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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [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: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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2
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Linciano S, Moro G, Zorzi A, Angelini A. Molecular analysis and therapeutic applications of human serum albumin-fatty acid interactions. J Control Release 2022; 348:115-126. [PMID: 35643382 DOI: 10.1016/j.jconrel.2022.05.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/16/2022] [Accepted: 05/21/2022] [Indexed: 11/16/2022]
Abstract
Human serum albumin (hSA) is the major carrier protein for fatty acids (FAs) in plasma. Its ability to bind multiple FA moieties with moderate to high affinity has inspired the use of FA conjugation as a safe and natural platform to generate long-lasting therapeutics with enhanced pharmacokinetic properties and superior efficacy. In this frame, the choice of the FA is crucial and a comprehensive elucidation of the molecular interactions of FAs with hSA cannot be left out of consideration. To this intent, we report here a comparative analysis of the binding mode of different FA moieties with hSA. The choice among different albumin-binding FAs and how this influence the pharmacokinetics properties of a broad spectrum of therapeutic molecules will be discussed including a critical description of some clinically relevant FA conjugated therapeutics.
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Affiliation(s)
- Sara Linciano
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Giulia Moro
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; AXES Research Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Alessandro Zorzi
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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3
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Interaction of esomeprazole with insulin detemir and human albumin: A potential cause of hypoglycemia. Biophys Chem 2022; 285:106809. [DOI: 10.1016/j.bpc.2022.106809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022]
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Potentials of Neuropeptides as Therapeutic Agents for Neurological Diseases. Biomedicines 2022; 10:biomedicines10020343. [PMID: 35203552 PMCID: PMC8961788 DOI: 10.3390/biomedicines10020343] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
Despite recent leaps in modern medicine, progress in the treatment of neurological diseases remains slow. The near impermeable blood-brain barrier (BBB) that prevents the entry of therapeutics into the brain, and the complexity of neurological processes, limits the specificity of potential therapeutics. Moreover, a lack of etiological understanding and the irreversible nature of neurological conditions have resulted in low tolerability and high failure rates towards existing small molecule-based treatments. Neuropeptides, which are small proteinaceous molecules produced by the body, either in the nervous system or the peripheral organs, modulate neurological function. Although peptide-based therapeutics originated from the treatment of metabolic diseases in the 1920s, the adoption and development of peptide drugs for neurological conditions are relatively recent. In this review, we examine the natural roles of neuropeptides in the modulation of neurological function and the development of neurological disorders. Furthermore, we highlight the potential of these proteinaceous molecules in filling gaps in current therapeutics.
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Hijazi Y. Prediction of Half-Life Extension of Peptides via Serum Albumin Binding: Current Challenges. Eur J Drug Metab Pharmacokinet 2021; 46:163-172. [PMID: 33386550 DOI: 10.1007/s13318-020-00664-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
The development of peptide therapeutics has increased enormously in recent decades. Many of the peptide drugs and antibody fragments that lack Fc backbone have a short half-life in circulation. In general, the half-life supports the design of the dosing regimen and frequency of administration, which are key aspects in the discovery of peptide drugs intended for long duration of action. Less frequent administration such as weekly or monthly can improve compliance and adherence to therapy. Serum albumin binding is a key approach to extend the half-life of peptide drugs. Despite the evidence of half-life prolongation of a variety of peptide drugs via albumin, quantitative prediction for humans is still a key question. Challenges in the measurement of albumin binding and in understanding the clearance mechanisms can limit quantitative prediction. We integrated pharmacokinetic concepts and albumin binding across species in a quantitative model to be used as a tool for prediction of half-life. Preliminary validation on a limited dataset indicated a good correlation between predicted and observed values. Further development of more quantitative models is warranted.
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Affiliation(s)
- Youssef Hijazi
- R&D, Drug Metabolism and Pharmacokinetics, Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, Bldg. H 831, C 0442, 65926, Frankfurt, Germany.
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Choi J, Wahlgren M, Ek V, Elofsson U, Fransson J, Nilsson L, Terry A, Söderberg CAG. Characterization of binding between model protein GA-Z and human serum albumin using asymmetrical flow field-flow fractionation and small angle X-ray scattering. PLoS One 2020; 15:e0242605. [PMID: 33232370 PMCID: PMC7685474 DOI: 10.1371/journal.pone.0242605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023] Open
Abstract
Protein-based drugs often require targeted drug delivery for optimal therapy. A successful strategy to increase the circulation time of the protein in the blood is to link the therapeutic protein with an albumin-binding domain. In this work, we characterized such a protein-based drug, GA-Z. Using asymmetrical flow field-flow fractionation coupled with multi-angle light scattering (AF4-MALS) we investigated the GA-Z monomer-dimer equilibrium as well as the molar binding ratio of GA-Z to HSA. Using small angle X-ray scattering, we studied the structure of GA-Z as well as the complex between GA-Z and HSA. The results show that GA-Z is predominantly dimeric in solution at pH 7 and that it binds to monomeric as well as dimeric HSA. Furthermore, GA-Z binds to HSA both as a monomer and a dimer, and thus, it can be expected to stay bound also upon dilution following injection in the blood stream. The results from SAXS and binding studies indicate that the GA-Z dimer is formed between two target domains (Z-domains). The results also indicate that the binding of GA-Z to HSA does not affect the ratio between HSA dimers and monomers, and that no higher order oligomers of the complex are seen other than those containing dimers of GA-Z and dimers of HSA.
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Affiliation(s)
- Jaeyeong Choi
- Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Marie Wahlgren
- Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Vilhelm Ek
- Swedish Orphan Biovitrum AB (Sobi), Stockholm, Sweden
| | - Ulla Elofsson
- Division of Bioscience and Materials, RISE Research Institutes of Sweden, Lund, Sweden
| | | | - Lars Nilsson
- Food Technology, Engineering and Nutrition, Faculty of Engineering LTH, Lund University, Lund, Sweden
| | - Ann Terry
- MAX IV Laboratory, Lund University, Lund, Sweden
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Faust C, Ochs C, Korn M, Werner U, Jung J, Dittrich W, Schiebler W, Schauder R, Rao E, Langer T. Production of a novel heterodimeric two-chain insulin-Fc fusion protein. Protein Eng Des Sel 2020; 33:5959880. [PMID: 33159202 DOI: 10.1093/protein/gzaa026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 01/12/2023] Open
Abstract
Insulin is a peptide hormone produced by the pancreas. The physiological role of insulin is the regulation of glucose metabolism. Under certain pathological conditions the insulin levels can be reduced leading to the metabolic disorder diabetes mellitus (DM). For type 1 DM and, dependent on the disease progression for type 2 DM, insulin substitution becomes indispensable. To relieve insulin substitution therapy for patients, novel insulin analogs with pharmacokinetic and pharmacodynamic profiles aiming for long-lasting or fast-acting insulins have been developed. The next step in the evolution of novel insulins should be insulin analogs with a time action profile beyond 1-2 days, preferable up to 1 week. Nowadays, insulin is produced in a recombinant manner. This approach facilitates the design and production of further insulin-analogs or insulin-fusion proteins. The usage of the Fc-domain from immunoglobulin as a fusion partner for therapeutic proteins and peptides is widely used to extend their plasma half-life. Insulin consists of two chains, the A- and B-chain, which are connected by two disulfide-bridges. To produce a novel kind of Fc-fusion protein we have fused the A-chain as well as the B-chain to Fc-fragments containing either 'knob' or 'hole' mutations. The 'knob-into-hole' technique is frequently used to force heterodimerization of the Fc-domain. Using this approach, we were able to produce different variants of two-chain-insulin-Fc-protein (tcI-Fc-protein) variants. The tcI-Fc-fusion variants retained activity as shown in in vitro assays. Finally, prolonged blood glucose lowering activity was demonstrated in normoglycemic rats. Overall, we describe here the production of novel insulin-Fc-fusion proteins with prolonged times of action.
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Affiliation(s)
- Christine Faust
- Sanofi-Aventis Deutschland GmbH, R&D Biologics Research, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Christian Ochs
- Sanofi-Aventis Deutschland GmbH, R&D Biologics Research, Industriepark Höchst, 65926 Frankfurt am Main, Germany.,Provadis School of International Management and Technology AG, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Marcus Korn
- Sanofi-Aventis Deutschland GmbH, R&D TA Diabetes, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Ulrich Werner
- Sanofi-Aventis Deutschland GmbH, R&D TA Diabetes, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Jennifer Jung
- Sanofi-Aventis Deutschland GmbH, R&D Biologics Research, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Werner Dittrich
- Sanofi-Aventis Deutschland GmbH, R&D Biologics Research, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Werner Schiebler
- Provadis School of International Management and Technology AG, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Rolf Schauder
- Provadis School of International Management and Technology AG, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Ercole Rao
- Sanofi-Aventis Deutschland GmbH, R&D Biologics Research, Industriepark Höchst, 65926 Frankfurt am Main, Germany
| | - Thomas Langer
- Sanofi-Aventis Deutschland GmbH, R&D Biologics Research, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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Feng S, Peters GHJ, Ohtake S, Schöneich C, Shalaev E. Water Distribution and Clustering on the Lyophilized IgG1 Surface: Insight from Molecular Dynamics Simulations. Mol Pharm 2020; 17:900-908. [PMID: 31990562 DOI: 10.1021/acs.molpharmaceut.9b01150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Water has a critical role in the stability of the higher-order structure of proteins. In addition, it is considered to be a major destabilization factor for the physical and chemical stability of freeze-dried proteins and peptides. Physical and chemical aspects of protein/water relationships are commonly studied with the use of water vapor sorption isotherms for amorphous lyophilized proteins, which, in turn, are commonly analyzed using the Brunauer-Emmett-Teller (BET) equation to obtain the parameters, Wm and CB. The parameter Wm is generally referred to as the "monolayer limit of adsorption" and has a narrow range of 6-8% for most proteins. In this study, the water distribution on an IgG1 surface is investigated by molecular dynamics (MD) simulations at different water contents. The monolayer of water molecules was found to have limited coverage of the protein surface, and the true monolayer coverage of the protein globule actually occurs at a hydration level above 30%. The distribution of water molecules on the IgG1 surface is also highly heterogeneous, and the heterogeneity is not considered in the BET theory. In this study, a mechanistic model has been developed to describe the water vapor sorption isotherm. This model is based on the analysis of the hydrogen bonding network extracted from the MD simulations. The model is consistent with the experimental Type-II isotherm, which is usually observed for proteins. The physical meaning of the BET monolayer was redefined as the onset of water cluster formation. A simple model to calculate the onset water level, Wm, is proposed based on the hydration of different amino acids, as determined from the MD simulations.
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Affiliation(s)
- Shaoxin Feng
- Department of Pharmaceutical Development, Allegan plc, Irvine, California 92612, United States
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Satoshi Ohtake
- BioTherapeutics Pharmaceutical Sciences, Pfizer, Chesterfield, Missouri 63017, United States
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Evgenyi Shalaev
- Department of Pharmaceutical Development, Allegan plc, Irvine, California 92612, United States
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Ryberg LA, Sønderby P, Bukrinski JT, Harris P, Peters GHJ. Investigations of Albumin–Insulin Detemir Complexes Using Molecular Dynamics Simulations and Free Energy Calculations. Mol Pharm 2019; 17:132-144. [DOI: 10.1021/acs.molpharmaceut.9b00839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Line A. Ryberg
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pernille Sønderby
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Pernille Harris
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Günther H. J. Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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