1
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Zhang YW, Lin NP, Guo X, Szabo-Fresnais N, Ortoleva PJ, Chou DHC. Omniligase-1-Mediated Phage-Peptide Library Modification and Insulin Engineering. ACS Chem Biol 2024; 19:506-515. [PMID: 38266161 DOI: 10.1021/acschembio.3c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Chemical and enzymatic modifications of peptide-displayed libraries have been successfully employed to expand the phage display library. However, the requirement of specific epitopes and scaffolds has limited the scope of protein engineering using phage display. In this study, we present a novel approach utilizing omniligase-1-mediated selective and specific ligation on the phage pIII protein, offering a high conversion rate and compatibility with commercially available phage libraries. We applied this method to perform high-throughput engineering of insulin analogues with randomized B chain C-terminal regions. Insulin analogues with different B chain C-terminal segments were selected and exhibited biological activity equivalent to that of human insulin. Molecular dynamics studies of insulin analogues revealed a novel interaction between the insulin B27 residue and insulin receptor L1 domain. In summary, our findings highlight the potential of omniligase-1-mediated phage display in the development and screening of disulfide-rich peptides and proteins. This approach holds promise for the creation of novel insulin analogues with enhanced therapeutic properties and exhibits potential for the development of other therapeutic compounds.
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Affiliation(s)
- Yi Wolf Zhang
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nai-Pin Lin
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
| | - Xu Guo
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicolas Szabo-Fresnais
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Peter J Ortoleva
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Danny Hung-Chieh Chou
- Department of Pediatrics, Division of Diabetes and Endocrinology, Stanford University, Palo Alto, California 94304, United States
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2
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Abstract
The ability to site-selectively modify equivalent functional groups in a molecule has the potential to streamline syntheses and increase product yields by lowering step counts. Enzymes catalyze site-selective transformations throughout primary and secondary metabolism, but leveraging this capability for non-native substrates and reactions requires a detailed understanding of the potential and limitations of enzyme catalysis and how these bounds can be extended by protein engineering. In this review, we discuss representative examples of site-selective enzyme catalysis involving functional group manipulation and C-H bond functionalization. We include illustrative examples of native catalysis, but our focus is on cases involving non-native substrates and reactions often using engineered enzymes. We then discuss the use of these enzymes for chemoenzymatic transformations and target-oriented synthesis and conclude with a survey of tools and techniques that could expand the scope of non-native site-selective enzyme catalysis.
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Affiliation(s)
- Dibyendu Mondal
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M Snodgrass
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christian A Gomez
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Jared C Lewis
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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3
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Jiráček J, Selicharová I, Žáková L. Mutations at hypothetical binding site 2 in insulin and insulin-like growth factors 1 and 2. VITAMINS AND HORMONES 2023; 123:187-230. [PMID: 37717985 DOI: 10.1016/bs.vh.2023.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Elucidating how insulin and the related insulin-like growth factors 1 and 2 (IGF-1 and IGF-2) bind to their cellular receptors (IR and IGF-1R) and how the receptors are activated has been the holy grail for generations of scientists. However, deciphering the 3D structure of tyrosine kinase receptors and their hormone-bound complexes has been complicated by the flexible and dimeric nature of the receptors and the dynamic nature of their interaction with hormones. Therefore, mutagenesis of hormones and kinetic studies first became an important tool for studying receptor interactions. It was suggested that hormones could bind to receptors through two binding sites on the hormone surface called site 1 and site 2. A breakthrough in knowledge came with the solution of cryoelectron microscopy (cryoEM) structures of hormone-receptor complexes. In this chapter, we document in detail the mutagenesis of insulin, IGF-1, and IGF-2 with emphasis on modifications of the hypothetical binding site 2 in the hormones, and we discuss the results of structure-activity studies in light of recent cryoEM structures of hormone complexes with IR and IGF-1R.
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Affiliation(s)
- Jiří Jiráček
- From Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic.
| | - Irena Selicharová
- From Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
| | - Lenka Žáková
- From Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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4
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Fryszkowska A, An C, Alvizo O, Banerjee G, Canada KA, Cao Y, DeMong D, Devine PN, Duan D, Elgart DM, Farasat I, Gauthier DR, Guidry EN, Jia X, Kong J, Kruse N, Lexa KW, Makarov AA, Mann BF, Milczek EM, Mitchell V, Nazor J, Neri C, Orr RK, Orth P, Phillips EM, Riggins JN, Schafer WA, Silverman SM, Strulson CA, Subramanian N, Voladri R, Yang H, Yang J, Yi X, Zhang X, Zhong W. A chemoenzymatic strategy for site-selective functionalization of native peptides and proteins. Science 2022; 376:1321-1327. [PMID: 35709255 DOI: 10.1126/science.abn2009] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The emergence of new therapeutic modalities requires complementary tools for their efficient syntheses. Availability of methodologies for site-selective modification of biomolecules remains a long-standing challenge, given the inherent complexity and the presence of repeating residues that bear functional groups with similar reactivity profiles. We describe a bioconjugation strategy for modification of native peptides relying on high site selectivity conveyed by enzymes. We engineered penicillin G acylases to distinguish among free amino moieties of insulin (two at amino termini and an internal lysine) and manipulate cleavable phenylacetamide groups in a programmable manner to form protected insulin derivatives. This enables selective and specific chemical ligation to synthesize homogeneous bioconjugates, improving yield and purity compared to the existing methods, and generally opens avenues in the functionalization of native proteins to access biological probes or drugs.
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Affiliation(s)
- Anna Fryszkowska
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Chihui An
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Oscar Alvizo
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | | | - Keith A Canada
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Yang Cao
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Duane DeMong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Paul N Devine
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Da Duan
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - David M Elgart
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Iman Farasat
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Donald R Gauthier
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Erin N Guidry
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Xiujuan Jia
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jongrock Kong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Nikki Kruse
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Katrina W Lexa
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Alexey A Makarov
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Benjamin F Mann
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Erika M Milczek
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Vesna Mitchell
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Jovana Nazor
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Claudia Neri
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Robert K Orr
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Peter Orth
- Discovery Chemistry, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Eric M Phillips
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - James N Riggins
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Wes A Schafer
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Steven M Silverman
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | | | | | - Rama Voladri
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Hao Yang
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Jie Yang
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Xiang Yi
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Xiyun Zhang
- Codexis Inc., 200 Penobscot Drive, Redwood City, CA 94063, USA
| | - Wendy Zhong
- Process Research and Development, Merck & Co., Inc., Rahway, NJ 07065, USA
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5
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Páníková T, Mitrová K, Halamová T, Mrzílková K, Pícha J, Chrudinová M, Kurochka A, Selicharová I, Žáková L, Jiráček J. Insulin Analogues with Altered Insulin Receptor Isoform Binding Specificities and Enhanced Aggregation Stabilities. J Med Chem 2021; 64:14848-14859. [PMID: 34591477 DOI: 10.1021/acs.jmedchem.1c01388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Insulin is a lifesaver for millions of diabetic patients. There is a need for new insulin analogues with more physiological profiles and analogues that will be thermally more stable than human insulin. Here, we describe the chemical engineering of 48 insulin analogues that were designed to have changed binding specificities toward isoforms A and B of the insulin receptor (IR-A and IR-B). We systematically modified insulin at the C-terminus of the B-chain, at the N-terminus of the A-chain, and at A14 and A18 positions. We discovered an insulin analogue that has Cα-carboxyamidated Glu at B31 and Ala at B29 and that has a more than 3-fold-enhanced binding specificity in favor of the "metabolic" IR-B isoform. The analogue is more resistant to the formation of insulin fibrils at 37 °C and is also more efficient in mice than human insulin. Therefore, [AlaB29,GluB31,amideB31]-insulin may be interesting for further clinical evaluation.
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Affiliation(s)
- Terezie Páníková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Technická 5, 166 28 Prague, Czech Republic
| | - Katarína Mitrová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Tereza Halamová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Karolína Mrzílková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Jan Pícha
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Martina Chrudinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Andrii Kurochka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 116 10 Prague 6, Czech Republic
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6
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021; 60:15972-15979. [PMID: 33844389 PMCID: PMC8361980 DOI: 10.1002/anie.202102343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/09/2021] [Indexed: 12/11/2022]
Abstract
The thiol group of the cysteine side chain is arguably the most versatile chemical handle in proteins. To expand the scope of established and commercially available thiol bioconjugation reagents, we genetically encoded a second such functional moiety in form of a latent thiol group that can be unmasked under mild physiological conditions. Phenylacetamidomethyl (Phacm) protected homocysteine (HcP) was incorporated and its latent thiol group unmasked on purified proteins using penicillin G acylase (PGA). The enzymatic deprotection depends on steric accessibility, but can occur efficiently within minutes on exposed positions in flexible sequences. The freshly liberated thiol group does not require treatment with reducing agents. We demonstrate the potential of this approach for protein modification with conceptually new schemes for regioselective dual labeling, thiol bioconjugation in presence of a preserved disulfide bond and formation of a novel intramolecular thioether crosslink.
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Affiliation(s)
| | - Pascal Meyer‐Ahrens
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Annika Aust
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Anna‐Lena Feldberg
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
| | - Henning D. Mootz
- Institute of BiochemistryUniversity of MünsterCorrensstraße 3648149MünsterGermany
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7
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Reille‐Seroussi M, Meyer‐Ahrens P, Aust A, Feldberg A, Mootz HD. Genetic Encoding and Enzymatic Deprotection of a Latent Thiol Side Chain to Enable New Protein Bioconjugation Applications. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Marie Reille‐Seroussi
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Pascal Meyer‐Ahrens
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Annika Aust
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Anna‐Lena Feldberg
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
| | - Henning D. Mootz
- Institute of Biochemistry University of Münster Corrensstraße 36 48149 Münster Germany
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8
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Reille-Seroussi M, Mayer SV, Dörner W, Lang K, Mootz HD. Expanding the genetic code with a lysine derivative bearing an enzymatically removable phenylacetyl group. Chem Commun (Camb) 2019; 55:4793-4796. [PMID: 30945708 DOI: 10.1039/c9cc00475k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We report the genetically encoded incorporation of phenylacetyl protected lysine (PacK) into proteins in Escherichia coli. This unnatural side-chain modification can be enzymatically removed using either penicillin G acylase (PGA) or, surprisingly, the sirtuin SrtN from Bacillus subtilis. Our approach expands the toolbox to reversibly control protein structure and function under very mild and non-denaturing conditions, as demonstrated by triggering the activity of the nonribosomal peptide synthetase GrsA.
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Affiliation(s)
- Marie Reille-Seroussi
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Str. 2, 48149 Münster, Germany.
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9
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Chrudinová M, Žáková L, Marek A, Socha O, Buděšínský M, Hubálek M, Pícha J, Macháčková K, Jiráček J, Selicharová I. A versatile insulin analog with high potency for both insulin and insulin-like growth factor 1 receptors: Structural implications for receptor binding. J Biol Chem 2018; 293:16818-16829. [PMID: 30213860 PMCID: PMC6204900 DOI: 10.1074/jbc.ra118.004852] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/05/2018] [Indexed: 12/02/2022] Open
Abstract
Insulin and insulin-like growth factor 1 (IGF-1) are closely related hormones involved in the regulation of metabolism and growth. They elicit their functions through activation of tyrosine kinase–type receptors: insulin receptors (IR-A and IR-B) and IGF-1 receptor (IGF-1R). Despite similarity in primary and three-dimensional structures, insulin and IGF-1 bind the noncognate receptor with substantially reduced affinity. We prepared [d-HisB24, GlyB31, TyrB32]-insulin, which binds all three receptors with high affinity (251 or 338% binding affinity to IR-A respectively to IR-B relative to insulin and 12.4% binding affinity to IGF-1R relative to IGF-1). We prepared other modified insulins with the aim of explaining the versatility of [d-HisB24, GlyB31, TyrB32]-insulin. Through structural, activity, and kinetic studies of these insulin analogs, we concluded that the ability of [d-HisB24, GlyB31, TyrB32]-insulin to stimulate all three receptors is provided by structural changes caused by a reversed chirality at the B24 combined with the extension of the C terminus of the B chain by two extra residues. We assume that the structural changes allow the directing of the B chain C terminus to some extra interactions with the receptors. These unusual interactions lead to a decrease of dissociation rate from the IR and conversely enable easier association with IGF-1R. All of the structural changes were made at the hormones' Site 1, which is thought to interact with the Site 1 of the receptors. The results of the study suggest that merely modifications of Site 1 of the hormone are sufficient to change the receptor specificity of insulin.
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Affiliation(s)
- Martina Chrudinová
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Lenka Žáková
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Aleš Marek
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Ondřej Socha
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Miloš Buděšínský
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Martin Hubálek
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jan Pícha
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Kateřina Macháčková
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Jiří Jiráček
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Irena Selicharová
- From the Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo n. 2, 166 10 Prague 6, Czech Republic
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10
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Křížková K, Chrudinová M, Povalová A, Selicharová I, Collinsová M, Vaněk V, Brzozowski AM, Jiráček J, Žáková L. Insulin–Insulin-like Growth Factors Hybrids as Molecular Probes of Hormone:Receptor Binding Specificity. Biochemistry 2016; 55:2903-13. [DOI: 10.1021/acs.biochem.6b00140] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Květoslava Křížková
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
- Charles University in Prague, Faculty of Science,
Department of Biochemistry, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Martina Chrudinová
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
- Charles University in Prague, Faculty of Science,
Department of Biochemistry, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Anna Povalová
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
- Charles University in Prague, Faculty of Science,
Department of Biochemistry, Hlavova 8, 128 43 Praha 2, Czech Republic
| | - Irena Selicharová
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Michaela Collinsová
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Václav Vaněk
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Andrzej M. Brzozowski
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Jiří Jiráček
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Lenka Žáková
- Institute
of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic v.v.i., Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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11
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Viková J, Collinsová M, Kletvíková E, Buděšínský M, Kaplan V, Žáková L, Veverka V, Hexnerová R, Aviñó RJT, Straková J, Selicharová I, Vaněk V, Wright DW, Watson CJ, Turkenburg JP, Brzozowski AM, Jiráček J. Rational steering of insulin binding specificity by intra-chain chemical crosslinking. Sci Rep 2016; 6:19431. [PMID: 26792393 PMCID: PMC4726324 DOI: 10.1038/srep19431] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/11/2015] [Indexed: 12/14/2022] Open
Abstract
Insulin is a key hormone of human metabolism with major therapeutic importance for both types of diabetes. New insulin analogues with more physiological profiles and better glycemic control are needed, especially analogues that preferentially bind to the metabolic B-isoform of insulin receptor (IR-B). Here, we aimed to stabilize and modulate the receptor-compatible conformation of insulin by covalent intra-chain crosslinking within its B22-B30 segment, using the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction of azides and alkynes. This approach resulted in 14 new, systematically crosslinked insulin analogues whose structures and functions were extensively characterized and correlated. One of the analogues, containing a B26-B29 triazole bridge, was highly active in binding to both IR isoforms, with a significant preference for IR-B. Our results demonstrate the potential of chemistry-driven modulation of insulin function, also shedding new light on the functional importance of hormone's B-chain C-terminus for its IR-B specificity.
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Affiliation(s)
- Jitka Viková
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Michaela Collinsová
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Emília Kletvíková
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Vojtěch Kaplan
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Roberto J. Tarazona Aviñó
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Jana Straková
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Irena Selicharová
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Václav Vaněk
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
| | - Daniel W. Wright
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Christopher J. Watson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Andrzej M. Brzozowski
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic
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Shcherbakova TA, Panin NV, Suplatov DA, Shapovalova IV, Švedas VK. The βD484N mutant of penicillin acylase from Escherichia coli is more resistant to inactivation by substrates and can effectively perform peptide synthesis in aqueous medium. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2014.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Žáková L, Kletvíková E, Veverka V, Lepsík M, Watson CJ, Turkenburg JP, Jirácek J, Brzozowski AM. Structural integrity of the B24 site in human insulin is important for hormone functionality. J Biol Chem 2013; 288:10230-40. [PMID: 23447530 DOI: 10.1074/jbc.m112.448050] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite the recent first structural insight into the insulin-insulin receptor complex, the role of the C terminus of the B-chain of insulin in this assembly remains unresolved. Previous studies have suggested that this part of insulin must rearrange to reveal amino acids crucial for interaction with the receptor. The role of the invariant Phe(B24), one of the key residues of the hormone, in this process remains unclear. For example, the B24 site functionally tolerates substitutions to D-amino acids but not to L-amino acids. Here, we prepared and characterized a series of B24-modified insulin analogues, also determining the structures of [D-HisB24]-insulin and [HisB24]-insulin. The inactive [HisB24]-insulin molecule is remarkably rigid due to a tight accommodation of the L-His side chain in the B24 binding pocket that results in the stronger tethering of B25-B28 residues to the protein core. In contrast, the highly active [D-HisB24]-insulin is more flexible, and the reverse chirality of the B24C(α) atom swayed the D-His(B24) side chain into the solvent. Furthermore, the pocket vacated by Phe(B24) is filled by Phe(B25), which mimics the Phe(B24) side and main chains. The B25→B24 downshift results in a subsequent downshift of Tyr(B26) into the B25 site and the departure of B26-B30 residues away from the insulin core. Our data indicate the importance of the aromatic L-amino acid at the B24 site and the structural invariance/integrity of this position for an effective binding of insulin to its receptor. Moreover, they also suggest limited, B25-B30 only, unfolding of the C terminus of the B-chain upon insulin activation.
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Affiliation(s)
- Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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Antolíková E, Žáková L, Turkenburg JP, Watson CJ, Hančlová I, Šanda M, Cooper A, Kraus T, Brzozowski AM, Jiráček J. Non-equivalent role of inter- and intramolecular hydrogen bonds in the insulin dimer interface. J Biol Chem 2011; 286:36968-77. [PMID: 21880708 PMCID: PMC3196076 DOI: 10.1074/jbc.m111.265249] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/03/2011] [Indexed: 11/06/2022] Open
Abstract
Apart from its role in insulin receptor (IR) activation, the C terminus of the B-chain of insulin is also responsible for the formation of insulin dimers. The dimerization of insulin plays an important role in the endogenous delivery of the hormone and in the administration of insulin to patients. Here, we investigated insulin analogues with selective N-methylations of peptide bond amides at positions B24, B25, or B26 to delineate their structural and functional contribution to the dimer interface. All N-methylated analogues showed impaired binding affinities to IR, which suggests a direct IR-interacting role for the respective amide hydrogens. The dimerization capabilities of analogues were investigated by isothermal microcalorimetry. Selective N-methylations of B24, B25, or B26 amides resulted in reduced dimerization abilities compared with native insulin (K(d) = 8.8 μM). Interestingly, although the N-methylation in [NMeTyrB26]-insulin or [NMePheB24]-insulin resulted in K(d) values of 142 and 587 μM, respectively, the [NMePheB25]-insulin did not form dimers even at high concentrations. This effect may be attributed to the loss of intramolecular hydrogen bonding between NHB25 and COA19, which connects the B-chain β-strand to the core of the molecule. The release of the B-chain β-strand from this hydrogen bond lock may result in its higher mobility, thereby shifting solution equilibrium toward the monomeric state of the hormone. The study was complemented by analyses of two novel analogue crystal structures. All examined analogues crystallized only in the most stable R(6) form of insulin oligomers (even if the dimer interface was totally disrupted), confirming the role of R(6)-specific intra/intermolecular interactions for hexamer stability.
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Affiliation(s)
- Emília Antolíková
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Lenka Žáková
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Johan P. Turkenburg
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom, and
| | - Christopher J. Watson
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom, and
| | - Ivona Hančlová
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Miloslav Šanda
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - Alan Cooper
- the School of Chemistry, Glasgow University, College of Science and Engineering, Glasgow G12 8QQ, Scotland, United Kingdom
| | - Tomáš Kraus
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
| | - A. Marek Brzozowski
- the York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, United Kingdom, and
| | - Jiří Jiráček
- From the Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 166 10 Prague 6, Czech Republic
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Implications for the active form of human insulin based on the structural convergence of highly active hormone analogues. Proc Natl Acad Sci U S A 2010; 107:1966-70. [PMID: 20133841 DOI: 10.1073/pnas.0911785107] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Insulin is a key protein hormone that regulates blood glucose levels and, thus, has widespread impact on lipid and protein metabolism. Insulin action is manifested through binding of its monomeric form to the Insulin Receptor (IR). At present, however, our knowledge about the structural behavior of insulin is based upon inactive, multimeric, and storage-like states. The active monomeric structure, when in complex with the receptor, must be different as the residues crucial for the interactions are buried within the multimeric forms. Although the exact nature of the insulin's induced-fit is unknown, there is strong evidence that the C-terminal part of the B-chain is a dynamic element in insulin activation and receptor binding. Here, we present the design and analysis of highly active (200-500%) insulin analogues that are truncated at residue 26 of the B-chain (B(26)). They show a structural convergence in the form of a new beta-turn at B(24)-B(26). We propose that the key element in insulin's transition, from an inactive to an active state, may be the formation of the beta-turn at B(24)-B(26) associated with a trans to cis isomerisation at the B(25)-B(26) peptide bond. Here, this turn is achieved with N-methylated L-amino acids adjacent to the trans to cis switch at the B(25)-B(26) peptide bond or by the insertion of certain D-amino acids at B(26). The resultant conformational changes unmask previously buried amino acids that are implicated in IR binding and provide structural details for new approaches in rational design of ligands effective in combating diabetes.
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Žáková L, Kazdová L, Hančlová I, Protivínská E, Šanda M, Buděšínský M, Jiráček J. Insulin Analogues with Modifications at Position B26. Divergence of Binding Affinity and Biological Activity. Biochemistry 2008; 47:5858-68. [DOI: 10.1021/bi702086w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lenka Žáková
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
| | - Ludmila Kazdová
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
| | - Ivona Hančlová
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
| | - Eva Protivínská
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
| | - Miloslav Šanda
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
| | - Jiří Jiráček
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic, and Institute for Clinical and Experimental Medicine, Vídeňská 1958/9, 140 21 Praha 4, Czech Republic
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