane glycoprotein named Podoplanin. We provide the full mechanism of this phenomenon in murine models and confirm SAA3 amyloidosis in failing human heart samples. Moreover, we developed a retro-inverso D-peptide therapeutic approach, "DRI-R5S," specifically designed to bind SAA3 monomers and prevent post-MI aggregation and deposition of SAA3 amyloid fibrils without interfering with the innate immune response.
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Firdessa-Fite R, Johnson SN, Bechi Genzano C, Leon MA, Ku A, Ocampo Gonzalez FA, Milner JD, Sestak JO, Berkland C, Creusot RJ. Soluble antigen arrays provide increased efficacy and safety over free peptides for tolerogenic immunotherapy. Front Immunol 2024; 15:1258369. [PMID: 38933266 PMCID: PMC11199391 DOI: 10.3389/fimmu.2024.1258369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Autoantigen-specific immunotherapy using peptides offers a more targeted approach to treat autoimmune diseases, but clinical implementation has been challenging. We previously showed that multivalent delivery of peptides as soluble antigen arrays (SAgAs) efficiently protects against spontaneous autoimmune diabetes in the non-obese diabetic (NOD) mouse model. Here, we compared the efficacy, safety, and mechanisms of action of SAgAs versus free peptides. SAgAs, but not their corresponding free peptides at equivalent doses, efficiently prevented the development of diabetes. SAgAs increased the frequency of regulatory T cells among peptide-specific T cells or induce their anergy/exhaustion or deletion, depending on the type of SAgA used (hydrolysable (hSAgA) and non-hydrolysable 'click' SAgA (cSAgA)) and duration of treatment, whereas their corresponding free peptides induced a more effector phenotype following delayed clonal expansion. Over time, the peptides induced an IgE-independent anaphylactic reaction, the incidence of which was significantly delayed when peptides were in SAgA form rather than in free form. Moreover, the N-terminal modification of peptides with aminooxy or alkyne linkers, which was needed for grafting onto hyaluronic acid to make hSAgA or cSAgA variants, respectively, influenced their stimulatory potency and safety, with alkyne-functionalized peptides being more potent and less anaphylactogenic than aminooxy-functionalized peptides. Immunologic anaphylaxis occurred in NOD mice in a dose-dependent manner but not in C57BL/6 or BALB/c mice; however, its incidence did not correlate with the level of anti-peptide antibodies. We provide evidence that SAgAs significantly improve the efficacy of peptides to induce tolerance and prevent autoimmune diabetes while at the same time reducing their anaphylactogenic potential.
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Affiliation(s)
- Rebuma Firdessa-Fite
- Columbia Center for Translational Immunology, Department of Medicine and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Stephanie N. Johnson
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Camillo Bechi Genzano
- Columbia Center for Translational Immunology, Department of Medicine and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Martin A. Leon
- Department of Chemistry, University of Kansas, Lawrence, KS, United States
| | - Amy Ku
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center and New York Presbyterian Hospital, New York, NY, United States
| | - Fernando A. Ocampo Gonzalez
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center and New York Presbyterian Hospital, New York, NY, United States
| | - Joshua D. Milner
- Department of Pediatrics, Division of Allergy and Immunology, Columbia University Irving Medical Center, New York, NY, United States
| | - Joshua O. Sestak
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
| | - Cory Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, United States
- Department of Chemical and Petroleum Engineering, University of Kansas, Lawrence, KS, United States
| | - Remi J. Creusot
- Columbia Center for Translational Immunology, Department of Medicine and Naomi Berrie Diabetes Center, Columbia University Irving Medical Center, New York, NY, United States
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3
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Xie X, Valiente PA, Kim J, Kim PM. HelixDiff, a Score-Based Diffusion Model for Generating All-Atom α-Helical Structures. ACS CENTRAL SCIENCE 2024; 10:1001-1011. [PMID: 38799672 PMCID: PMC11117309 DOI: 10.1021/acscentsci.3c01488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 05/29/2024]
Abstract
Here, we present HelixDiff, a score-based diffusion model for generating all-atom helical structures. We developed a hot spot-specific generation algorithm for the conditional design of α-helices targeting critical hotspot residues in bioactive peptides. HelixDiff generates α-helices with near-native geometries for most test scenarios with root-mean-square deviations (RMSDs) less than 1 Å. Significantly, HelixDiff outperformed our prior GAN-based model with regard to sequence recovery and Rosetta scores for unconditional and conditional generations. As a proof of principle, we employed HelixDiff to design an acetylated GLP-1 D-peptide agonist that activated the glucagon-like peptide-1 receptor (GLP-1R) cAMP accumulation without stimulating the glucagon-like peptide-2 receptor (GLP-2R). We predicted that this D-peptide agonist has a similar orientation to GLP-1 and is substantially more stable in MD simulations than our earlier D-GLP-1 retro-inverse design. This D-peptide analogue is highly resistant to protease degradation and induces similar levels of AKT phosphorylation in HEK293 cells expressing GLP-1R compared to the native GLP-1. We then discovered that matching crucial hotspots for the GLP-1 function is more important than the sequence orientation of the generated D-peptides when constructing D-GLP-1 agonists.
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Affiliation(s)
- Xuezhi Xie
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Pedro A Valiente
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Jisun Kim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Philip M Kim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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Tseng TS, Lee CC, Chen PJ, Lin CY, Chen WC, Lee YC, Lin JH, Chen KW, Tsai KC. Structure-Guided Discovery of PD-1/PD-L1 Interaction Inhibitors: Peptide Design, Screening, and Optimization via Computation-Aided Phage Display Engineering. J Chem Inf Model 2024; 64:1615-1627. [PMID: 38356220 DOI: 10.1021/acs.jcim.3c01500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Cancer immunotherapy harnesses the immune system to combat tumors and has emerged as a major cancer treatment modality. The PD-1/PD-L1 immune checkpoint modulates interactions between tumor cells and T cells and has been extensively targeted in cancer immunotherapy. However, the monoclonal antibodies known to target this immune checkpoint have considerable side effects, and novel PD-1/PD-L1 inhibitors are therefore required. Herein, a peptide inhibitor to disrupt PD-1/PD-L1 interactions was designed through structure-driven phage display engineering coupled to computational modification and optimization. BetaPb, a novel peptide library constructed by using the known structure of PD-1/PD-L, was used to develop inhibitors against the immune checkpoint, and specific peptides with high affinity toward PD-1 were screened through enzyme-linked immunosorbent assays, homogeneous time-resolved fluorescence, and biolayer interferometry. A potential inhibitor, B8, was preliminarily screened through biopanning. The binding affinity of B8 toward PD-1 was confirmed through computation-aided optimization. Assessment of B8 variants (B8.1, B8.2, B8.3, B8.4, and B8.5) demonstrated their attenuation of PD-1/PD-L1 interactions. B8.4 exhibited the strongest attenuation efficiency at a half-maximal effective concentration of 0.1 μM and the strongest binding affinity to PD-1 (equilibrium dissociation constant = 0.1 μM). B8.4 outperformed the known PD-1/PD-L1 interaction inhibitor PL120131 in disrupting PD-1/PD-L1 interactions, revealing that B8.4 has remarkable potential for modification to yield an antitumor agent. This study provides valuable information for the future development of peptide-based drugs, therapeutics, and immunotherapies for cancer.
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Affiliation(s)
- Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40202, Taiwan
| | - Chao-Chang Lee
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Po-Juei Chen
- Institute of Molecular Biology, National Chung Hsing University, Taichung 40202, Taiwan
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Chiu-Yuen Lin
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Wang-Chuan Chen
- The School of Chinese Medicine for Post Baccalaureate, I-Shou University, Kaohsiung 824005, Taiwan
- Department of Chinese Medicine, E-Da Hospital, Kaohsiung 824005, Taiwan
| | - Yu-Ching Lee
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Jiun-Han Lin
- Department of Industrial Technology, Ministry of Economic Affairs, Taipei 100210, Taiwan
- Food Industry Research and Development Institute, Hsinchu 30062, Taiwan
| | - Kaun-Wen Chen
- Molecular Science and Digital Innovation Center, Genetics Generation Advancement Corporation, Taipei 11949, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: A new OSPREY-based algorithm for designing de novo D-peptide inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.12.579944. [PMID: 38405797 PMCID: PMC10888900 DOI: 10.1101/2024.02.12.579944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan, which enable exponential reductions in the size of the peptide sequence search space. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a new framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead therapeutic candidates. We provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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6
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Sarkar T, Ghosh S, Sundaravadivelu PK, Pandit G, Debnath S, Thummer RP, Satpati P, Chatterjee S. Mechanism of Protease Resistance of D-Amino Acid Residue Containing Cationic Antimicrobial Heptapeptides. ACS Infect Dis 2024; 10:562-581. [PMID: 38294842 DOI: 10.1021/acsinfecdis.3c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Antimicrobial peptides (AMPs) have been an alternate promising class of therapeutics in combating global antibiotic resistance threat. However, the short half-life of AMPs, owing to protease degradability, is one of the major bottlenecks in its commercial success. In this study, we have developed all-D-amino acid containing small cationic peptides P4C and P5C, which are completely protease-resistant, noncytotoxic, nonhemolytic, and potent against the ESKAPE pathogens in comparison to their L analogues. MD simulations suggested marginal improvement in the peptide-binding affinity to the membrane-mimetic SDS micelle (∼ 1 kcal/mol) in response to L → D conversion, corroborating the marginal improvement in the antimicrobial activity. However, L → D chirality conversion severely compromised the peptide:protease (trypsin) binding affinity (≥10 kcal/mol). The relative distance between the scissile peptide carbonyl and the catalytic triad of the protease (H57, D102, and S195) was found to be significantly altered in the D-peptide:protease complex (inactive conformation) relative to the active L-peptide:protease complex. Thus, the poor binding affinity between D-peptides and the protease, resulting in the inactive complex formation, explained their experimentally observed proteolytic stability. This mechanistic insight might be extended to the proteolytic stability of the D-peptides in general and stimulate the rational design of protease-resistant AMPs.
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Affiliation(s)
- Tanumoy Sarkar
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Suvankar Ghosh
- Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | | | - Gopal Pandit
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Swapna Debnath
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Rajkumar P Thummer
- Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Priyadarshi Satpati
- Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
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7
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Wang Y, Sun Y, Zeng X, Zhuang R, Huang J, Zhang X, Guo Z, Li Y. 68Ga-Labeled TMTP1 Modified with d-Amino Acid for Positron Emission Tomography Diagnosis of Highly Metastatic Hepatocellular Carcinoma. J Med Chem 2024; 67:2165-2175. [PMID: 38270637 DOI: 10.1021/acs.jmedchem.3c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
TMTP1 (NVVRQ) has been proven to selectively target various highly metastatic tumor cells. Nonetheless, existing TMTP1 probes encounter challenges such as rapid blood clearance, limited tumor uptake, and inadequate suitability for therapeutic interventions. To overcome these constraints, we designed and synthesized eight peptide probes, employing innovative chemical modification strategies involving d-amino acid modification and retro-inverso isomerization. Notably, [68Ga]TV2 exhibited particularly impressive performance, displaying an 88.88, 76.90, and 90.32% improvement in uptake at 15, 30, and 60 min, respectively, while maintaining a high target-to-nontarget ratio. Further research has demonstrated that [68Ga]TV2 also exhibits remarkable diagnostic potential for detecting in situ microtumors in the liver. The results suggest that through the implementation of innovative chemical modification strategies, we successfully developed a peptide precursor, NOTA-G-NVvRQ, with specific affinity for highly metastatic tumors, enhanced in vivo pharmacokinetic profile, and heightened stability in vivo, rendering it well suited for prospective investigations in combination therapy studies.
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Affiliation(s)
- Yanjie Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yuan Sun
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Xueyuan Zeng
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Rongqiang Zhuang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Jinxiong Huang
- Department of Nuclear Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, China
| | - Xianzhong Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
- Theranostics and Translational Research Center, Institute of Clinical Medicine, Department of Nuclear Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Zhide Guo
- State Key Laboratory of Vaccines for Infectious Diseases, Center for Molecular Imaging and Translational Medicine, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Yesen Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, China
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8
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Guerin N, Childs H, Zhou P, Donald BR. DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors. Protein Eng Des Sel 2024; 37:gzae007. [PMID: 38757573 PMCID: PMC11099876 DOI: 10.1093/protein/gzae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 04/17/2024] [Indexed: 05/18/2024] Open
Abstract
With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains play a central role in modulating polarization, signaling, and trafficking pathways. Mutations in PDZ domains lead to diseases such as cancer and cystic fibrosis, making PDZ domains attractive targets for therapeutic intervention. D-peptide inhibitors offer unique advantages as therapeutics, including increased metabolic stability and low immunogenicity. Here, we introduce DexDesign, a novel OSPREY-based algorithm for computationally designing de novo D-peptide inhibitors. DexDesign leverages three novel techniques that are broadly applicable to computational protein design: the Minimum Flexible Set, K*-based Mutational Scan, and Inverse Alanine Scan. We apply these techniques and DexDesign to generate novel D-peptide inhibitors of two biomedically important PDZ domain targets: CAL and MAST2. We introduce a framework for analyzing de novo peptides-evaluation along a replication/restitution axis-and apply it to the DexDesign-generated D-peptides. Notably, the peptides we generated are predicted to bind their targets tighter than their targets' endogenous ligands, validating the peptides' potential as lead inhibitors. We also provide an implementation of DexDesign in the free and open source computational protein design software OSPREY.
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Affiliation(s)
- Nathan Guerin
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
| | - Henry Childs
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
| | - Bruce R Donald
- Department of Computer Science, Duke University, 308 Research Drive, Durham, NC 27708, United States
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, United States
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 22710, United States
- Department of Mathematics, Duke University, 120 Science Drive, Durham, NC 27708, United States
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9
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Lee Y, Chong S, Lee C, Kim J, Choi SQ. Structural Determinants of Chirally Selective Transport of Amino Acids through the α-Hemolysin Protein Nanopores of Free-Standing Planar Lipid Membranes. NANO LETTERS 2024; 24:681-687. [PMID: 38185873 DOI: 10.1021/acs.nanolett.3c03976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Despite the importance of the enantioselective transport of amino acids through transmembrane protein nanopores from fundamental and practical perspectives, little has been explored to date. Here, we study the transport of amino acids through α-hemolysin (αHL) protein pores incorporated into a free-standing lipid membrane. By measuring the transport of 13 different amino acids through the αHL pores, we discover that the molecular size of the amino acids and their capability to form hydrogen bonds with the pore surface determine the chiral selectivity. Molecular dynamics simulations corroborate our findings by revealing the enantioselective molecular-level interactions between the amino acid enantiomers and the αHL pore. Our work is the first to present the determinants for chiral selectivity using αHL protein as a molecular filter.
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Affiliation(s)
- Yohan Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sanggyu Chong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Chiwoo Lee
- Chiral Technology Korea (CTK), Daejeon 34013, Republic of Korea
| | - Jihan Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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10
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Guo RC, Wang N, Wang W, Zhang Z, Luo W, Wang Y, Du H, Xu Y, Li G, Yu Z. Artificial Peptide-Protein Necrosomes Promote Cell Death. Angew Chem Int Ed Engl 2023; 62:e202314578. [PMID: 37870078 DOI: 10.1002/anie.202314578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/12/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
The presence of disordered region or large interacting surface within proteins significantly challenges the development of targeted drugs, commonly known as the "undruggable" issue. Here, we report a heterogeneous peptide-protein assembling strategy to selectively phosphorylate proteins, thereby activating the necroptotic signaling pathway and promoting cell necroptosis. Inspired by the structures of natural necrosomes formed by receptor interacting protein kinases (RIPK) 1 and 3, the kinase-biomimetic peptides are rationally designed by incorporating natural or D -amino acids, or connecting D -amino acids in a retro-inverso (DRI) manner, leading to one RIPK3-biomimetic peptide PR3 and three RIPK1-biomimetic peptides. Individual peptides undergo self-assembly into nanofibrils, whereas mixing RIPK1-biomimetic peptides with PR3 accelerates and enhances assembly of PR3. In particular, RIPK1-biomimetic peptide DRI-PR1 exhibits reliable binding affinity with protein RIPK3, resulting in specific cytotoxicity to colon cancer cells that overexpress RIPK3. Mechanistic studies reveal the increased phosphorylation of RIPK3 induced by RIPK1-biomimetic peptides, elucidating the activation of the necroptotic signaling pathway responsible for cell death without an obvious increase in secretion of inflammatory cytokines. Our findings highlight the potential of peptide-protein hybrid aggregation as a promising approach to address the "undruggable" issue and provide alternative strategies for overcoming cancer resistance in the future.
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Affiliation(s)
- Ruo-Chen Guo
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Ning Wang
- State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Weishu Wang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Zeyu Zhang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Wendi Luo
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory for Biological Effects of Nanomaterials & Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yushi Wang
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Haiqin Du
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Yifei Xu
- State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Gongyu Li
- State Key Laboratory of Medicinal Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
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11
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Kumar Sharma A, Sharma R, Dev Sarma H, Mukherjee A, Das T, Satpati D. Design, synthesis and evaluation of 177Lu-labeled inverso and retro-inverso A9 peptide variants targeting HER2-overexpression. Bioorg Chem 2023; 140:106761. [PMID: 37586132 DOI: 10.1016/j.bioorg.2023.106761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023]
Abstract
Several HER2-specific peptides are being continuously explored to find a candidate with suitable pharmacokinetic properties for development of effective radiopharmaceutical that can find applications for clinical screening of breast cancer patients. In the present work with an aim of preparing a radiopeptide with improved metabolic stability and in vivo pharmacokinetic performance we modified our previously reported [177Lu]DOTA-L-A9 peptide. Here we designed an 'inverso' peptide with all d-amino acids and a 'retro-inverso' peptide where sequence of d-amino acids was reversed. Higher secondary structure stabilization of retro- inverso A9 variant compared to inverso A9 peptide was evident by circular dichroism studies. The two radiopeptides [177Lu]DOTA-D-A9 and [177Lu]DOTA-rD-A9 exhibited significantly improved in vivo metabolic stability over the original l-peptide. The retro-inverso variant, [177Lu]DOTA-rD-A9 demonstrated better pharmacokinetic behavior with significantly higher tumor uptake than the inverso peptide, [177Lu]DOTA-D-A9 and the original peptide, [177Lu]DOTA-L-A9. In the present case of A9 peptide, reversal of the peptide sequence of d-amino acids boosted the uptake and retention of radioactivity in HER2-positive tumor. The present study can thus guide the design and development of newer and improved versions of peptides.
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Affiliation(s)
- Amit Kumar Sharma
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Rohit Sharma
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Haladhar Dev Sarma
- Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Archana Mukherjee
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Tapas Das
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Drishty Satpati
- Radiopharmaceuticals Division, Bhabha Atomic Research Centre, Mumbai, India; Homi Bhabha National Institute, Mumbai, India.
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12
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Lindman J, Yadav A, Gising J, Larhed M. Two-Chamber Aminocarbonylation of Aryl Bromides and Triflates Using Amino Acids as Nucleophiles. J Org Chem 2023; 88:12978-12985. [PMID: 37639573 PMCID: PMC10507664 DOI: 10.1021/acs.joc.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Indexed: 08/31/2023]
Abstract
A palladium(0)-catalyzed aminocarbonylation reaction employing molybdenum hexacarbonyl as a carbon monoxide precursor for the production of N-capped amino acids using aryl and heteroaryl bromides and triflates is reported. The carbon monoxide is formed ex situ through the use of a two-chamber system, where carbon monoxide generated in one chamber is free to diffuse over and be consumed in the other palladium-catalyzed reaction chamber. Using this method, two series of aryl bromides and aryl triflates were utilized to synthesize 21 N-capped amino acids in isolated yields between 40 and 91%.
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Affiliation(s)
- Jens Lindman
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
| | - Anubha Yadav
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
| | - Johan Gising
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Uppsala University, Husargatan 3, SE-751
23 Uppsala, Sweden
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13
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Du S, Wey M, Armstrong DW. d-Amino acids in biological systems. Chirality 2023; 35:508-534. [PMID: 37074214 DOI: 10.1002/chir.23562] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 04/20/2023]
Abstract
Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.
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Affiliation(s)
- Siqi Du
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Michael Wey
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
| | - Daniel W Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas, USA
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14
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Bu H, Lan X, Cheng H, Pei C, Ouyang M, Chen Y, Huang X, Yu L, Tan Y. Development of an interfering peptide M1-20 with potent anti-cancer effects by targeting FOXM1. Cell Death Dis 2023; 14:533. [PMID: 37598210 PMCID: PMC10439915 DOI: 10.1038/s41419-023-06056-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023]
Abstract
Disrupting protein-protein interactions (PPIs) has emerged as a promising strategy for cancer drug development. Interfering peptides disrupting PPIs can be rationally designed based on the structures of natural sequences mediating these interactions. Transcription factor FOXM1 overexpresses in multiple cancers and is considered an effective target for cancer therapeutic drug development. Using a rational design approach, we have generated a peptide library from the FOXM1 C-terminal sequence and screened FOXM1-binding peptides. Combining FOXM1 binding and cell inhibitory results, we have obtained a FOXM1-targeting interfering peptide M1-20 that is optimized from the natural parent peptide to the D-retro-inverso peptide. With improved stability characteristics, M1-20 inhibits proliferation and migration, and induces apoptosis of cancer cells. Mechanistically, M1-20 inhibits FOXM1 transcriptional activities by disrupting its interaction between the MuvB complex and the transcriptional co-activator CBP. These are consistent with the results that M1-20 suppresses cancer progression and metastasis without noticeable toxic and side effects in wild-type mice. These findings reveal that M1-20 has the potential to be developed as an anti-cancer drug candidate targeting FOXM1.
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Affiliation(s)
- Huitong Bu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Xianling Lan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Haojie Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Chaozhu Pei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Min Ouyang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Yan Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Xiaoqin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Li Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China
| | - Yongjun Tan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Engineering Research Center for Anticancer Targeted Protein Pharmaceuticals, Hunan University, Changsha, Hunan, 410082, China.
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15
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Valiente P, Nim S, Kim J, Kim PM. Computational Design of Potent and Selective d-Peptide Agonists of the Glucagon-like Peptide-2 Receptor. J Med Chem 2023; 66:10342-10353. [PMID: 37491005 PMCID: PMC10424673 DOI: 10.1021/acs.jmedchem.3c00464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Indexed: 07/27/2023]
Abstract
Here, we designed three d-GLP-2 agonists that activated the glucagon-like peptide-2 receptor (GLP-2R) cyclic adenosine monophosphate (cAMP) accumulation without stimulating the glucagon-like peptide-1 receptor (GLP-1R). All the d-GLP-2 agonists increased the protein kinase B phosphorylated (p-AKT) expression levels in a time- and concentration-dependent manner in vitro. The most effective d-GLP-2 analogue boosted the AKT phosphorylation 2.28 times more effectively compared to the native l-GLP-2. The enhancement in the p-AKT levels induced by the d-GLP-2 analogues could be explained by GLP-2R's more prolonged activation, given that the d-GLP-2 analogues induce a lower β-arrestin recruitment. The higher stability to protease degradation of our d-GLP-2 agonists helps us envision their potential applications in enhancing intestinal absorption and treating inflammatory bowel illness while lowering the high dosage required by the current treatments.
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Affiliation(s)
- Pedro
A. Valiente
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Satra Nim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Jisun Kim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Philip M. Kim
- Donnelly
Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 3E1, Canada
- Department
of Computer Science, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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16
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Marciano Y, Nayeem N, Dave D, Ulijn RV, Contel M. N-Acetylation of Biodegradable Supramolecular Peptide Nanofilaments Selectively Enhances Their Proteolytic Stability for Targeted Delivery of Gold-Based Anticancer Agents. ACS Biomater Sci Eng 2023; 9:3379-3389. [PMID: 37192486 PMCID: PMC10699682 DOI: 10.1021/acsbiomaterials.3c00312] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Peptide materials are promising for various biomedical applications; however, a significant concern is their lack of stability and rapid degradation in vivo due to non-specific proteolysis. For materials specifically designed to respond to disease-specific proteases, it would be desirable to retain high susceptibility to target proteases while minimizing the impact of non-specific proteolysis. We describe N-terminal acetylation as a simple synthetic modification of amphiphilic self-assembling peptides that contain an MMP-9-cleavable segment and form soluble, nanoscale filaments. We found that the N-terminus capping of these peptides did not significantly impact their self-assembly behavior, critical aggregation concentration, or ability to encapsulate hydrophobic payloads. By contrast, their proteolytic stability in human plasma (especially for anionic peptide sequences) was considerably increased while susceptibility to hydrolysis by MMP-9 was retained when compared to non-acetylated peptides, especially during the first 12 h. We note, however, that due to the longer time scale required for in vitro studies (72 h), non-specific proteolysis of both anionic acetylated peptides leads to similar activity in vitro despite differing MMP-9 kinetics during the early stages. Overall, the enhanced stability against non-specific proteases, combined with the ability of these nanofilaments to enhance the effectiveness of gold-based drugs toward cancerous cells compared to healthy cells, brings these acetylated peptide filaments a step closer toward clinical translation.
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Affiliation(s)
- Yaron Marciano
- Department of Chemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Nazia Nayeem
- Department of Chemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- PhD Program Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Dhwanit Dave
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Rein V. Ulijn
- Advanced Science Research Center at The Graduate Center of the City University of New York, 85 Saint Nicholas Terrace, New York, NY 10031, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
| | - Maria Contel
- Department of Chemistry, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- PhD Program in Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- PhD Program Biology, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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17
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Bonaccorso A, Privitera A, Grasso M, Salamone S, Carbone C, Pignatello R, Musumeci T, Caraci F, Caruso G. The Therapeutic Potential of Novel Carnosine Formulations: Perspectives for Drug Development. Pharmaceuticals (Basel) 2023; 16:778. [PMID: 37375726 DOI: 10.3390/ph16060778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/29/2023] Open
Abstract
Carnosine (beta-alanyl-L-histidine) is an endogenous dipeptide synthesized via the activity of the ATP-dependent enzyme carnosine synthetase 1 and can be found at a very high concentration in tissues with a high metabolic rate, including muscles (up to 20 mM) and brain (up to 5 mM). Because of its well-demonstrated multimodal pharmacodynamic profile, which includes anti-aggregant, antioxidant, and anti-inflammatory activities, as well as its ability to modulate the energy metabolism status in immune cells, this dipeptide has been investigated in numerous experimental models of diseases, including Alzheimer's disease, and at a clinical level. The main limit for the therapeutic use of carnosine is related to its rapid hydrolysis exerted by carnosinases, especially at the plasma level, reason why the development of new strategies, including the chemical modification of carnosine or its vehiculation into innovative drug delivery systems (DDS), aiming at increasing its bioavailability and/or at facilitating the site-specific transport to different tissues, is of utmost importance. In the present review, after a description of carnosine structure, biological activities, administration routes, and metabolism, we focused on different DDS, including vesicular systems and metallic nanoparticles, as well as on possible chemical derivatization strategies related to carnosine. In particular, a basic description of the DDS employed or the derivatization/conjugation applied to obtain carnosine formulations, followed by the possible mechanism of action, is given. To the best of our knowledge, this is the first review that includes all the new formulations of carnosine (DDS and derivatives), allowing a decrease or complete prevention of the hydrolysis of this dipeptide exerted by carnosinases, the simultaneous blood-brain barrier crossing, the maintenance or enhancement of carnosine biological activity, and the site-specific transport to different tissues, which then offers perspectives for the development of new drugs.
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Affiliation(s)
- Angela Bonaccorso
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- NANOMED-Research Centre for Nanomedicine and Pharmaceutical Nanotechnology, University of Catania, 95125 Catania, Italy
| | - Anna Privitera
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Margherita Grasso
- Unit of Neuropharmacology and Translational Neurosciences, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Sonya Salamone
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
| | - Claudia Carbone
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- NANOMED-Research Centre for Nanomedicine and Pharmaceutical Nanotechnology, University of Catania, 95125 Catania, Italy
| | - Rosario Pignatello
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- NANOMED-Research Centre for Nanomedicine and Pharmaceutical Nanotechnology, University of Catania, 95125 Catania, Italy
| | - Teresa Musumeci
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- NANOMED-Research Centre for Nanomedicine and Pharmaceutical Nanotechnology, University of Catania, 95125 Catania, Italy
| | - Filippo Caraci
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Unit of Neuropharmacology and Translational Neurosciences, Oasi Research Institute-IRCCS, 94018 Troina, Italy
| | - Giuseppe Caruso
- Department of Drug and Health Sciences, University of Catania, 95125 Catania, Italy
- Unit of Neuropharmacology and Translational Neurosciences, Oasi Research Institute-IRCCS, 94018 Troina, Italy
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18
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Nag A, Mafi A, Das S, Yu MB, Alvarez-Villalonga B, Kim SK, Su Y, Goddard WA, Heath JR. Stereochemical engineering yields a multifunctional peptide macrocycle inhibitor of Akt2 by fine-tuning macrocycle-cell membrane interactions. Commun Chem 2023; 6:95. [PMID: 37202473 DOI: 10.1038/s42004-023-00890-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 04/26/2023] [Indexed: 05/20/2023] Open
Abstract
Macrocycle peptides are promising constructs for imaging and inhibiting extracellular, and cell membrane proteins, but their use for targeting intracellular proteins is typically limited by poor cell penetration. We report the development of a cell-penetrant high-affinity peptide ligand targeted to the phosphorylated Ser474 epitope of the (active) Akt2 kinase. This peptide can function as an allosteric inhibitor, an immunoprecipitation reagent, and a live cell immunohistochemical staining reagent. Two cell penetrant stereoisomers were prepared and shown to exhibit similar target binding affinities and hydrophobic character but 2-3-fold different rates of cell penetration. Experimental and computational studies resolved that the ligands' difference in cell penetration could be assigned to their differential interactions with cholesterol in the membrane. These results expand the tool kit for designing new chiral-based cell-penetrant ligands.
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Affiliation(s)
- Arundhati Nag
- California Institute of Technology, Pasadena, CA, USA
- Clark University, Worcester, MA, USA
| | - Amirhossein Mafi
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - Samir Das
- California Institute of Technology, Pasadena, CA, USA
- Clark University, Worcester, MA, USA
| | - Mary Beth Yu
- California Institute of Technology, Pasadena, CA, USA
| | | | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - Yapeng Su
- California Institute of Technology, Pasadena, CA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, USA
| | - James R Heath
- California Institute of Technology, Pasadena, CA, USA.
- Institute for Systems Biology, Seattle, WA, USA.
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19
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Firdessa-Fite R, Johnson SN, Leon MA, Sestak JO, Berkland C, Creusot RJ. Soluble antigen arrays improve the efficacy and safety of peptide-based tolerogenic immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539161. [PMID: 37205572 PMCID: PMC10187310 DOI: 10.1101/2023.05.05.539161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Autoantigen-specific immunotherapy using peptides offers a more targeted approach to treat autoimmune diseases, but the limited in vivo stability and uptake of peptides impedes clinical implementation. We previously showed that multivalent delivery of peptides as soluble antigen arrays (SAgAs) efficiently protects against spontaneous autoimmune diabetes in the non-obese diabetic (NOD) mouse model. Here, we compared the efficacy, safety, and mechanisms of action of SAgAs versus free peptides. SAgAs, but not their corresponding free peptides at equivalent doses, efficiently prevented the development of diabetes. SAgAs increased the frequency of regulatory T cells among peptide-specific T cells or induce their anergy/exhaustion or deletion, depending on the type of SAgA (hydrolysable (hSAgA) and non-hydrolysable 'click' SAgA (cSAgA)) and duration of treatment, whereas their corresponding free peptides induced a more effector phenotype following delayed clonal expansion. Moreover, the N-terminal modification of peptides with aminooxy or alkyne linkers, which was needed for grafting onto hyaluronic acid to make hSAgA or cSAgA variants, respectively, influenced their stimulatory potency and safety, with alkyne-functionalized peptides being more potent and less anaphylactogenic than aminooxy-functionalized peptides. Both SAgA variants significantly delayed anaphylaxis compared to their respective free peptides. The anaphylaxis, which occurred in NOD mice but not in C57BL/6 mice, was dose-dependent but did not correlate with the production of IgG1 or IgE against the peptides. We provide evidence that SAgAs significantly improve the efficacy and safety of peptide-based immunotherapy.
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Affiliation(s)
- Rebuma Firdessa-Fite
- Columbia Center for Translational Immunology, Department of Medicine and Naomi Berrie Diabetes Center, Columbia University Medical Center, 650 West 168 St, New York, NY 10032
| | - Stephanie N. Johnson
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047
| | - Martin A. Leon
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Drive, Lawrence, KS 66045
| | - Joshua O. Sestak
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047
| | - Cory Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047
- Department of Chemical and Petroleum Engineering, University of Kansas,1530 West 15 Street, Lawrence, KS 66045
| | - Remi J. Creusot
- Columbia Center for Translational Immunology, Department of Medicine and Naomi Berrie Diabetes Center, Columbia University Medical Center, 650 West 168 St, New York, NY 10032
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20
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Nim S, O'Hara DM, Corbi-Verge C, Perez-Riba A, Fujisawa K, Kapadia M, Chau H, Albanese F, Pawar G, De Snoo ML, Ngana SG, Kim J, El-Agnaf OMA, Rennella E, Kay LE, Kalia SK, Kalia LV, Kim PM. Disrupting the α-synuclein-ESCRT interaction with a peptide inhibitor mitigates neurodegeneration in preclinical models of Parkinson's disease. Nat Commun 2023; 14:2150. [PMID: 37076542 PMCID: PMC10115881 DOI: 10.1038/s41467-023-37464-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 03/14/2023] [Indexed: 04/21/2023] Open
Abstract
Accumulation of α-synuclein into toxic oligomers or fibrils is implicated in dopaminergic neurodegeneration in Parkinson's disease. Here we performed a high-throughput, proteome-wide peptide screen to identify protein-protein interaction inhibitors that reduce α-synuclein oligomer levels and their associated cytotoxicity. We find that the most potent peptide inhibitor disrupts the direct interaction between the C-terminal region of α-synuclein and CHarged Multivesicular body Protein 2B (CHMP2B), a component of the Endosomal Sorting Complex Required for Transport-III (ESCRT-III). We show that α-synuclein impedes endolysosomal activity via this interaction, thereby inhibiting its own degradation. Conversely, the peptide inhibitor restores endolysosomal function and thereby decreases α-synuclein levels in multiple models, including female and male human cells harboring disease-causing α-synuclein mutations. Furthermore, the peptide inhibitor protects dopaminergic neurons from α-synuclein-mediated degeneration in hermaphroditic C. elegans and preclinical Parkinson's disease models using female rats. Thus, the α-synuclein-CHMP2B interaction is a potential therapeutic target for neurodegenerative disorders.
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Affiliation(s)
- Satra Nim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Darren M O'Hara
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Carles Corbi-Verge
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Albert Perez-Riba
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Kazuko Fujisawa
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Minesh Kapadia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Hien Chau
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Federica Albanese
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Grishma Pawar
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Mitchell L De Snoo
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Sophie G Ngana
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Jisun Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Omar M A El-Agnaf
- Neurological Disorders Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Suneil K Kalia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, ON, Canada.
| | - Lorraine V Kalia
- Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada.
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada.
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.
| | - Philip M Kim
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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21
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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22
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A Review on Forced Degradation Strategies to Establish the Stability of Therapeutic Peptide Formulations. Int J Pept Res Ther 2023. [DOI: 10.1007/s10989-023-10492-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
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23
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Xie X, Valiente PA, Kim PM. HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures. Bioinformatics 2023; 39:6991169. [PMID: 36651657 PMCID: PMC9887083 DOI: 10.1093/bioinformatics/btad036] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/19/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION Protein and peptide engineering has become an essential field in biomedicine with therapeutics, diagnostics and synthetic biology applications. Helices are both abundant structural feature in proteins and comprise a major portion of bioactive peptides. Precise design of helices for binding or biological activity is still a challenging problem. RESULTS Here, we present HelixGAN, the first generative adversarial network method to generate de novo left-handed and right-handed alpha-helix structures from scratch at an atomic level. We developed a gradient-based search approach in latent space to optimize the generation of novel α-helical structures by matching the exact conformations of selected hotspot residues. The designed α-helical structures can bind specific targets or activate cellular receptors. There is a significant agreement between the helix structures generated with HelixGAN and PEP-FOLD, a well-known de novo approach for predicting peptide structures from amino acid sequences. HelixGAN outperformed RosettaDesign, and our previously developed structural similarity method to generate D-peptides matching a set of given hotspots in a known L-peptide. As proof of concept, we designed a novel D-GLP1_1 analog that matches the conformations of critical hotspots for the GLP1 function. MD simulations revealed a stable binding mode of the D-GLP1_1 analog coupled to the GLP1 receptor. This novel D-peptide analog is more stable than our previous D-GLP1 design along the MD simulations. We envision HelixGAN as a critical tool for designing novel bioactive peptides with specific properties in the early stages of drug discovery. AVAILABILITY AND IMPLEMENTATION https://github.com/xxiexuezhi/helix_gan. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xuezhi Xie
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada,Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Pedro A Valiente
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
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24
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Tripathi AK, Vishwanatha JK. Role of Anti-Cancer Peptides as Immunomodulatory Agents: Potential and Design Strategy. Pharmaceutics 2022; 14:pharmaceutics14122686. [PMID: 36559179 PMCID: PMC9781574 DOI: 10.3390/pharmaceutics14122686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 11/27/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022] Open
Abstract
The usage of peptide-based drugs to combat cancer is gaining significance in the pharmaceutical industry. The collateral damage caused to normal cells due to the use of chemotherapy, radiotherapy, etc. has given an impetus to the search for alternative methods of cancer treatment. For a long time, antimicrobial peptides (AMPs) have been shown to display anticancer activity. However, the immunomodulatory activity of anti-cancer peptides has not been researched very extensively. The interconnection of cancer and immune responses is well-known. Hence, a search and design of molecules that can show anti-cancer and immunomodulatory activity can be lead molecules in this field. A large number of anti-cancer peptides show good immunomodulatory activity by inhibiting the pro-inflammatory responses that assist cancer progression. Here, we thoroughly review both the naturally occurring and synthetic anti-cancer peptides that are reported to possess both anti-cancer and immunomodulatory activity. We also assess the structural and biophysical parameters that can be utilized to improve the activity. Both activities are mostly reported by different groups, however, we discuss them together to highlight their interconnection, which can be used in the future to design peptide drugs in the field of cancer therapeutics.
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25
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Lu S, Lin J, Jin J, Zhang L, Guan Y, Chen H, Wu Y, Zhang W, Luan X. Tachyplesin I and its derivatives: A pharmaco-chemical perspective on their antimicrobial and antitumor potential. Expert Opin Drug Discov 2022; 17:1407-1423. [PMID: 36503335 DOI: 10.1080/17460441.2023.2157402] [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: 12/14/2022]
Abstract
INTRODUCTION Increasing evidence suggests that intratumor microbiota are an intrinsic component in the tumor microenvironment across multiple cancer types, and that there is a close relationship between microbiota and tumor progression. Therefore, how to address the interaction between bacteria and malignances has become a growing concern. Tachyplesin I (TPI), a peptide with dual antimicrobial and antitumor effects, holds great promise as a therapeutic alternative for the aforementioned diseases, with the advantage of broad-spectrum activities, quick killing efficacy, and a low tendency to induce resistance. AREAS COVERED This review comprehensively summarizes the pharmacological mechanisms of TPI with an emphasis on its antimicrobial and antitumor potential. Furthermore, it presents advances in TPI derivatives and gives a perspective on their future development. The article is based on literature searches using PubMed and SciFinder to retrieve the most up-to-date information of TPI. EXPERT OPINION Bacterial infections and cancer both pose a serious threat to health due to their symbiotic interactions and drug resistance. TPI is anticipated to be a novel agent to control pathogenic bacteria and various tumors through multiple mechanisms of action. Indeed, the continuous advancements in chemical modification and innovative applications of TPI give hope for future improvements in therapeutic efficacy.
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Affiliation(s)
- Shengxin Lu
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
| | - Jiayi Lin
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
| | - Jinmei Jin
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
| | - Lijun Zhang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
| | - Yingyun Guan
- Department of Pharmacy, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Municipality, Shanghai, China
| | - Hongzhuan Chen
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
| | - Ye Wu
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
| | - Weidong Zhang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China.,School of Pharmacy, Naval Medical University, Municipality, Shanghai, China
| | - Xin Luan
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Municipality, Shanghai, China
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26
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Yu Z, Cary BP, Kim TW, Nguyen KD, Gardella TJ, Gellman SH. Kinetic and Thermodynamic Insights into Agonist Interactions with the Parathyroid Hormone Receptor-1 from a New NanoBRET Assay. ACS Chem Biol 2022; 17:3148-3158. [PMID: 36282520 PMCID: PMC9747329 DOI: 10.1021/acschembio.2c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Polypeptides that activate the parathyroid hormone receptor-1 (PTHR1) are important in human physiology and medicine. Most previous studies of peptide binding to this receptor have involved the displacement of a radiolabeled ligand. We report a new assay format based on bioluminescence resonance energy transfer (BRET). Fusion of a NanoLuc luciferase (nLuc) unit to the N-terminus of the PTHR1 allows the direct detection of binding by an agonist peptide bearing a tetramethylrhodamine (TMR) unit. Affinity measurements from the BRET assay align well with results previously obtained via radioligand displacement. The BRET assay offers substantial operational benefits relative to affinity measurements involving radioactive compounds. The convenience of the new assay allowed us to explore several questions raised by earlier reports. For example, we show that although the first two residues of PTH(1-34) (the drug teriparatide) are critical for PTHR1 activation, these two residues contribute little or nothing to affinity. Comparisons among the well-studied agonists PTH(1-34), PTHrP(1-34), and "long-acting PTH" (LA-PTH) reveal that the high affinity of LA-PTH arises largely from a diminished rate constant for dissociation relative to the other two. A D-peptide recently reported to be comparable to PTH(1-34) as an agonist of the PTHR1 was found not to bind detectably to the receptor and to be a very weak agonist.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Brian P. Cary
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Tae Wook Kim
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Kevin D. Nguyen
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Thomas J. Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114 USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
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27
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Abstract
While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Ordy Gnewou
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Armin Solemanifar
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- School of Chemical Engineering, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Vincent P Conticello
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, United States
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28
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Yu X, Zhang B, Fan C, Yan Q, Wang S, Hu H, Dong Q, Du G, Gao Y, Zeng C. Rapid, enantioselective and colorimetric detection of D-arginine. iScience 2022; 25:104964. [PMID: 36060051 PMCID: PMC9437853 DOI: 10.1016/j.isci.2022.104964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 12/02/2022] Open
Abstract
D-amino acids are of biological significance yet are not clearly understood due to the lack of powerful analytical tools for their identification. Thus, the specific detection of a single enantiomer of a particular amino acid remains a great challenge due to their structural similarity. Here, we report a strategy to incorporate multiple reaction sites on a chiral 1,1′-bi-2,2′-naphthol-based fluorescent probe. It can respond specifically to D-arginine, while producing no response when in contact with all other amino acids. The probe can report arginine’s concentration, and enantiomeric configuration and colorimetric studies enable its qualitative determination. A new strategy to form a fluorescent probe (S)-3 with multiple reaction sites Specific response to D-arginine among 39 chiral amino acids Metal-free detection, quick responses within a minute Qualitative determination of arginine through colorimetric studies
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29
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van Dijk A, Anten J, Bakker A, Evers N, Hoekstra AT, Chang JC, Scheenstra MR, Veldhuizen EJA, Netea MG, Berkers CR, Haagsman HP. Innate Immune Training of Human Macrophages by Cathelicidin Analogs. Front Immunol 2022; 13:777530. [PMID: 35958593 PMCID: PMC9360325 DOI: 10.3389/fimmu.2022.777530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/15/2022] [Indexed: 11/21/2022] Open
Abstract
Trained innate immunity can be induced in human macrophages by microbial ligands, but it is unknown if exposure to endogenous alarmins such as cathelicidins can have similar effects. Previously, we demonstrated sustained protection against infection by the chicken cathelicidin-2 analog DCATH-2. Thus, we assessed the capacity of cathelicidins to induce trained immunity. PMA-differentiated THP-1 (dTHP1) cells were trained with cathelicidin analogs for 24 hours and restimulated after a 3-day rest period. DCATH-2 training of dTHP-1 cells amplified their proinflammatory cytokine response when restimulated with TLR2/4 agonists. Trained cells displayed a biased cellular metabolism towards mTOR-dependent aerobic glycolysis and long-chain fatty acid accumulation and augmented microbicidal activity. DCATH-2-induced trained immunity was inhibited by histone acetylase inhibitors, suggesting epigenetic regulation, and depended on caveolae/lipid raft-mediated uptake, MAPK p38 and purinergic signaling. To our knowledge, this is the first report of trained immunity by host defense peptides.
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Affiliation(s)
- Albert van Dijk
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- *Correspondence: Albert van Dijk,
| | - Jennifer Anten
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anne Bakker
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Noah Evers
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Anna T. Hoekstra
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jung-Chin Chang
- Division Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Maaike R. Scheenstra
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Edwin J. A. Veldhuizen
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine, Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Celia R. Berkers
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Division Cell Biology, Metabolism & Cancer, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Henk P. Haagsman
- Division Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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30
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Jerath G, Darvin P, Christian Y, Trivedi V, Kumar TRS, Ramakrishnan V. Delivery of Small Molecules by Syndiotactic Peptides for Breast Cancer Therapy. Mol Pharm 2022; 19:2877-2887. [PMID: 35839086 DOI: 10.1021/acs.molpharmaceut.2c00238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The utilization of peptide-based drug delivery systems has been suboptimal due to their poor proteolytic susceptibility, poor cell permeability, and limited tumor homing capabilities. Earlier attempts in using d-enantiomers in peptide sequences increased proteolytic stability but have compromised the overall penetration capability. We designed a series of peptides (STRAPs) with a syndiotactic polypeptide backbone that can potentially form a spatial array of cationic groups, an important feature that facilitates cellular uptake. The peptides penetrate cell membranes through a combination of active and passive modes. Furthermore, the cellular uptake of the peptides was unaffected by the presence of or treatment with bovine serum and human plasma. The designed peptides successfully delivered methotrexate, an anticancer drug, to the in vitro and in vivo models of breast cancer, with the best performing peptide STRAP-4-MTX conjugate having an EC50 value of 1.34 μM. Peptide drug delivery in mouse xenograft models showed a greater reduction of primary tumor and metastasis of breast cancer, in comparison to methotrexate of the same dose. The in vivo biodistribution assay of the STRAP-4 peptide suggests that the peptide accumulates at the tumor site after 2 h of treatment, and in the absence of tumors, the peptide gets metabolized and excreted from the system.
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Affiliation(s)
- Gaurav Jerath
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pramod Darvin
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Yvonne Christian
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Vishal Trivedi
- Malaria Research Group, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - T R Santhosh Kumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Vibin Ramakrishnan
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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31
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Zheng S, Ye Z, Ji Y, Li N, Zhang L. Development of the Antithrombotic Peptide LEKNSTY Targeting the Collagen Surface: II. Improvement of Plasma Stability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7114-7120. [PMID: 35623058 DOI: 10.1021/acs.langmuir.2c00587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The development of antithrombotic peptides targeting collagen was proven effective, and an effective antithrombotic peptide LEKNSTY was obtained in part I. However, the plasma stability of LEKNSTY was found to be not good enough. In this part, the LEKNSTY was further optimized for improvement in plasma stability by substitution using d-amino acid residues. Two novel antithrombotic peptides LekNStY and lEKnsTy were designed, where lowercase letters represent d-amino acid residues. Improvements in plasma stability of both LekNStY and lEKnsTy were experimentally confirmed. Moreover, good binding of these antithrombotic peptides on the collagen surface was confirmed by molecular dynamics simulation and experimental validation. For example, a Kd of only 0.75 ± 0.10 μM was observed for lEKnsTy. Moreover, LekNStY and lEKnsTy were found to inhibit platelet adhesion on the collagen surface more effectively than LEKNSTY, and the IC50 of lEKnsTy was only 2/5 of that of LEKNSTY. These results confirmed the successful design of LekNStY and lEKnsTy that had good plasma stability and could effectively inhibit arterial thrombosis, which would be helpful for the research into interfaces involved in thrombus formation and the development of antithrombotic nanomedicine.
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Affiliation(s)
- Si Zheng
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Zhao Ye
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Yufan Ji
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Nanxing Li
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
| | - Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, People's Republic of China
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32
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Hu K, Wu W, Xie L, Geng H, Zhang Y, Hanyu M, Zhang L, Liu Y, Nagatsu K, Suzuki H, Guo J, Wu Y, Li Z, Wang F, Zhang M. Whole-body PET tracking of a d-dodecapeptide and its radiotheranostic potential for PD-L1 overexpressing tumors. Acta Pharm Sin B 2022; 12:1363-1376. [PMID: 35530129 PMCID: PMC9069398 DOI: 10.1016/j.apsb.2021.09.016] [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: 07/13/2021] [Revised: 09/02/2021] [Accepted: 09/14/2021] [Indexed: 02/06/2023] Open
Abstract
Peptides that are composed of dextrorotary (d)-amino acids have gained increasing attention as a potential therapeutic class. However, our understanding of the in vivo fate of d-peptides is limited. This highlights the need for whole-body, quantitative tracking of d-peptides to better understand how they interact with the living body. Here, we used mouse models to track the movement of a programmed death-ligand 1 (PD-L1)-targeting d-dodecapeptide antagonist (DPA) using positron emission tomography (PET). More specifically, we profiled the metabolic routes of [64Cu]DPA and investigated the tumor engagement of [64Cu/68Ga]DPA in mouse models. Our results revealed that intact [64Cu/68Ga]DPA was primarily eliminated by the kidneys and had a notable accumulation in tumors. Moreover, a single dose of [64Cu]DPA effectively delayed tumor growth and improved the survival of mice. Collectively, these results not only deepen our knowledge of the in vivo fate of d-peptides, but also underscore the utility of d-peptides as radiopharmaceuticals.
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Affiliation(s)
- Kuan Hu
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Wenyu Wu
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Lin Xie
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Hao Geng
- State Key Laboratory of Chemical Oncogenomics, the School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
| | - Yiding Zhang
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Masayuki Hanyu
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Lulu Zhang
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Yinghuan Liu
- State Key Laboratory of Chemical Oncogenomics, the School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
| | - Kotaro Nagatsu
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Hisashi Suzuki
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Jialin Guo
- Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yundong Wu
- State Key Laboratory of Chemical Oncogenomics, the School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518038, China
- Corresponding authors. Tel./fax: +81 43 3823709 (Mingrong Zhang), +86 25 52271455 (Feng Wang), +86 755 26033616 (Zigang Li), +86 755 26611113 (Yundong Wu).
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, the School of Chemical Biology and Biotechnology, Peking University, Shenzhen Graduate School, Shenzhen 518055, China
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
- Corresponding authors. Tel./fax: +81 43 3823709 (Mingrong Zhang), +86 25 52271455 (Feng Wang), +86 755 26033616 (Zigang Li), +86 755 26611113 (Yundong Wu).
| | - Feng Wang
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
- Corresponding authors. Tel./fax: +81 43 3823709 (Mingrong Zhang), +86 25 52271455 (Feng Wang), +86 755 26033616 (Zigang Li), +86 755 26611113 (Yundong Wu).
| | - Mingrong Zhang
- Department of Advanced Nuclear Medicine Sciences, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
- Corresponding authors. Tel./fax: +81 43 3823709 (Mingrong Zhang), +86 25 52271455 (Feng Wang), +86 755 26033616 (Zigang Li), +86 755 26611113 (Yundong Wu).
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Cesaro A, Torres MDT, Gaglione R, Dell'Olmo E, Di Girolamo R, Bosso A, Pizzo E, Haagsman HP, Veldhuizen EJA, de la Fuente-Nunez C, Arciello A. Synthetic Antibiotic Derived from Sequences Encrypted in a Protein from Human Plasma. ACS NANO 2022; 16:1880-1895. [PMID: 35112568 DOI: 10.1021/acsnano.1c04496] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Encrypted peptides have been recently found in the human proteome and represent a potential class of antibiotics. Here we report three peptides derived from the human apolipoprotein B (residues 887-922) that exhibited potent antimicrobial activity against drug-resistant Klebsiella pneumoniae, Acinetobacter baumannii, and Staphylococci both in vitro and in an animal model. The peptides had excellent cytotoxicity profiles, targeted bacteria by depolarizing and permeabilizing their cytoplasmic membrane, inhibited biofilms, and displayed anti-inflammatory properties. Importantly, the peptides, when used in combination, potentiated the activity of conventional antibiotics against bacteria and did not select for bacterial resistance. To ensure translatability of these molecules, a protease resistant retro-inverso variant of the lead encrypted peptide was synthesized and demonstrated anti-infective activity in a preclinical mouse model. Our results provide a link between human plasma and innate immunity and point to the blood as a source of much-needed antimicrobials.
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Affiliation(s)
- Angela Cesaro
- Department of Chemical Sciences, University of Naples Federico II, Naples I-80126, Italy
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, Naples I-80126, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome 00136, Italy
| | - Eliana Dell'Olmo
- Department of Chemical Sciences, University of Naples Federico II, Naples I-80126, Italy
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Naples Federico II, Naples I-80126, Italy
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II, Naples I-80126, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, Naples I-80126, Italy
| | - Henk P Haagsman
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Section Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
| | - Edwin J A Veldhuizen
- Department of Biomolecular Health Sciences, Division of Infectious Diseases and Immunology, Section Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CL, The Netherlands
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, Naples I-80126, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome 00136, Italy
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Lawler JT, Harrilal CP, DeBlase AF, Sibert EL, McLuckey SA, Zwier TS. Single-conformation spectroscopy of cold, protonated DPG-containing peptides: switching β-turn types and formation of a sequential type II/II' double β-turn. Phys Chem Chem Phys 2022; 24:2095-2109. [PMID: 35019911 DOI: 10.1039/d1cp04852j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
D-Proline (DPro, DP) is widely utilized to form β-hairpin loops in engineered peptides that would otherwise be unstructured, most often as part of a DPG sub-unit that forms a β-turn. To observe whether DPG facilitated this effect in short protonated peptides, conformation specific IR-UV double resonance photofragment spectra of the cold (∼10 K) protonated DP and LP diastereomers of the pentapeptide YAPGA was carried out in the hydride stretch (2800-3700 cm-1) and amide I/II (1400-1800 cm-1) regions. A model localized Hamiltonian was developed to better describe the 1600-1800 cm-1 region commonly associated with the amide I vibrations. The CO stretch fundamentals experience extensive mixing with the N-H bending fundamentals of the NH3+ group in these protonated peptides. The model Hamiltonian accounts for experiment in quantitative detail. In the DP diastereomer, all the population is funneled into a single conformer which presented as a type II β-turn with A and DP in the i + 1 and i + 2 positions, respectively. This structure was not the anticipated type II' β-turn across DPG that we had hypothesized based on solution-phase propensities. Analysis of the conformational energy landscape shows that both steric and charge-induced effects play a role in the preferred formation of the type II β-turn. In contrast, the LP isomer forms three conformations with very different structures, none of which were type II/II' β-turns, confirming that LPG is not a β-turn former. Finally, single-conformation spectroscopy was also carried out on the extended peptide [YAADPGAAA + H]+ to determine whether moving the protonated N-terminus further from DPG would lead to β-hairpin formation. Despite funneling its entire population into a single peptide backbone structure, the assigned structure is not a β-hairpin, but a concatenated type II/type II' double β-turn that displaces the peptide backbone laterally by about 7.5 Å, but leaves the backbone oriented in its original direction.
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Affiliation(s)
- John T Lawler
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | | | - Andrew F DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Edwin L Sibert
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA. .,Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, CA 94550, USA
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35
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Hernández González JE, Eberle RJ, Willbold D, Coronado MA. A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease. Front Mol Biosci 2022; 8:816166. [PMID: 35187076 PMCID: PMC8852625 DOI: 10.3389/fmolb.2021.816166] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/30/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 main protease, also known as 3-chymotrypsin-like protease (3CLpro), is a cysteine protease responsible for the cleavage of viral polyproteins pp1a and pp1ab, at least, at eleven conserved sites, which leads to the formation of mature nonstructural proteins essential for the replication of the virus. Due to its essential role, numerous studies have been conducted so far, which have confirmed 3CLpro as an attractive drug target to combat Covid-19 and have reported a vast number of inhibitors and their co-crystal structures. Despite all the ongoing efforts, D-peptides, which possess key advantages over L-peptides as therapeutic agents, have not been explored as potential drug candidates against 3CLpro. The current work fills this gap by reporting an in silico approach for the discovery of D-peptides capable of inhibiting 3CLpro that involves structure-based virtual screening (SBVS) of an in-house library of D-tripeptides and D-tetrapeptides into the protease active site and subsequent rescoring steps, including Molecular Mechanics Generalized-Born Surface Area (MM-GBSA) free energy calculations and molecular dynamics (MD) simulations. In vitro enzymatic assays conducted for the four top-scoring D-tetrapeptides at 20 μM showed that all of them caused 55–85% inhibition of 3CLpro activity, thus highlighting the suitability of the devised approach. Overall, our results present a promising computational strategy to identify D-peptides capable of inhibiting 3CLpro, with broader application in problems involving protein inhibition.
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Affiliation(s)
- Jorge E. Hernández González
- Multiuser Center for Biomolecular Innovation, IBILCE, Universidade Estadual Paulista (UNESP), São Jose do Rio Preto, Brazil
- Laboratory for Molecular Modeling and Dynamics, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitária Ilha do Fundão, Rio de Janeiro, Brazil
| | - Raphael J. Eberle
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
| | - Dieter Willbold
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Düsseldorf, Germany
- JuStruct: Jülich Centre for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Mônika A. Coronado
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- *Correspondence: Mônika A. Coronado,
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36
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Engel H, Guischard F, Krause F, Nandy J, Kaas P, Höfflin N, Köhn M, Kilb N, Voigt K, Wolf S, Aslan T, Baezner F, Hahne S, Ruckes C, Weygant J, Zinina A, Akmeriç EB, Antwi EB, Dombrovskij D, Franke P, Lesch KL, Vesper N, Weis D, Gensch N, Di Ventura B, Öztürk MA. finDr: A web server for in silico D-peptide ligand identification. Synth Syst Biotechnol 2021; 6:402-413. [PMID: 34901479 PMCID: PMC8632724 DOI: 10.1016/j.synbio.2021.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/20/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
In the rapidly expanding field of peptide therapeutics, the short in vivo half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display. This technique is extremely powerful, but it requires the synthesis of the target in D-form, which is challenging for large proteins. Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. In a separate, heuristic approach to search the chemical space of 12-mer peptides, finDr executes a customizable evolutionary algorithm (EA) for the de novo identification or optimization of D-peptide ligands. As a proof of principle, we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3 (PSMα3), a toxin of methicillin-resistant Staphylococcus aureus (MRSA). We validate the predictions using in vitro binding assays, supporting the success of this approach. Compared to conventional methods, finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation. We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.
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Key Words
- D-AA, dextrorotatory amino acid
- D-peptide
- EA, evolutionary algorithm
- Evolutionary algorithm
- L-AA, levorotatory amino acid
- MD, molecular dynamics
- MIEA, mirror-image evolutionary algorithm
- MIPD, mirror-image phage display
- MIVS, mirror-image virtual screening
- MRSA, methicillin-resistant Staphylococcus aureus
- Mirror-image phage display
- Molecular docking
- NCL, native chemical ligation
- PD-1, receptor programmed death 1
- PPI, protein-protein interaction
- PSMα3, phenol soluble modulin alpha 3
- Peptide design
- SPPS, solid phase peptide synthesis
- Web server
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Affiliation(s)
- Helena Engel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Felix Guischard
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Krause
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Janina Nandy
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Paulina Kaas
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nico Höfflin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Normann Kilb
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- AG Roth-Lab for MicroarrayCopying, ZBSA–Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Karsten Voigt
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3a, 79104, Freiburg, Germany
| | - Tahira Aslan
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Baezner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Salomé Hahne
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Carolin Ruckes
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Joshua Weygant
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Alisa Zinina
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Emir Bora Akmeriç
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Enoch B. Antwi
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Dennis Dombrovskij
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Philipp Franke
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Klara L. Lesch
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
- Internal Medicine IV, Department of Medicine, Medical Center, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - Niklas Vesper
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Daniel Weis
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nicole Gensch
- Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Corresponding author. Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Barbara Di Ventura
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Mehmet Ali Öztürk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
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Fumagalli G, Carbajo RJ, Nissink JWM, Tart J, Dou R, Thomas AP, Spring DR. Targeting a Novel KRAS Binding Site: Application of One-Component Stapling of Small (5-6-mer) Peptides. J Med Chem 2021; 64:17287-17303. [PMID: 34787423 DOI: 10.1021/acs.jmedchem.1c01334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RAS proteins are central in the proliferation of many types of cancer, but a general approach toward the identification of pan-mutant RAS inhibitors has remained unresolved. In this work, we describe the application of a binding pharmacophore identified from analysis of known RAS binding peptides to the design of novel peptides. Using a chemically divergent approach, we generated a library of small stapled peptides from which we identified compounds with weak binding activity. Exploration of structure-activity relationships (SARs) and optimization of these early compounds led to low-micromolar binders of KRAS that block nucleotide exchange.
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Affiliation(s)
- Gabriele Fumagalli
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K.,Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Jonathan Tart
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Rongxuan Dou
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Andrew P Thomas
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - David R Spring
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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38
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Hendrikse SIS, Contreras-Montoya R, Ellis AV, Thordarson P, Steed JW. Biofunctionality with a twist: the importance of molecular organisation, handedness and configuration in synthetic biomaterial design. Chem Soc Rev 2021; 51:28-42. [PMID: 34846055 DOI: 10.1039/d1cs00896j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The building blocks of life - nucleotides, amino acids and saccharides - give rise to a large variety of components and make up the hierarchical structures found in Nature. Driven by chirality and non-covalent interactions, helical and highly organised structures are formed and the way in which they fold correlates with specific recognition and hence function. A great amount of effort is being put into mimicking these highly specialised biosystems as biomaterials for biomedical applications, ranging from drug discovery to regenerative medicine. However, as well as lacking the complexity found in Nature, their bio-activity is sometimes low and hierarchical ordering is missing or underdeveloped. Moreover, small differences in folding in natural biomolecules (e.g., caused by mutations) can have a catastrophic effect on the function they perform. In order to develop biomaterials that are more efficient in interacting with biomolecules, such as proteins, DNA and cells, we speculate that incorporating order and handedness into biomaterial design is necessary. In this review, we first focus on order and handedness found in Nature in peptides, nucleotides and saccharides, followed by selected examples of synthetic biomimetic systems based on these components that aim to capture some aspects of these ordered features. Computational simulations are very helpful in predicting atomic orientation and molecular organisation, and can provide invaluable information on how to further improve on biomaterial designs. In the last part of the review, a critical perspective is provided along with considerations that can be implemented in next-generation biomaterial designs.
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Affiliation(s)
- Simone I S Hendrikse
- Department of Chemical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia. .,School of Chemistry, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
| | | | - Amanda V Ellis
- Department of Chemical Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia.
| | - Pall Thordarson
- School of Chemistry, University of New South Wales (UNSW), Sydney, NSW 2052, Australia
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39
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Valiente PA, Wen H, Nim S, Lee J, Kim HJ, Kim J, Perez-Riba A, Paudel YP, Hwang I, Kim KD, Kim S, Kim PM. Computational Design of Potent D-Peptide Inhibitors of SARS-CoV-2. J Med Chem 2021; 64:14955-14967. [PMID: 34624194 PMCID: PMC8525337 DOI: 10.1021/acs.jmedchem.1c00655] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Blocking the association between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein receptor-binding domain (RBD) and the human angiotensin-converting enzyme 2 (ACE2) is an attractive therapeutic approach to prevent the virus from entering human cells. While antibodies and other modalities have been developed to this end, d-amino acid peptides offer unique advantages, including serum stability, low immunogenicity, and low cost of production. Here, we designed potent novel D-peptide inhibitors that mimic the ACE2 α1-binding helix by searching a mirror-image version of the PDB. The two best designs bound the RBD with affinities of 29 and 31 nM and blocked the infection of Vero cells by SARS-CoV-2 with IC50 values of 5.76 and 6.56 μM, respectively. Notably, both D-peptides neutralized with a similar potency the infection of two variants of concern: B.1.1.7 and B.1.351 in vitro. These potent D-peptide inhibitors are promising lead candidates for developing SARS-CoV-2 prophylactic or therapeutic treatments.
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Affiliation(s)
- Pedro A. Valiente
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Han Wen
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Satra Nim
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - JinAh Lee
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Hyeon Ju Kim
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Jinhee Kim
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Albert Perez-Riba
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Yagya Prasad Paudel
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
| | - Insu Hwang
- Center for Convergent Research of Emerging Virus
Infection, Korea Research Institute of Chemical Technology,
Daejeon 34114, Republic of Korea
| | - Kyun-Do Kim
- Center for Convergent Research of Emerging Virus
Infection, Korea Research Institute of Chemical Technology,
Daejeon 34114, Republic of Korea
| | - Seungtaek Kim
- Zoonotic Virus Laboratory, Institut
Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil Bundang-gu, Seongnam-si,
Gyeonggi-do 13488, Republic of Korea
| | - Philip M. Kim
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, Toronto, Ontario M5S 3E1,
Canada
- Department of Molecular Genetics,
University of Toronto, Toronto, Ontario M5S 3E1,
Canada
- Department of Computer Science,
University of Toronto, Toronto, Ontario M5S 3E1,
Canada
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40
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Recent Applications of Retro-Inverso Peptides. Int J Mol Sci 2021; 22:ijms22168677. [PMID: 34445382 PMCID: PMC8395423 DOI: 10.3390/ijms22168677] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 12/14/2022] Open
Abstract
Natural and de novo designed peptides are gaining an ever-growing interest as drugs against several diseases. Their use is however limited by the intrinsic low bioavailability and poor stability. To overcome these issues retro-inverso analogues have been investigated for decades as more stable surrogates of peptides composed of natural amino acids. Retro-inverso peptides possess reversed sequences and chirality compared to the parent molecules maintaining at the same time an identical array of side chains and in some cases similar structure. The inverted chirality renders them less prone to degradation by endogenous proteases conferring enhanced half-lives and an increased potential as new drugs. However, given their general incapability to adopt the 3D structure of the parent peptides their application should be careful evaluated and investigated case by case. Here, we review the application of retro-inverso peptides in anticancer therapies, in immunology, in neurodegenerative diseases, and as antimicrobials, analyzing pros and cons of this interesting subclass of molecules.
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41
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Cui Z, Luo Q, Bannon MS, Gray VP, Bloom TG, Clore MF, Hughes MA, Crawford MA, Letteri RA. Molecular engineering of antimicrobial peptide (AMP)-polymer conjugates. Biomater Sci 2021; 9:5069-5091. [PMID: 34096936 PMCID: PMC8493962 DOI: 10.1039/d1bm00423a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
As antimicrobial resistance becomes an increasing threat, bringing significant economic and health burdens, innovative antimicrobial treatments are urgently needed. While antimicrobial peptides (AMPs) are promising therapeutics, exhibiting high activity against resistant bacterial strains, limited stability and toxicity to mammalian cells has hindered clinical development. Attaching AMPs to polymers provides opportunities to present AMPs in a way that maximizes bacterial killing while enhancing compatibility with mammalian cells, stability, and solubility. Conjugation of an AMP to a linear hydrophilic polymer yields the desired improvements in stability, mammalian cell compatibility, and solubility, yet often markedly reduces bactericidal effects. Non-linear polymer architectures and supramolecular assemblies that accommodate multiple AMPs per polymer chain afford AMP-polymer conjugates that strike a superior balance of antimicrobial activity, mammalian cell compatibility, stability, and solubility. Therefore, we review the design criteria, building blocks, and synthetic strategies for engineering AMP-polymer conjugates, emphasizing the connection between molecular architecture and antimicrobial performance to inspire and enable further innovation to advance this emerging class of biomaterials.
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Affiliation(s)
- Zixian Cui
- Department of Chemical Engineering, University of Virginia, Charlottesville, VA, 22903, USA.
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42
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Schmitthenner HF, Barrett TM, Beach SA, Heese LE, Weidman C, Dobson DE, Mahoney ER, Schug NC, Jones KG, Durmaz C, Otasowie O, Aronow S, Lee YP, Ophardt HD, Becker AE, Hornak JP, Evans IM, Ferran MC. Modular Synthesis of Peptide-Based Single- and Multimodal Targeted Molecular Imaging Agents. ACS APPLIED BIO MATERIALS 2021; 4:5435-5448. [PMID: 35006725 DOI: 10.1021/acsabm.1c00157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A practical, modular synthesis of targeted molecular imaging agents (TMIAs) containing near-infrared dyes for optical molecular imaging (OMI) or chelated metals for magnetic resonance imaging (MRI) and single-photon emission correlation tomography (SPECT) or positron emission tomography (PET) has been developed. In the method, imaging modules are formed early in the synthesis by attaching imaging agents to the side chain of protected lysines. These modules may be assembled to provide a given set of single- or dual-modal imaging agents, which may be conjugated in the last steps of the synthesis under mild conditions to linkers and targeting groups. A key discovery was the ability of a metal such as gadolinium, useful in MRI, to serve as a protecting group for the chelator, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). It was further discovered that two lanthanide metals, La and Ce, can double as protecting groups and placeholder metals, which may be transmetalated under mild conditions by metals used for PET in the final step. The modular method enabled the synthesis of discrete targeted probes with two of the same or different dyes, two same or different metals, or mixtures of dyes and metals. The approach was exemplified by the synthesis of single- or dual-modal imaging modules for MRI-OMI, PET-OMI, and PET-MRI, followed by conjugation to the integrin-seeking peptide, c(RGDyK). For Gd modules, their efficacy for MRI was verified by measuring the NMR spin-lattice relaxivity. To validate functional imaging of TMIAs, dual-modal agents containing Cy5.5 were shown to target A549 cancer cells by confocal fluorescence microscopy.
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Affiliation(s)
- Hans F Schmitthenner
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Taylor M Barrett
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Stephanie A Beach
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Lauren E Heese
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Chelsea Weidman
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Damien E Dobson
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Emily R Mahoney
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Nicholas C Schug
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Kelsea G Jones
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Ceyda Durmaz
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Osarhuwense Otasowie
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Sean Aronow
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Yin Peng Lee
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Henry D Ophardt
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Amy E Becker
- Chester Carlson Center for Imaging Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Joseph P Hornak
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States.,Chester Carlson Center for Imaging Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Irene M Evans
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Maureen C Ferran
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
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43
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Parisi G, Palopoli N, Tosatto SC, Fornasari MS, Tompa P. "Protein" no longer means what it used to. Curr Res Struct Biol 2021; 3:146-152. [PMID: 34308370 PMCID: PMC8283027 DOI: 10.1016/j.crstbi.2021.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/02/2023] Open
Abstract
Every biologist knows that the word protein describes a group of macromolecules essential to sustain life on Earth. As biologists, we are invariably trained under a protein paradigm established since the early twentieth century. However, in recent years, the term protein unveiled itself as an euphemism to describe the overwhelming heterogeneity of these compounds. Most of our current studies are targeted on carefully selected subsets of proteins, but we tend to think and write about these as representative of the whole population. Here we discuss how seeking for universal definitions and general rules in any arbitrarily segmented study would be misleading about the conclusions. Of course, it is not our purpose to discourage the use of the word protein. Instead, we suggest to embrace the extended universe of proteins to reach a deeper understanding of their full potential, realizing that the term encompasses a group of molecules very heterogeneous in terms of size, shape, chemistry and functions, i.e. the term protein no longer means what it used to.
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Affiliation(s)
- Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Nicolas Palopoli
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | | | - María Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Peter Tompa
- VIB-VUB Center for Structural Biology (CSB), Brussels, Belgium
- Structural Biology Brussels (SBB), Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
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44
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Sokullu E, Gauthier MS, Coulombe B. Discovery of Antivirals Using Phage Display. Viruses 2021; 13:v13061120. [PMID: 34200959 PMCID: PMC8230593 DOI: 10.3390/v13061120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
The latest coronavirus disease outbreak, COVID-19, has brought attention to viral infections which have posed serious health threats to humankind throughout history. The rapid global spread of COVID-19 is attributed to the increased human mobility of today's world, yet the threat of viral infections to global public health is expected to increase continuously in part due to increasing human-animal interface. Development of antiviral agents is crucial to combat both existing and novel viral infections. Recently, there is a growing interest in peptide/protein-based drug molecules. Antibodies are becoming especially predominant in the drug market. Indeed, in a remarkably short period, four antibody therapeutics were authorized for emergency use in COVID-19 treatment in the US, Russia, and India as of November 2020. Phage display has been one of the most widely used screening methods for peptide/antibody drug discovery. Several phage display-derived biologics are already in the market, and the expiration of intellectual property rights of phage-display antibody discovery platforms suggests an increment in antibody drugs in the near future. This review summarizes the most common phage display libraries used in antiviral discovery, highlights the approaches employed to enhance the antiviral potency of selected peptides/antibody fragments, and finally provides a discussion about the present status of the developed antivirals in clinic.
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Affiliation(s)
- Esen Sokullu
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
| | - Marie-Soleil Gauthier
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada;
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Correspondence: (E.S.); (B.C.)
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45
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Kandeel M, Yamamoto M, Tani H, Kobayashi A, Gohda J, Kawaguchi Y, Park BK, Kwon HJ, Inoue JI, Alkattan A. Discovery of New Fusion Inhibitor Peptides against SARS-CoV-2 by Targeting the Spike S2 Subunit. Biomol Ther (Seoul) 2021; 29:282-289. [PMID: 33424013 PMCID: PMC8094075 DOI: 10.4062/biomolther.2020.201] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 12/31/2022] Open
Abstract
A novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), caused a worldwide pandemic. Our aim in this study is to produce new fusion inhibitors against SARS-CoV-2, which can be the basis for developing new antiviral drugs. The fusion core comprising the heptad repeat domains (HR1 and HR2) of SARS-CoV-2 spike (S) were used to design the peptides. A total of twelve peptides were generated, comprising a short or truncated 24-mer (peptide #1), a long 36-mer peptide (peptide #2), and ten peptide #2 analogs. In contrast to SARS-CoV, SARS-CoV-2 S-mediated cell-cell fusion cannot be inhibited with a minimal length, 24-mer peptide. Peptide #2 demonstrated potent inhibition of SARS-CoV-2 S-mediated cell-cell fusion at 1 µM concentration. Three peptide #2 analogs showed IC50 values in the low micromolar range (4.7-9.8 µM). Peptide #2 inhibited the SARS-CoV-2 pseudovirus assay at IC50=1.49 µM. Given their potent inhibition of viral activity and safety and lack of cytotoxicity, these peptides provide an attractive avenue for the development of new prophylactic and therapeutic agents against SARS-CoV-2.
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Affiliation(s)
- Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia.,Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Mizuki Yamamoto
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama 939-0363, Japan
| | - Ayako Kobayashi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jin Gohda
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasushi Kawaguchi
- Research Center for Asian Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Division of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Byoung Kwon Park
- Department of Microbiology, Hallym University College of Medicine, Chuncheon 24252, Republic of Korea
| | - Hyung-Joo Kwon
- Department of Microbiology, Hallym University College of Medicine, Chuncheon 24252, Republic of Korea
| | - Jun-Ichiro Inoue
- Senior Professor Office, The University of Tokyo, Tokyo 108-8639, Japan
| | - Abdallah Alkattan
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
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46
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Patient-centric design for peptide delivery: Trends in routes of administration and advancement in drug delivery technologies. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2020.100079] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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47
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Torres MDT, Cao J, Franco OL, Lu TK, de la Fuente-Nunez C. Synthetic Biology and Computer-Based Frameworks for Antimicrobial Peptide Discovery. ACS NANO 2021; 15:2143-2164. [PMID: 33538585 PMCID: PMC8734659 DOI: 10.1021/acsnano.0c09509] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Antibiotic resistance is one of the greatest challenges of our time. This global health problem originated from a paucity of truly effective antibiotic classes and an increased incidence of multi-drug-resistant bacterial isolates in hospitals worldwide. Indeed, it has been recently estimated that 10 million people will die annually from drug-resistant infections by the year 2050. Therefore, the need to develop out-of-the-box strategies to combat antibiotic resistance is urgent. The biological world has provided natural templates, called antimicrobial peptides (AMPs), which exhibit multiple intrinsic medical properties including the targeting of bacteria. AMPs can be used as scaffolds and, via engineering, can be reconfigured for optimized potency and targetability toward drug-resistant pathogens. Here, we review the recent development of tools for the discovery, design, and production of AMPs and propose that the future of peptide drug discovery will involve the convergence of computational and synthetic biology principles.
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Affiliation(s)
- Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jicong Cao
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília, Brasília, DF 70790160, Brazil
- S-inova Biotech, Universidade Católica Dom Bosco, Campo Grande, MS 79117010, Brazil
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Department of Biological Engineering and Electrical Engineering and Computer Science, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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48
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Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
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Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
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Lalani S, Gew LT, Poh CL. Antiviral peptides against Enterovirus A71 causing hand, foot and mouth disease. Peptides 2021; 136:170443. [PMID: 33171280 PMCID: PMC7648656 DOI: 10.1016/j.peptides.2020.170443] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022]
Abstract
The emergence of new and resistant viruses is a serious global burden. Conventional antiviral therapy with small molecules has led to the development of resistant mutants. In the case of hand, foot and mouth disease (HFMD), the absence of a US-FDA approved vaccine calls for urgent need to develop an antiviral that could serve as a safe, potent and robust therapy against the neurovirulent Enterovirus A71 (EV-A71). Natural peptides such as lactoferrin, melittin and synthetic peptides such as SP40, RGDS and LVLQTM have been studied against EV-A71 and have shown promising results as potent antivirals in pre-clinical studies. Peptides are considered safe, efficacious and pose fewer chances of resistance. Poor pharmacokinetic features of peptides can be overcome by the use of chemical modifications to improve in vivo delivery particularly by oral route. The use of nanotechnology can remarkably assist in the oral delivery of peptides and enhance stability in vivo. This can greatly increase patient compliance and make it more attractive as antiviral therapy.
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Affiliation(s)
- Salima Lalani
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Subang Jaya, Selangor 47500, Malaysia; Department of Biological Sciences, Sunway University, Bandar Sunway, Malaysia Department, University, City, Country, Subang Jaya, Selangor 47500, Malaysia
| | - Lai Ti Gew
- Department of Biological Sciences, Sunway University, Bandar Sunway, Malaysia Department, University, City, Country, Subang Jaya, Selangor 47500, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, Sunway University, Bandar Sunway, Subang Jaya, Selangor 47500, Malaysia.
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50
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Wen Z, Zhan J, Li H, Xu G, Ma S, Zhang J, Li Z, Ou C, Yang Z, Cai Y, Chen M. Dual-ligand supramolecular nanofibers inspired by the renin-angiotensin system for the targeting and synergistic therapy of myocardial infarction. Theranostics 2021; 11:3725-3741. [PMID: 33664858 PMCID: PMC7914367 DOI: 10.7150/thno.53644] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Rationale: The compensatory activation of the renin-angiotensin system (RAS) after myocardial infarction (MI) plays a crucial role in the pathogenesis of heart failure. Most existing studies on this subject focus on mono- or dual-therapy of blocking the RAS, which exhibit limited efficacy and often causes serious adverse reactions. Few studies have been conducted on targeted therapy based on the activated RAS post-MI. Thus, the development of multiple-functional nanomedicine with concurrent targeting ability and synergistic therapeutic effect against RAS may show great promise in improving cardiac function post-MI. Methods: We utilized a cooperative self-assembly strategy constructing supramolecular nanofibers— telmisartan-doped co-assembly nanofibers (TDCNfs) to counter-regulate RAS through targeted delivery and combined therapy. TDCNfs were prepared through serial steps of solvent exchange, heating incubation, gelation, centrifugation, and lyophilization, in which the telmisartan was doped in the self-assembly process of Ang1-7 to obtain the co-assembly nanofibers wherein they act as both therapeutic agents and target-guide agents. Results: TDCNfs exhibited the desired binding affinity to the two different receptors, AT1R and MasR. Through the dual ligand-receptor interactions to mediate the coincident downstream pathways, TDCNfs not only displayed favorably targeted properties to hypoxic cardiomyocytes, but also exerted synergistic therapeutic effects in apoptosis reduction, inflammatory response alleviation, and fibrosis inhibition in vitro and in vivo, significantly protecting cardiac function and mitigating post-MI adverse outcomes. Conclusion: A dual-ligand nanoplatform was successfully developed to achieve targeted and synergistic therapy against cardiac deterioration post-MI. We envision that the integration of multiple therapeutic agents through supramolecular self-assembly would offer new insight for the systematic and targeted treatment of cardiovascular diseases.
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