1
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Sharma A, Yadav A, Nandy A, Ghatak S. Insight into the Functional Dynamics and Challenges of Exosomes in Pharmaceutical Innovation and Precision Medicine. Pharmaceutics 2024; 16:709. [PMID: 38931833 PMCID: PMC11206934 DOI: 10.3390/pharmaceutics16060709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Of all the numerous nanosized extracellular vesicles released by a cell, the endosomal-originated exosomes are increasingly recognized as potential therapeutics, owing to their inherent stability, low immunogenicity, and targeted delivery capabilities. This review critically evaluates the transformative potential of exosome-based modalities across pharmaceutical and precision medicine landscapes. Because of their precise targeted biomolecular cargo delivery, exosomes are posited as ideal candidates in drug delivery, enhancing regenerative medicine strategies, and advancing diagnostic technologies. Despite the significant market growth projections of exosome therapy, its utilization is encumbered by substantial scientific and regulatory challenges. These include the lack of universally accepted protocols for exosome isolation and the complexities associated with navigating the regulatory environment, particularly the guidelines set forth by the U.S. Food and Drug Administration (FDA). This review presents a comprehensive overview of current research trajectories aimed at addressing these impediments and discusses prospective advancements that could substantiate the clinical translation of exosomal therapies. By providing a comprehensive analysis of both the capabilities and hurdles inherent to exosome therapeutic applications, this article aims to inform and direct future research paradigms, thereby fostering the integration of exosomal systems into mainstream clinical practice.
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Affiliation(s)
| | | | | | - Subhadip Ghatak
- McGowan Institute for Regenerative Medicine, Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15219, USA; (A.S.); (A.Y.); (A.N.)
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2
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Asar M, Newton-Northup J, Soendergaard M. Improving Pharmacokinetics of Peptides Using Phage Display. Viruses 2024; 16:570. [PMID: 38675913 PMCID: PMC11055145 DOI: 10.3390/v16040570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Phage display is a versatile method often used in the discovery of peptides that targets disease-related biomarkers. A major advantage of this technology is the ease and cost efficiency of affinity selection, also known as biopanning, to identify novel peptides. While it is relatively straightforward to identify peptides with optimal binding affinity, the pharmacokinetics of the selected peptides often prove to be suboptimal. Therefore, careful consideration of the experimental conditions, including the choice of using in vitro, in situ, or in vivo affinity selections, is essential in generating peptides with high affinity and specificity that also demonstrate desirable pharmacokinetics. Specifically, in vivo biopanning, or the combination of in vitro, in situ, and in vivo affinity selections, has been proven to influence the biodistribution and clearance of peptides and peptide-conjugated nanoparticles. Additionally, the marked difference in properties between peptides and nanoparticles must be considered. While peptide biodistribution depends primarily on physiochemical properties and can be modified by amino acid modifications, the size and shape of nanoparticles also affect both absorption and distribution. Thus, optimization of the desired pharmacokinetic properties should be an important consideration in biopanning strategies to enable the selection of peptides and peptide-conjugated nanoparticles that effectively target biomarkers in vivo.
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Affiliation(s)
- Mallika Asar
- College of Osteopathic Medicine, Kansas City University, Kansas City, MO 64106, USA;
| | | | - Mette Soendergaard
- Cell Origins LLC, 1601 South Providence Road Columbia, Columbia, MO 65203, USA;
- Department of Chemistry, Western Illinois University, Macomb, IL 61455, USA
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3
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Kobayashi T, Yamazaki K, Shinada J, Mizunuma M, Furukawa K, Chuman Y. Identification of Inhibitors of the Disease-Associated Protein Phosphatase Scp1 Using Antibody Mimetic Molecules. Int J Mol Sci 2024; 25:3737. [PMID: 38612548 PMCID: PMC11011526 DOI: 10.3390/ijms25073737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
Protein phosphorylation is a prevalent translational modification, and its dysregulation has been implicated in various diseases, including cancer. Despite its significance, there is a lack of specific inhibitors of the FCP/SCP-type Ser/Thr protein phosphatase Scp1, characterized by high specificity and affinity. In this study, we focused on adnectin, an antibody-mimetic protein, aiming to identify Scp1-specific binding molecules with a broad binding surface that target the substrate-recognition site of Scp1. Biopanning of Scp1 was performed using an adnectin-presenting phage library with a randomized FG loop. We succeeded in identifying FG-1Adn, which showed high affinity and specificity for Scp1. Ala scanning analysis of the Scp1-binding sequence in relation to the FG-1 peptide revealed that hydrophobic residues, including aromatic amino acids, play important roles in Scp1 recognition. Furthermore, FG-1Adn was found to co-localize with Scp1 in cells, especially on the plasma membrane. In addition, Western blotting analysis showed that FG-1Adn increased the phosphorylation level of the target protein of Scp1 in cells, indicating that FG-1Adn can inhibit the function of Scp1. These results suggest that FG-1Adn can be used as a specific inhibitor of Scp1.
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Affiliation(s)
| | | | | | | | | | - Yoshiro Chuman
- Department of Chemistry, Faculty of Science, Niigata University, Niigata 950-2181, Japan; (T.K.); (K.Y.); (J.S.); (M.M.); (K.F.)
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4
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Miyamoto E, Sato T, Matsubara T. Cyclization of Peptides Enhances the Inhibitory Activity against Ganglioside-Induced Aβ Fibril Formation. ACS Chem Neurosci 2023; 14:4199-4207. [PMID: 37971427 DOI: 10.1021/acschemneuro.3c00589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
Alzheimer's disease is a progressive neurodegenerative disease and is the most common cause of dementia. It has been reported that the assembly of amyloid β-protein (Aβ) on the cell membrane is induced by the interaction of the Aβ monomer with gangliosides such as GM1. The ganglioside-bound Aβ (GAβ) complex acts as a seed to promote the toxic assembly of the Aβ fibrils. In a previous study, we found that a GM1 cluster-binding peptide (GCBP) specifically recognizes Aβ-sensitive ganglioside nanoclusters and inhibits the assembly of Aβ on a GM1-containing lipid membrane. In this study, cysteine-substituted double mutants of GCBP were designed and cyclized by intramolecular disulfide bond formation. Affinity assays indicated that one of the cyclic peptides had a higher affinity to a GM1-containing membrane compared to that of GCBP. Furthermore, surface topography analysis indicated that this peptide recognizes GM1 nanoclusters on the lipid membrane. An evaluation of the inhibitory kinetics indicated that the cyclic peptide could inhibit the formation of Aβ fibrils with an IC50 value of 1.2 fM, which is 10,000-fold higher than that of GCBP. The cyclic peptide was also shown to have a clearance effect on Aβ fibrils deposited on the lipid membrane and suppressed the formation of toxic Aβ assemblies. Our results indicate that the cyclic peptide that binds to the Aβ-sensitive ganglioside nanocluster is a potential novel inhibitor of ganglioside-induced Aβ assembly.
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Affiliation(s)
- Erika Miyamoto
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan
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5
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Wong JYK, Ekanayake AI, Kharchenko S, Kirberger SE, Qiu R, Kelich P, Sarkar S, Li J, Fernandez KX, Alvizo-Paez ER, Miao J, Kalhor-Monfared S, John JD, Kang H, Choi H, Nuss JM, Vederas JC, Lin YS, Macauley MS, Vukovic L, Pomerantz WCK, Derda R. Genetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo. Nat Commun 2023; 14:5654. [PMID: 37704629 PMCID: PMC10499988 DOI: 10.1038/s41467-023-41427-y] [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: 08/25/2022] [Accepted: 08/17/2023] [Indexed: 09/15/2023] Open
Abstract
Peptide-based therapeutics have gained attention as promising therapeutic modalities, however, their prevalent drawback is poor circulation half-life in vivo. In this paper, we report the selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine SNAr chemistry, with decafluoro-diphenylsulfone (DFS). Testing of the binding of the selected peptides to albumin identified SICRFFC as the lead sequence. We replaced DFS with isosteric pentafluorophenyl sulfide (PFS) and the PFS-SICRFFCGG exhibited KD = 4-6 µM towards human serum albumin. When injected in mice, the concentration of the PFS-SICRFFCGG in plasma was indistinguishable from the reference peptide, SA-21. More importantly, a conjugate of PFS-SICRFFCGG and peptide apelin-17 analogue (N3-PEG6-NMe17A2) showed retention in circulation similar to SA-21; in contrast, apelin-17 analogue was cleared from the circulation after 2 min. The PFS-SICRFFC is the smallest known peptide macrocycle with a significant affinity for human albumin and substantial in vivo circulation half-life. It is a productive starting point for future development of compact macrocycles with extended half-life in vivo.
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Affiliation(s)
- Jeffrey Y K Wong
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Arunika I Ekanayake
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Serhii Kharchenko
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Steven E Kirberger
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ryan Qiu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Payam Kelich
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, 79968, USA
| | - Susmita Sarkar
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jiaqian Li
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | | | - Edgar R Alvizo-Paez
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Jiayuan Miao
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | | | - J Dwyer John
- Ferring Research Institute, San Diego, CA, 92121, USA
| | - Hongsuk Kang
- Quantum Intelligence Corp., 31F, One IFC, 10 Gukjegeumyung-ro, Yeongdeungpo-gu-Seoul, Republic of Korea
| | - Hwanho Choi
- Quantum Intelligence Corp., 31F, One IFC, 10 Gukjegeumyung-ro, Yeongdeungpo-gu-Seoul, Republic of Korea
| | - John M Nuss
- Ferring Research Institute, San Diego, CA, 92121, USA
| | - John C Vederas
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, 02155, USA
| | - Matthew S Macauley
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Lela Vukovic
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso, TX, 79968, USA
| | | | - Ratmir Derda
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada.
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6
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Zhang Q, Sioud M. Tumor-Associated Macrophage Subsets: Shaping Polarization and Targeting. Int J Mol Sci 2023; 24:7493. [PMID: 37108657 PMCID: PMC10138703 DOI: 10.3390/ijms24087493] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
The tumor microenvironment (TME) is a critical regulator of tumor growth, progression, and metastasis. Among the innate immune cells recruited to the tumor site, macrophages are the most abundant cell population and are present at all stages of tumor progression. They undergo M1/M2 polarization in response to signals derived from TME. M1 macrophages suppress tumor growth, while their M2 counterparts exert pro-tumoral effects by promoting tumor growth, angiogenesis, metastasis, and resistance to current therapies. Several subsets of the M2 phenotype have been observed, often denoted as M2a, M2b, M2c, and M2d. These are induced by different stimuli and differ in phenotypes as well as functions. In this review, we discuss the key features of each M2 subset, their implications in cancers, and highlight the strategies that are being developed to harness TAMs for cancer treatment.
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Affiliation(s)
- Qindong Zhang
- Division of Cancer Medicine, Department of Cancer Immunology, Oslo University Hospital, University of Oslo, Ullernchausseen 70, 0379 Oslo, Norway;
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Blindern, P.O. Box 1068, 0316 Oslo, Norway
| | - Mouldy Sioud
- Division of Cancer Medicine, Department of Cancer Immunology, Oslo University Hospital, University of Oslo, Ullernchausseen 70, 0379 Oslo, Norway;
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7
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Hourani T, Holden JA, Li W, Lenzo JC, Hadjigol S, O’Brien-Simpson NM. Tumor Associated Macrophages: Origin, Recruitment, Phenotypic Diversity, and Targeting. Front Oncol 2021; 11:788365. [PMID: 34988021 PMCID: PMC8722774 DOI: 10.3389/fonc.2021.788365] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/30/2021] [Indexed: 12/20/2022] Open
Abstract
The tumor microenvironment (TME) is known to have a strong influence on tumorigenesis, with various components being involved in tumor suppression and tumor growth. A protumorigenic TME is characterized by an increased infiltration of tumor associated macrophages (TAMs), where their presence is strongly associated with tumor progression, therapy resistance, and poor survival rates. This association between the increased TAMs and poor therapeutic outcomes are stemming an increasing interest in investigating TAMs as a potential therapeutic target in cancer treatment. Prominent mechanisms in targeting TAMs include: blocking recruitment, stimulating repolarization, and depletion methods. For enhancing targeting specificity multiple nanomaterials are currently being explored for the precise delivery of chemotherapeutic cargo, including the conjugation with TAM-targeting peptides. In this paper, we provide a focused literature review of macrophage biology in relation to their role in tumorigenesis. First, we discuss the origin, recruitment mechanisms, and phenotypic diversity of TAMs based on recent investigations in the literature. Then the paper provides a detailed review on the current methods of targeting TAMs, including the use of nanomaterials as novel cancer therapeutics.
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Affiliation(s)
| | | | | | | | | | - Neil M. O’Brien-Simpson
- Antimicrobial, Cancer Therapeutics and Vaccines (ACTV) Research Group, Melbourne Dental School, Centre for Oral Health Research, Royal Dental Hospital, The University of Melbourne, Melbourne, VIC, Australia
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8
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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9
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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: 55] [Impact Index Per Article: 18.3] [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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10
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Cardle II, Jensen MC, Pun SH, Sellers DL. Optimized serum stability and specificity of an αvβ6 integrin-binding peptide for tumor targeting. J Biol Chem 2021; 296:100657. [PMID: 33857478 PMCID: PMC8138772 DOI: 10.1016/j.jbc.2021.100657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/03/2022] Open
Abstract
The integrin αvβ6 is an antigen expressed at low levels in healthy tissue but upregulated during tumorigenesis, which makes it a promising target for cancer imaging and therapy. A20FMDV2 is a 20-mer peptide derived from the foot-and-mouth disease virus that exhibits nanomolar and selective affinity for αvβ6 versus other integrins. Despite this selectivity, A20FMDV2 has had limited success in imaging and treating αvβ6+ tumors in vivo because of its poor serum stability. Here, we explore the cyclization and modification of the A20FMDV2 peptide to improve its serum stability without sacrificing its affinity and specificity for αvβ6. Using cysteine amino acid substitutions and cyclization by perfluoroarylation with decafluorobiphenyl, we synthesized six cyclized A20FMDV2 variants and discovered that two retained binding to αvβ6 with modestly improved serum stability. Further d-amino acid substitutions and C-terminal sequence optimization outside the cyclized region greatly prolonged peptide serum stability without reducing binding affinity. While the cyclized A20FMDV2 variants exhibited increased nonspecific integrin binding compared with the original peptide, additional modifications with the non-natural amino acids citrulline, hydroxyproline, and d-alanine were found to restore binding specificity, with some modifications leading to greater αvβ6 integrin selectivity than the original A20FMDV2 peptide. The peptide modifications detailed herein greatly improve the potential of utilizing A20FMDV2 to target αvβ6 in vivo, expanding opportunities for cancer targeting and therapy.
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Affiliation(s)
- Ian I Cardle
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; Seattle Children's Therapeutics, Seattle, Washington, USA
| | - Michael C Jensen
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; Seattle Children's Therapeutics, Seattle, Washington, USA; Department of Pediatrics, University of Washington, Seattle, Washington, USA; Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Drew L Sellers
- Department of Bioengineering, University of Washington, Seattle, Washington, USA.
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11
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Sindhikara D, Wagner M, Gkeka P, Güssregen S, Tiwari G, Hessler G, Yapici E, Li Z, Evers A. Automated Design of Macrocycles for Therapeutic Applications: From Small Molecules to Peptides and Proteins. J Med Chem 2020; 63:12100-12115. [PMID: 33017535 DOI: 10.1021/acs.jmedchem.0c01500] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Macrocycles and cyclic peptides are increasingly attractive therapeutic modalities as they often have improved affinity, are able to bind to extended protein surfaces, and otherwise have favorable properties. Macrocyclization of a known binder may stabilize its bioactive conformation and improve its metabolic stability, cell permeability, and in certain cases oral bioavailability. Herein, we present implementation and application of an approach that automatically generates, evaluates, and proposes cyclizations utilizing a library of well-established chemical reactions and reagents. Using the three-dimensional (3D) conformation of the linear molecule in complex with a target protein as the starting point, this approach identifies attachment points, generates linkers, evaluates their geometric compatibility, and ranks the resulting molecules with respect to their predicted conformational stability and interactions with the target protein. As we show here with prospective and retrospective case studies, this procedure can be applied for the macrocyclization of small molecules and peptides and even PROteolysis TArgeting Chimeras (PROTACs) and proteins.
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Affiliation(s)
- Dan Sindhikara
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Michael Wagner
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Paraskevi Gkeka
- Integrated Drug Discovery, Sanofi R&D, 1 Avenue Pierre Brossolette, 91385 Chilly-Mazarin, France
| | - Stefan Güssregen
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Garima Tiwari
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Gerhard Hessler
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Engin Yapici
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ziyu Li
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
| | - Andreas Evers
- Integrated Drug Discovery, Sanofi-Aventis Deutschland GmbH, Industriepark Hoechst, 65926 Frankfurt am Main, Germany
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12
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Lee LCC, Tsang AWY, Liu HW, Lo KKW. Photofunctional Cyclometalated Iridium(III) Polypyridine Complexes Bearing a Perfluorobiphenyl Moiety for Bioconjugation, Bioimaging, and Phototherapeutic Applications. Inorg Chem 2020; 59:14796-14806. [DOI: 10.1021/acs.inorgchem.0c01343] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lawrence Cho-Cheung Lee
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| | - Ada Wun-Yu Tsang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| | - Hua-Wei Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
| | - Kenneth Kam-Wing Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
- State Key Laboratory of Terahertz and Millimeter Waves, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
- Center of Functional Photonics, City University of Hong Kong, Tat Chee Avenue, Hong Kong, P. R. China
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13
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Huang Y, Nawatha M, Livneh I, Rogers JM, Sun H, Singh SK, Ciechanover A, Brik A, Suga H. Affinity Maturation of Macrocyclic Peptide Modulators of Lys48‐Linked Diubiquitin by a Twofold Strategy. Chemistry 2020; 26:8022-8027. [DOI: 10.1002/chem.202000273] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Yichao Huang
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
| | - Mickal Nawatha
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Ido Livneh
- The Rappaport Faculty of Medicine and Research InstituteTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Joseph M. Rogers
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
| | - Hao Sun
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Sumeet K. Singh
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Aaron Ciechanover
- The Rappaport Faculty of Medicine and Research InstituteTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Ashraf Brik
- Schulich Faculty of ChemistryTechnion-Israel Institute of Technology Haifa 3200008 Israel
| | - Hiroaki Suga
- Department of ChemistrySchool of ScienceThe University of Tokyo 7-3-1 Hongo Bunkyo Tokyo 113-0033 Japan
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Sellers DL, Tan JKY, Pineda JMB, Peeler DJ, Porubsky VL, Olden BR, Salipante SJ, Pun SH. Targeting Ligands Deliver Model Drug Cargo into the Central Nervous System along Autonomic Neurons. ACS NANO 2019; 13:10961-10971. [PMID: 31589023 PMCID: PMC7651855 DOI: 10.1021/acsnano.9b01515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While biologic drugs such as proteins, peptides, or nucleic acids have shown promise in the treatment of neurodegenerative diseases, the blood-brain barrier (BBB) severely limits drug delivery to the central nervous system (CNS) after systemic administration. Consequently, drug delivery challenges preclude biological drug candidates from the clinical armamentarium. In order to target drug delivery and uptake into to the CNS, we used an in vivo phage display screen to identify peptides able to target drug-uptake by the vast array of neurons of the autonomic nervous system (ANS). Using next-generation sequencing, we identified 21 candidate targeted ANS-to-CNS uptake ligands (TACL) that enriched bacteriophage accumulation and delivered protein-cargo into the CNS after intraperitoneal (IP) administration. The series of TACL peptides were synthesized and tested for their ability to deliver a model enzyme (NeutrAvidin-horseradish peroxidase fusion) to the brain and spinal cord. Three TACL-peptides facilitated significant active enzyme delivery into the CNS, with limited accumulation in off-target organs. Peptide structure and serum stability is increased when internal cysteine residues are cyclized by perfluoroarylation with decafluorobiphenyl, which increased delivery to the CNS further. TACL-peptide was demonstrated to localize in parasympathetic ganglia neurons in addition to neuronal structures in the hindbrain and spinal cord. By targeting uptake into ANS neurons, we demonstrate the potential for TACL-peptides to bypass the blood-brain barrier and deliver a model drug into the brain and spinal cord.
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Affiliation(s)
- Drew L. Sellers
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, 98195, USA
| | - James-Kevin Y. Tan
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
| | - Julio Marco B. Pineda
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
| | - David J. Peeler
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
| | - Veronica L. Porubsky
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
| | - Brynn R. Olden
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Suzie H. Pun
- Department of Bioengineering, University of Washington, Seattle, Washington, 98195, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington, 98195, USA
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Zhang C, Vinogradova EV, Spokoyny AM, Buchwald SL, Pentelute BL. Arylation Chemistry for Bioconjugation. Angew Chem Int Ed Engl 2019; 58:4810-4839. [PMID: 30399206 PMCID: PMC6433541 DOI: 10.1002/anie.201806009] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Indexed: 12/20/2022]
Abstract
Bioconjugation chemistry has been used to prepare modified biomolecules with functions beyond what nature intended. Central to these techniques is the development of highly efficient and selective bioconjugation reactions that operate under mild, biomolecule compatible conditions. Methods that form a nucleophile-sp2 carbon bond show promise for creating bioconjugates with new modifications, sometimes resulting in molecules with unparalleled functions. Here we outline and review sulfur, nitrogen, selenium, oxygen, and carbon arylative bioconjugation strategies and their applications to modify peptides, proteins, sugars, and nucleic acids.
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Affiliation(s)
- Chi Zhang
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
| | - Ekaterina V. Vinogradova
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
- Dr. E. V. Vinogradova, The Skaggs Institute for Chemical Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexander M. Spokoyny
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
- Prof. Dr. A. M. Spokoyny, Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Stephen L. Buchwald
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
| | - Bradley L. Pentelute
- Dr. C. Zhang, Dr. E. V. Vinogradova, Prof. Dr. A. M. Spokoyny, Prof. Dr. S. L. Buchwald, Prof. Dr. B. L. Pentelute, Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA, ,
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Zhang C, Vinogradova EV, Spokoyny AM, Buchwald SL, Pentelute BL. Arylierungschemie für die Biokonjugation. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201806009] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Chi Zhang
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Ekaterina V. Vinogradova
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- The Skaggs Institute for Chemical Biology and Department of Molecular MedicineThe Scripps Research Institute La Jolla CA 92037 USA
| | - Alexander M. Spokoyny
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
- Department of Chemistry and BiochemistryUniversity of California, Los Angeles 607 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Stephen L. Buchwald
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of Technology 77 Massachusetts Avenue Cambridge MA 02139 USA
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Seek & Destroy, use of targeting peptides for cancer detection and drug delivery. Bioorg Med Chem 2017; 26:2797-2806. [PMID: 28893601 DOI: 10.1016/j.bmc.2017.08.052] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/14/2017] [Accepted: 08/30/2017] [Indexed: 12/21/2022]
Abstract
Accounting for 16 million new cases and 9 million deaths annually, cancer leaves a great number of patients helpless. It is a complex disease and still a major challenge for the scientific and medical communities. The efficacy of conventional chemotherapies is often poor and patients suffer from off-target effects. Each neoplasm exhibits molecular signatures - sometimes in a patient specific manner - that may completely differ from the organ of origin, may be expressed in markedly higher amounts and/or in different location compared to the normal tissue. Although adding layers of complexity in the understanding of cancer biology, this cancer-specific signature provides an opportunity to develop targeting agents for early detection, diagnosis, and therapeutics. Chimeric antibodies, recombinant proteins or synthetic polypeptides have emerged as excellent candidates for specific homing to peripheral and central nervous system cancers. Specifically, peptide ligands benefit from their small size, easy and affordable production, high specificity, and remarkable flexibility regarding their sequence and conjugation possibilities. Coupled to imaging agents, chemotherapies and/or nanocarriers they have shown to increase the on-site delivery, thus allowing better tumor mass contouring in imaging and increased efficacy of the chemotherapies associated with reduced adverse effects. Therefore, some of the peptides alone or in combination have been tested in clinical trials to treat patients. Peptides have been well-tolerated and shown absence of toxicity. This review aims to offer a view on tumor targeting peptides that are either derived from natural peptide ligands or identified using phage display screening. We also include examples of peptides targeting the high-grade malignant tumors of the central nervous system as an example of the complex therapeutic management due to the tumor's location. Peptide vaccines are outside of the scope of this review.
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Ngambenjawong C, Pun SH. Multivalent polymers displaying M2 macrophage-targeting peptides improve target binding avidity and serum stability. ACS Biomater Sci Eng 2017; 3:2050-2053. [PMID: 29430522 DOI: 10.1021/acsbiomaterials.7b00332] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Tumor-associated macrophages (TAMs) display a spectrum of phenotypes ranging from pro-tumoral/anti-inflammatory "M2-like" to anti-tumoral/pro-inflammatory "M1-like" subtypes and, consequently, high intratumoral M2-to-M1 ratios are typically indicative of poor disease prognosis. Cancer immunotherapies that selectively modulate M2-like TAMs, enabling reversal of the M2-to-M1 ratio, represent a promising anti-cancer intervention but are difficult to implement due to the lack of effective targeting systems. In this study, we report the development of high avidity, M2 macrophage-selective targeted drug delivery platforms based on M2 macrophage-targeting peptides (M2pep) grafted onto poly(N-(2-hydroxypropyl) methacrylamide). Furthermore, these M2pep-grafted polymers also exhibit improved serum stability along with M2 macrophage-selective toxicity.
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Affiliation(s)
- Chayanon Ngambenjawong
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, United States
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, United States
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Ngambenjawong C, Gustafson HH, Pun SH. Progress in tumor-associated macrophage (TAM)-targeted therapeutics. Adv Drug Deliv Rev 2017; 114:206-221. [PMID: 28449873 DOI: 10.1016/j.addr.2017.04.010] [Citation(s) in RCA: 502] [Impact Index Per Article: 71.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 02/06/2023]
Abstract
As an essential innate immune population for maintaining body homeostasis and warding off foreign pathogens, macrophages display high plasticity and perform diverse supportive functions specialized to different tissue compartments. Consequently, aberrance in macrophage functions contributes substantially to progression of several diseases including cancer, fibrosis, and diabetes. In the context of cancer, tumor-associated macrophages (TAMs) in tumor microenvironment (TME) typically promote cancer cell proliferation, immunosuppression, and angiogenesis in support of tumor growth and metastasis. Oftentimes, the abundance of TAMs in tumor is correlated with poor disease prognosis. Hence, significant attention has been drawn towards development of cancer immunotherapies targeting these TAMs; either depleting them from tumor, blocking their pro-tumoral functions, or restoring their immunostimulatory/tumoricidal properties. This review aims to introduce readers to various aspects in development and evaluation of TAM-targeted therapeutics in pre-clinical and clinical stages.
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Affiliation(s)
- Chayanon Ngambenjawong
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, United States
| | - Heather H Gustafson
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, United States
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98195, United States.
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