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Wu Y, Williams J, Calder EDD, Walport LJ. Strategies to expand peptide functionality through hybridisation with a small molecule component. RSC Chem Biol 2021; 2:151-165. [PMID: 34458778 PMCID: PMC8341444 DOI: 10.1039/d0cb00167h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
Combining different compound classes gives molecular hybrids that can offer access to novel chemical space and unique properties. Peptides provide ideal starting points for such molecular hybrids, which can be easily modified with a variety of molecular entities. The addition of small molecules can improve the potency, stability and cell permeability of therapeutically relevant peptides. Furthermore, they are often applied to create peptide-based tools in chemical biology. In this review, we discuss general methods that allow the discovery of this compound class and highlight key examples of peptide-small molecule hybrids categorised by the application and function of the small molecule entity.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Jack Williams
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Ewen D D Calder
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
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52
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Wang L, Yang J, Li S, Li Q, Liu S, Zheng W, Jiang X. Oral Administration of Starting Materials for In Vivo Synthesis of Antibacterial Gold Nanoparticles for Curing Remote Infections. NANO LETTERS 2021; 21:1124-1131. [PMID: 33459020 DOI: 10.1021/acs.nanolett.0c04578] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Oral administration is a facile and safe way for medication. However, most of the reported nanomedicines could not be taken orally, partially due to their unsatisfied stability, poor absorbance, or toxicity in the gastrointestinal tract. Here, we demonstrate that we could robustly synthesize gold nanoparticles (GNPs) in vivo by orally administering two starting materials, tetrachloroauric acid and aminophenyl boronic acid (ABA). The ABA-activated GNPs (A-GNPs) synthesized in vivo could be absorbed by the gastrointestinal tract and reach the remote infection lesions such as peritonitis caused by multidrug resistant (MDR) bacteria in mice. The A-GNPs exhibit excellent antibacterial efficacy (MIC, 3 μg/mL), long half-life (16-17 h), effective clearance (residual concentration is near 0 within 72 h), and high biosafety (safe dose/effective dose, 8 times). Our study is a pioneering attempt for synthesizing and taking nanomedicines orally just like preparing and drinking a cocktail.
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Affiliation(s)
- Le Wang
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Road, Nangang District, Harbin 150001, P.R. China
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088 Xueyuan Rd, Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Junchuan Yang
- The GBA National Institute for Nanotechnology Innovation, CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, No. 11 Zhongguancun Beiyitiao, Beijing, 100190, P.R. China
| | - Sixiang Li
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088 Xueyuan Rd, Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Qizhen Li
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088 Xueyuan Rd, Nanshan District, Shenzhen, Guangdong 518055, P.R. China
| | - Shaoqin Liu
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Road, Nangang District, Harbin 150001, P.R. China
| | - Wenfu Zheng
- The GBA National Institute for Nanotechnology Innovation, CAS Key Lab for Biological Effects of Nanomaterials and Nanosafety, National Center for NanoScience and Technology, No. 11 Zhongguancun Beiyitiao, Beijing, 100190, P.R. China
| | - Xingyu Jiang
- School of Life Science and Technology, Harbin Institute of Technology, 2 Yikuang Road, Nangang District, Harbin 150001, P.R. China
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088 Xueyuan Rd, Nanshan District, Shenzhen, Guangdong 518055, P.R. China
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Dotter H, Boll M, Eder M, Eder AC. Library and post-translational modifications of peptide-based display systems. Biotechnol Adv 2021; 47:107699. [PMID: 33513435 DOI: 10.1016/j.biotechadv.2021.107699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/04/2021] [Accepted: 01/14/2021] [Indexed: 12/27/2022]
Abstract
Innovative biotechnological methods empower the successful identification of new drug candidates. Phage, ribosome and mRNA display represent high throughput screenings, allowing fast and efficient progress in the field of targeted drug discovery. The identification range comprises low molecular weight peptides up to whole antibodies. However, a major challenge poses the stability and affinity in particular of peptides. Chemical modifications e.g. the introduction of unnatural amino acids or cyclization, have been proven to be essential tools to overcome these limitations. This review article particularly focuses on available methods for the targeted chemical modification of peptides and peptide libraries in selected display approaches.
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Affiliation(s)
- Hanna Dotter
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie Boll
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Ann-Christin Eder
- Department of Nuclear Medicine, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany; Division of Radiopharmaceutical Development, German Cancer Consortium, partner site Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany, and German Cancer Research Center, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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54
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Apostolopoulos V, Bojarska J, Chai TT, Elnagdy S, Kaczmarek K, Matsoukas J, New R, Parang K, Lopez OP, Parhiz H, Perera CO, Pickholz M, Remko M, Saviano M, Skwarczynski M, Tang Y, Wolf WM, Yoshiya T, Zabrocki J, Zielenkiewicz P, AlKhazindar M, Barriga V, Kelaidonis K, Sarasia EM, Toth I. A Global Review on Short Peptides: Frontiers and Perspectives. Molecules 2021; 26:E430. [PMID: 33467522 PMCID: PMC7830668 DOI: 10.3390/molecules26020430] [Citation(s) in RCA: 153] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.
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Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (V.A.); (J.M.); (V.B.)
| | - Joanna Bojarska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Tsun-Thai Chai
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia;
| | - Sherif Elnagdy
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamaa St., Giza 12613, Egypt; (S.E.); (M.A.)
| | - Krzysztof Kaczmarek
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (K.K.); (J.Z.)
| | - John Matsoukas
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (V.A.); (J.M.); (V.B.)
- NewDrug, Patras Science Park, 26500 Patras, Greece;
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Roger New
- Vaxcine (UK) Ltd., c/o London Bioscience Innovation Centre, London NW1 0NH, UK;
- Faculty of Science & Technology, Middlesex University, The Burroughs, London NW4 4BT, UK;
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA;
| | - Octavio Paredes Lopez
- Centro de Investigación y de Estudios Avanzados del IPN, Departamento de Biotecnología y Bioquímica, Irapuato 36824, Guanajuato, Mexico;
| | - Hamideh Parhiz
- Infectious Disease Division, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6073, USA;
| | - Conrad O. Perera
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Monica Pickholz
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina;
- Instituto de Física de Buenos Aires (IFIBA, UBA-CONICET), Argentina, Buenos Aires 1428, Argentina
| | - Milan Remko
- Remedika, Luzna 9, 85104 Bratislava, Slovakia;
| | - Michele Saviano
- Institute of Crystallography (CNR), Via Amendola 122/o, 70126 Bari, Italy;
| | - Mariusz Skwarczynski
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (M.S.); (I.T.)
| | - Yefeng Tang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (MOE), School of Pharma Ceutical Sciences, Tsinghua University, Beijing 100084, China;
| | - Wojciech M. Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | | | - Janusz Zabrocki
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (K.K.); (J.Z.)
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
- Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Maha AlKhazindar
- Botany and Microbiology Department, Faculty of Science, Cairo University, Gamaa St., Giza 12613, Egypt; (S.E.); (M.A.)
| | - Vanessa Barriga
- Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia; (V.A.); (J.M.); (V.B.)
| | | | | | - Istvan Toth
- School of Chemistry & Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (M.S.); (I.T.)
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
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Abstract
Supramolecular biopolymers (SBPs) are those polymeric units derived from macromolecules that can assemble with each other by noncovalent interactions. Macromolecular structures are commonly found in living systems such as proteins, DNA/RNA, and polysaccharides. Bioorganic chemistry allows the generation of sequence-specific supramolecular units like SBPs that can be tailored for novel applications in tissue engineering (TE). SBPs hold advantages over other conventional polymers previously used for TE; these materials can be easily functionalized; they are self-healing, biodegradable, stimuli-responsive, and nonimmunogenic. These characteristics are vital for the further development of current trends in TE, such as the use of pluripotent cells for organoid generation, cell-free scaffolds for tissue regeneration, patient-derived organ models, and controlled delivery systems of small molecules. In this review, we will analyse the 3 subtypes of SBPs: peptide-, nucleic acid-, and oligosaccharide-derived. Then, we will discuss the role that SBPs will be playing in TE as dynamic scaffolds, therapeutic scaffolds, and bioinks. Finally, we will describe possible outlooks of SBPs for TE.
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56
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Iskandar SE, Haberman VA, Bowers AA. Expanding the Chemical Diversity of Genetically Encoded Libraries. ACS COMBINATORIAL SCIENCE 2020; 22:712-733. [PMID: 33167616 PMCID: PMC8284915 DOI: 10.1021/acscombsci.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
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Affiliation(s)
- Sabrina E Iskandar
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Victoria A Haberman
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Albert A Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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57
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Sasikumar PG, Ramachandra M. Peptide and peptide-inspired checkpoint inhibitors: Protein fragments to cancer immunotherapy. MEDICINE IN DRUG DISCOVERY 2020. [DOI: 10.1016/j.medidd.2020.100073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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58
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Kong XD, Carle V, Díaz-Perlas C, Butler K, Heinis C. Generation of a Large Peptide Phage Display Library by Self-Ligation of Whole-Plasmid PCR Product. ACS Chem Biol 2020; 15:2907-2915. [PMID: 33125222 DOI: 10.1021/acschembio.0c00497] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The success of phage display, used for developing target-specific binders based on peptides and proteins, depends on the size and diversity of the library screened, but generating large libraries of phage-encoded polypeptides remains challenging. New peptide phage display libraries developed in recent years rarely contained more than 1 billion clones, which appears to have become the upper size limit for libraries generated with reasonable effort. Here, we established a strategy based on whole-plasmid PCR and self-ligation to clone a library with more than 2 × 1010 members. The enormous library size could be obtained through amplifying the entire vector DNA by PCR, which omitted the step of vector isolation from bacterial cells, and through appending DNA coding for the peptide library via a PCR primer, which enabled efficient DNA circularization by end-ligation to facilitate the difficult step of vector-insertion of DNA fragments. Panning the peptide repertoires against a target yielded high-affinity ligands and validated the quality of the library and thus the new library cloning strategy. This simple and efficient strategy places larger libraries within reach for nonspecialist researchers to hopefully expand the possible targets of phage display applications.
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Affiliation(s)
- Xu-Dong Kong
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Vanessa Carle
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Kaycie Butler
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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59
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Li H, Ren J, Li J, Zhang Z, Chang N, Qin C. Greener liquid-phase synthesis and the ACE inhibitory structure-activity relationship of an anti-SARS octapeptide. Org Biomol Chem 2020; 18:8433-8442. [PMID: 33057549 DOI: 10.1039/d0ob01948h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A high-efficiency strategy for resin-free and large scale liquid phase synthesis of the anti-SARS octapeptide AVLQSGFR is described. Herein, tri(4'-diphenylphosphonyloxylbenzoyl phenyl)phosphate (TDPBP) derivatives were designed as C-terminal supports to aid octapeptide intermediate purification without the need for chromatographic separation. Furthermore, the ACE inhibitory structure-activity relationship (SAR) of the anti-SARS octapeptide and its alanine-scanning analogues was systematically studied by in vitro assay and 3D-QSAR via molecular docking. This paper provides a new strategy for the development of peptide-based drugs. Simultaneously, a study on the ACE inhibition and structure-activity relationship of the anti-SARS octapeptide also lays a foundation for further understanding how the anti-SARS octapeptide acts as an ACE inhibitor.
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Affiliation(s)
- Haidi Li
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Jin Ren
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Junyou Li
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Zixin Zhang
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Ninghui Chang
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
| | - Chuanguang Qin
- Shaanxi Key Laboratory of Polymer Science & Technology, OME Key Laboratory of Supernormal Material Physics & Chemistry, School of Chemistry and Chemical Engineering, Northwestern Polytechnical University, Xi'an, 710072, P. R. China.
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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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Inyushin M, Zayas-Santiago A, Rojas L, Kucheryavykh L. On the Role of Platelet-Generated Amyloid Beta Peptides in Certain Amyloidosis Health Complications. Front Immunol 2020; 11:571083. [PMID: 33123145 PMCID: PMC7567018 DOI: 10.3389/fimmu.2020.571083] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
As do many other immunity-related blood cells, platelets release antimicrobial peptides that kill bacteria, fungi, and even certain viruses. Here we review the literature suggesting that there is a similarity between the antimicrobials released by other blood cells and the amyloid-related Aβ peptide released by platelets. Analyzing the literature, we also propose that platelet-generated Aβ amyloidosis may be more common than currently recognized. This systemic Aβ from a platelet source may participate in various forms of amyloidosis in pathologies ranging from brain cancer, glaucoma, skin Aβ accumulation, and preeclampsia to Alzheimer’s disease and late-stage Parkinson’s disease. We also discuss the advantages and disadvantages of specific animal models for studying platelet-related Aβ. This field is undergoing rapid change, as it evaluates competing ideas in the light of new experimental observations. We summarized both in order to clarify the role of platelet-generated Aβ peptides in amyloidosis-related health disorders, which may be helpful to researchers interested in this growing area of investigation.
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Affiliation(s)
- Mikhail Inyushin
- Department of Physiology, Universidad Central del Caribe, Bayamon, Puerto Rico
| | - Astrid Zayas-Santiago
- Department of Pathology & Laboratory Medicine, Universidad Central del Caribe, Bayamon, Puerto Rico
| | - Legier Rojas
- Department of Physiology, Universidad Central del Caribe, Bayamon, Puerto Rico
| | - Lilia Kucheryavykh
- Department of Biochemistry, Universidad Central del Caribe, Bayamon, Puerto Rico
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Faucher F, Bennett JM, Bogyo M, Lovell S. Strategies for Tuning the Selectivity of Chemical Probes that Target Serine Hydrolases. Cell Chem Biol 2020; 27:937-952. [PMID: 32726586 PMCID: PMC7484133 DOI: 10.1016/j.chembiol.2020.07.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 02/08/2023]
Abstract
Serine hydrolases comprise a large family of enzymes that have diverse roles in key cellular processes, such as lipid metabolism, cell signaling, and regulation of post-translation modifications of proteins. They are also therapeutic targets for multiple human pathologies, including viral infection, diabetes, hypertension, and Alzheimer disease; however, few have well-defined substrates and biological functions. Activity-based probes (ABPs) have been used as effective tools to both profile activity and screen for selective inhibitors of serine hydrolases. One broad-spectrum ABP containing a fluorophosphonate electrophile has been used extensively to advance our understanding of diverse serine hydrolases. Due to the success of this single reagent, several robust chemistries have been developed to further diversify and tune the selectivity of ABPs used to target serine hydrolases. In this review, we highlight approaches to identify selective serine hydrolase ABPs and suggest new synthetic methodologies that could be applied to further advance probe development.
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Affiliation(s)
- Franco Faucher
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - John M Bennett
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Scott Lovell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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