Amino Acids, Peptides and Proteins

in Organic Chemistry

Edited by

Andrew B. Hughes

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Amino Acids, Peptides and Proteinsin Organic Chemistry

Volume 2 - Modified Amino Acids, Organocatalysisand Enzymes

Edited byAndrew B. Hughes

The Editor

Andrew B. HughesLa Trobe UniversityDepartment of ChemistryVictoria 3086Australia

All books published by Wiley-VCH are carefullyproduced. Nevertheless, authors, editors, andpublisher do not warrant the information containedin these books, including this book, to be free oferrors. Readers are advised to keep in mind thatstatements, data, illustrations, procedural details orother items may inadvertently be inaccurate.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication DataA catalogue record for this book is available from theBritish Library.

Bibliographic information published bythe Deutsche NationalbibliothekThe Deutsche Nationalbibliothek lists thispublication in the Deutsche Nationalbibliografie;detailed bibliographic data are available in theInternet at http://dnb.d-nb.de.

# 2009 WILEY-VCH Verlag GmbH & Co. KGaA,Weinheim

All rights reserved (including those of translation intoother languages). No part of this book may bereproduced in any form – by photoprinting,microfilm, or any other means – nor transmitted ortranslated into a machine language without writtenpermission from the publishers. Registered names,trademarks, etc. used in this book, even when notspecifically marked as such, are not to be consideredunprotected by law.

Composition Thomson Digital, Noida, IndiaPrinting Betz-Druck GmbH, DarmstadtBookbinding Litges & Dopf GmbH, HeppenheimCover Design Schulz Grafik Design, Fußgönheim

Printed in the Federal Republic of GermanyPrinted on acid-free paper

ISBN: 978-3-527-32098-1

Contents

List of Contributors XIX

Part One Synthesis and Chemistry of Modified Amino Acids 1

1 Synthesis and Chemistry of a,b-Didehydroamino Acids 3Uli Kazmaier

1.1 Introduction 31.2 Synthesis of DDAAs 31.2.1 DDAAs via Eliminations 31.2.1.1 DDAAs via b-Elimination 31.2.1.1.1 From b-Hydroxy Amino Acids 31.2.1.1.2 From b-Thio- and Selenoamino Acids 51.2.1.2 Elimination from N-Hydroxylated and -Chlorinated Amino Acids

and Peptides 61.2.1.3 DDAAs from a-Oxo Acids and Amides 61.2.1.4 DDAAs from Azides 71.2.2 DDAAs via C¼C Bond Formation 71.2.2.1 DDAAs via Azlactones [5(4H)-Oxazolones] 71.2.2.2 DDAAs via Horner–Emmons and Wittig Reactions 81.2.2.3 DDAAs via Enolates of Nitro- and Isocyano- and Iminoacetates 101.2.3 DDAAs via C–C Bond Formation 121.2.3.1 DDAAs via Heck Reaction 121.2.3.2 DDAAs via Cross-Coupling Reactions 131.3 Reactions of DDAAs 141.3.1 Additions to the C¼C Bond 141.3.1.1 Nucleophilic Additions 141.3.1.2 Radical Additions 151.3.1.3 Cycloadditions 171.3.1.3.1 [3þ2] Cycloadditions 18

Amino Acids, Peptides and Proteins in Organic Chemistry.Vol.2 – Modified Amino Acids, Organocatalysis and Enzymes. Edited by Andrew B. HughesCopyright � 2009 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 978-3-527-32098-1

V

1.3.1.3.2 [4þ2] Cycloadditions 191.3.1.4 Catalytic Hydrogenations 191.3.2 Halogenations of DDAAs 211.4 Conclusions 211.5 Experimental Procedures 221.5.1 General Procedure for the Two-Step Synthesis of Dehydroisoleucine

Derivatives 221.5.2 General Procedure for the Synthesis of a,b-Didehydroamino Acid Esters

by the Phosphorylglycine Ester Method using DBU 221.5.3 General Procedure for the Synthesis of a-Chloroglycine Derivatives 231.5.4 General Procedure for the Synthesis of Homomeric Dimers 231.5.5 General Procedure for the Synthesis of (Z)-g-Alkyl-a,

b-Didehydroglutamates from Imino Glycinates 241.5.6 Palladium-Catalyzed Trifold Heck Coupling 251.5.7 General Experimental Procedure for Conjugate Addition of Alkyl

iodides to Chiral a,b-Unsaturated Amino Acid Derivatives 251.5.8 Bromination of N-tert-Butyloxycarbonyldehydroamino Acids 26

References 26

2 Synthesis and Chemistry of a-Hydrazino Acids 35Joëlle Vidal

2.1 Introduction 352.1.1 a-Hydrazino Acids are Potent Inhibitors of Pyridoxal

Phosphate Enzymes 352.1.2 Natural Products Containing the N–N–C–C¼O Fragment 362.1.3 Synthetic Bioactive Products Containing the N–N–C–C¼O

Fragment 392.1.4 The CO–N–N–C–CO–NH Fragment is a Turn Inducer in

Pseudopeptides 402.2 Synthesis 412.2.1 Disconnection 1a: Reaction of Hydrazine Derivatives with

Carbon Electrophiles 412.2.1.1 Reaction of Hydrazine Derivatives with Enantiopure

a-Halogeno Acids 422.2.1.2 Reaction of Hydrazine Derivatives with Enantiopure Activated

a-Hydroxy Esters 422.2.1.3 Mitsunobu Reaction of Aminophthalimide Derivatives with

Enantiopure a-Hydroxy Esters 432.2.1.4 Reaction of Hydrazine Derivatives with Nonracemic Epoxides 432.2.1.5 Enantioselective Conjugate Addition of Hydrazines to

a,b-Unsaturated Imides 442.2.2 Disconnection 1b: Stereoselective Synthesis using

Azodicarboxylates 442.2.2.1 Stereoselective a-Hydrazination of Chiral Carbonyl Compounds

using Azodicarboxylates 45

VI Contents

2.2.2.2 Catalytic Enantioselective a-Hydrazination of Carbonyl Compoundsusing Azodicarboxylates 46

2.2.2.3 Stereoselective a-Hydrazination of Chiral a,b-UnsaturatedCarboxylates using Azodicarboxylates 50

2.2.3 Disconnection 2: Synthesis from Chiral Nonracemic a-AminoAcids 52

2.2.3.1 Schestakow Rearrangement of Hydantoic Acids Prepared froma-Amino Acids 52

2.2.3.2 Reduction of N-Nitroso-a-Amino Esters 522.2.3.3 Amination of a-Amino Acids by Hydroxylamine Derivatives 522.2.3.4 Amination of a-Amino Acids by Oxaziridines 532.2.4 Disconnections 3, 4, and 5: Syntheses from Hydrazones or

a-Diazoesters 552.2.4.1 Catalytic Enantioselective Hydrogenation of Hydrazones 562.2.4.2 Stereoselective and Catalytic Enantioselective

Strecker Reaction 562.2.4.3 Stereoselective Addition of Organometallic Reagents to

Hydrazones 572.2.4.4 Stereoselective or Catalytic Enantioselective Mannich-Type

Reaction with Hydrazones 582.2.4.5 Enantioselective Friedel–Crafts Alkylations with Hydrazones 592.2.4.6 Diastereoselective Zinc-Mediated Carbon Radical Addition

to Hydrazones 592.2.4.7 Catalytic Enantioselective Reaction of a-Diazoesters with Aldehydes

and Subsequent Stereoselective Reduction 592.2.5 Piperazic Acid and Derivatives by Cycloaddition Reactions 612.2.5.1 Diels–Alder Cycloaddition 612.2.5.2 1,3-Dipolar Cycloaddition 622.3 Chemistry 632.3.1 Cleavage of the N–N Bond 632.3.2 Reactivity of the Hydrazino Function 672.3.2.1 Reaction of Unprotected a-Hydrazino Acid Derivatives with

Acylating Reagents 672.3.2.2 Reaction of N1-Substituted a-Hydrazino Acid Derivatives with

Acylating Reagents 692.3.2.3 Reaction of N2-Protected a-Hydrazino Acid Derivatives with

Acylating Reagents 692.3.2.4 Reaction with Aldehydes and Ketones 692.3.3 Reactivity of the Carboxyl Function 732.3.4 Synthesis of Heterocycles 742.3.4.1 Cyclization Leading to Piperazic Acid Derivatives 742.3.4.2 Other Heterocycles 752.4 Conclusions 782.5 Experimental Procedures 792.5.1 (S)-2-hydrazinosuccinic Acid Monohydrate 79

Contents VII

2.5.2 (�)-(R)-N1,N2-dibenzyloxycarbonyl-2-hydrazino-2-phenyl PropionicAcid, Methyl Ester 80

2.5.3 (þ)-(R)-N1,N2-Bis(benzyloxycarbonyl)-1-hydrazino-2-oxocyclopentaneCarboxylic Acid, Ethyl Ester 81

2.5.4 (�)-L-N-Aminovaline 812.5.5 (þ)-L-N-benzyl-N-(tert-butoxycarbonylamino)tryptophan,

Hexylamine Salt 822.5.6 (R)-2-(N2-benzoylhydrazino)-2-(4-dimethylaminophenyl)

Acetonitrile 832.5.7 tert-Butoxycarbonylamino-(4-dimethylamino-2-methoxy-phenyl)-acetic

Acid Ethyl Ester by Reduction using SmI2 842.5.8 (R)-1,2-bis(benzyloxycarbonyl)piperazine-3-carboxylic Acid 84

References 86

3 Hydroxamic Acids: Chemistry, Bioactivity, and Solution-and Solid-Phase Synthesis 93Darren Griffith, Marc Devocelle, and Celine J. Marmion

3.1 Introduction 933.2 Chemistry, Bioactivity, and Clinical Utility 933.2.1 Chemistry 933.2.2 Bioactivity and Clinical Utility 953.2.2.1 Hydroxamic Acids as Siderophores 953.2.2.2 Hydroxamic Acids as Enzyme Inhibitors 973.2.2.2.1 MMP Inhibitors 983.2.2.2.2 HDAC Inhibitors 1023.2.2.2.3 PGHS Inhibitors 1043.3 Solution-Phase Synthesis of Hydroxamic Acids 1063.3.1 Synthesis of Hydroxamic Acids Derived from Carboxylic

Acid Derivatives 1063.3.1.1 From Esters 1073.3.1.2 From Acid Halides 1083.3.1.3 From Anhydrides 1093.3.1.4 From [1.3.5]Triazine-Coupled Carboxylic Acids 1103.3.1.5 From Carbodiimide-Coupled Carboxylic Acids 1113.3.1.6 From Acyloxyphosphonium Ions 1113.3.1.7 From Carboxylic Acids Coupled with other Agents 1133.3.2 Synthesis of Hydroxamic Acids from N-acyloxazolidinones 1143.3.3 Synthesis of Hydroxamic Acids from gem-Dicyanoepoxides 1153.3.4 Synthesis of Hydroxamic Acids from Aldehydes 1153.3.5 Synthesis of Hydroxamic Acids from Nitro Compounds 1163.3.6 Synthesis of Hydroxamic Acids via a Palladium-Catalyzed

Cascade Reaction 1163.3.7 Synthesis of N-Formylhydroxylamine (Formohydroxamic Acid) 1173.3.8 Synthesis of Reverse or Retro-Hydroxamates 1173.3.9 Synthesis of Acylhydroxamic Acids 120

VIII Contents

3.4 Solid-Phase Synthesis of Hydroxamic Acids 1213.4.1 Acidic Cleavage 1223.4.1.1 O-Tethered Hydroxylamine 1223.4.1.1.1 Cleavage with 30–90% TFA 1223.4.1.1.2 Super Acid-Sensitive Linkers 1243.4.1.2 N-Tethered Hydroxylamine 1263.4.1.3 Other Methods of Solid-Phase Synthesis of Hydroxamic Acids

based on an Acidic Cleavage 1263.4.2 Nucleophilic Cleavage 1283.4.2.1 Other Methods 1293.5 Conclusions 1303.6 Experimental Procedures 1303.6.1 Synthesis of 3-Pyridinehydroxamic Acid 1303.6.2 Synthesis of O-benzylbenzohydroxamic Acid 1313.6.3 Synthesis of N-methylbenzohydroxamic Acid 1313.6.4 Synthesis of Isobutyrohydroxamic Acid 1323.6.5 Synthesis of O-benzyl-2-phenylpropionohydroxamic Acid 1323.6.6 Synthesis of Methyl 3-(2-quinolinylmethoxy)benzeneacetohydroxamic

Acid 1333.6.7 Synthesis of the Chlamydocin Hydroxamic Acid Analog,

cyclo(L-Asu(NHOH)–Aib-L-Phe–D-Pro) 1333.6.8 Synthesis of O-benzyl-4-methoxybenzohydroxamic Acid 1343.6.9 Synthesis of O-benzylbenzohydroxamic acid 1343.6.10 Synthesis of a 4-chlorophenyl Substituted-a-bromohydroxamic

acid 1343.6.11 Synthesis of 4-Chlorobenzohydroxamic Acid 1353.6.12 Synthesis of Acetohydroxamic Acid 1353.6.13 Synthesis of N-hydroxy Lactam 1363.6.14 Synthesis of O-tert-butyl-N-formylhydroxylamine 1363.6.15 Synthesis of Triacetylsalicylhydroxamic Acid 137

References 137

4 Chemistry of a-Aminoboronic Acids and their Derivatives 145Valery M. Dembitsky and Morris Srebnik

4.1 Introduction 1454.2 Synthesis of a-Aminoboronic Acids 1464.3 Synthesis of a-Amidoboronic Acid Derivatives 1464.4 Asymmetric Synthesis via a-Haloalkylboronic Esters 1514.5 Synthesis of Glycine a-Aminoboronic Acids 1544.6 Synthesis of Proline a-Aminoboronic Acids 1554.7 Synthesis of Alanine a-Aminoboronic Acids 1624.8 Synthesis of Ornithine a-Aminoboronic Acids 1644.9 Synthesis of Arginine a-Aminoboronic Acids 1674.10 Synthesis of Phenethyl Peptide Boronic Acids 1704.11 Synthesis via Zirconocene Species 172

Contents IX

4.12 Synthesis and Activity of Amine-Carboxyboranes andtheir Derivatives 174

4.13 Synthesis of Boron Analogs of Phosphonoacetates 1794.14 Conclusions 183

References 183

5 Chemistry of Aminophosphonic Acids and Phosphonopeptides 189Valery P. Kukhar and Vadim D. Romanenko

5.1 Introduction 1895.2 Physical/Chemical Properties and Analysis 1915.3 Synthesis of a-Aminophosphonic Acids 1935.3.1 Amidoalkylation in the ‘‘Carbonyl Compound–Amine–Phosphite’’

Three-Component System 1935.3.2 Kabachnik–Fields Reaction 1955.3.3 Direct Hydrophosphonylation of C¼N Bonds 1995.3.4 Syntheses using C–N and C–C Bond-Forming Reactions 2065.4 Synthesis of b-Aminophosphonates 2125.5 Synthesis of g-Aminophosphonates and Higher Homologs 2195.6 Phosphono- and Phosphinopeptides 2275.6.1 General Strategies for the Phosphonopeptide Synthesis 2295.6.2 Peptides Containing P-terminal Aminophosphonate or

Aminophosphinate Moiety 2305.6.3 Peptides Containing an Aminophosphinic Acid Unit 2335.6.4 Peptides Containing a Phosphonamide or

Phosphinamide Bond 2365.6.5 Phosphonodepsipeptides Containing a Phosphonoester Moiety 2395.6.6 Peptides Containing a Phosphonic or Phosphinic Acid Moiety

in the Side-Chain 2405.7 Remarks on the Practical Utility of Aminophosphonates 2405.8 Conclusions 2455.9 Experimental Procedures 2465.9.1 Synthesis of N-Protected a-aminophosphinic Acid 10

(R1 ¼ EtOCOCH2, R2 ¼ Me) 246

5.9.2 Synthesis of Phosphonomethylaminocyclopentane-1-carboxylicAcid (17) 246

5.9.3 General Procedure for Catalytic Asymmetric Hydrophosphonylation.Synthesis of a-Aminophosphonate 39 (R1 ¼ C5H11, R

2 ¼ Ph2CH) 2475.9.4 General Procedure of the Asymmetric Aminohydroxylation

Reaction: Synthesis of b-Amino-a-hydroxyphosphonates 87 2475.9.5 Dimethyl (S,S)-(�)3-N,N-bis(a-Methylbenzyl) amino-2-

oxopropylphosphonate (S,S)-100 and Dimethyl 3-[(S,S)-N,N-bis(a-methylbenzylamino)-(2R)-hydroxypropylphosphonate(R,S,S)-101 248

5.9.6 General Procedure for the Preparation of Dialkyl Phenyl(4-pyridylcarbonylamino) methyl-phosphonates 126 249

X Contents

5.9.7 Synthesis of 1-[(Benzyloxy) carbonyl] prolyl-N1-{[1,10-biphenyl-4-yl-methyl)(methoxy) phosphoryl] methyl}leucinamide (159a) 249References 249

6 Chemistry of Silicon-Containing Amino Acids 261Yingmei Qi and Scott McN. Sieburth

6.1 Introduction 2616.1.1 Stability of Organosilanes 2616.1.2 Sterics and Electronics 2626.2 Synthesis of Silicon-Containing Amino Acids 2636.2.1 Synthesis of a-Silyl Amino Acids and Derivatives 2636.2.2 Synthesis of b-Silylalanine and Derivatives 2636.2.3 Synthesis of o-Silyl Amino Acids and Derivatives 2676.2.4 Synthesis of Silyl-Substituted Phenylalanines 2696.2.5 Synthesis of Amino Acids with Silicon a to Nitrogen 2696.2.6 Synthesis of Proline Analogs with Silicon in the Ring 2696.3 Reactions of Silicon-Containing Amino Acids 2716.3.1 Stability of the Si–C Bond 2726.3.2 Functional Group Protection 2726.3.3 Functional Group Deprotection 2726.4 Bioactive Peptides Incorporating Silicon-Substituted Amino Acids 2726.4.1 Use of b-Silylalanine 2726.4.2 Use of N-Silylalkyl Amino Acids 2746.4.3 Use of Silaproline 2746.5 Conclusions 2756.6 Experimental Procedures 2766.6.1 L-b-Trimethylsilylalanine 23 2766.6.2 (�)-b-Trimethylsilylalanine 23 2766.6.3 L-b-Trimethylsilylalanine 23 2776.6.4 (�)-p-Trimethylsilylphenylalanine 60 2776.6.5 L-4-Dimethylsilaproline 100 278

References 278

Part Two Amino Acid Organocatalysis 281

7 Catalysis of Reactions by Amino Acids 283Haibo Xie, Thomas Hayes, and Nicholas Gathergood

7.1 Introduction 2837.2 Aldol Reaction 2857.2.1 Intramolecular Aldol Reaction and Mechanisms 2857.2.1.1 Intramolecular Aldol Reaction 2857.2.1.2 Mechanisms 2877.2.2 Intermolecular Aldol Reaction and Mechanisms 2897.2.2.1 Intermolecular Aldol Reaction 289

Contents XI

7.2.2.2 Mechanisms 2927.2.3 Carbohydrate Synthesis 2947.2.3.1 Carbohydrate Synthesis 2947.2.3.2 Synthesis of Amino Sugars 2977.3 Mannich Reaction 2987.3.1 a-Aminomethylation 2987.3.2 Direct Mannich Reaction 2987.3.3 Indirect Mannich Reaction using Ketone Donors 3037.3.4 anti-Mannich Reactions 3037.4 a-Amination Reaction 3067.5 Michael Reaction 3087.5.1 Mechanism for Iminium Ion-Catalyzed Michael Reaction 3097.5.1.1 Iminium Ion-Catalyzed Intermolecular Michael Reactions 3097.5.2 Mechanism for the Enamine-Catalyzed Michael Reaction 3137.5.2.1 Enamine-Catalyzed Intramolecular Michael Reactions 3137.5.2.2 Enamine-Catalyzed Intermolecular Michael Reactions 3137.6 Morita–Baylis–Hillman Reaction and Its Aza-Counterpart 3197.6.1 Morita–Baylis–Hillman Reactions 3197.6.2 Aza-Morita–Baylis–Hillman Reactions 3207.7 Miscellaneous Amino Acid-Catalyzed Reactions 3217.7.1 Diels–Alder Reaction 3227.7.2 Knoevenagel Condensation 3227.7.3 Reduction and Oxidation 3237.7.4 Rosenmund–von Braun Reaction 3267.7.5 Activation of Epoxides 3267.7.6 a-Fluorination of Aldehydes and Ketones 3277.7.7 SN2 Alkylation 3287.8 Sustainability of Amino Acid Catalysis 3287.8.1 Toxicity and Ecotoxicity of Amino Acid Catalysis 3287.8.2 Amino Acid Catalysis and Green Chemistry 3297.9 Conclusions and Expectations 3307.10 Typical Procedures for Preferred Catalysis of Reactions

by Amino Acids 330References 333

Part Three Enzymes 339

8 Proteases as Powerful Catalysts for Organic Synthesis 341Andrés Illanes, Fanny Guzmán, and Sonia Barberis

8.1 Enzyme Biocatalysis 3418.2 Proteolytic Enzymes: Mechanisms and Characteristics 3458.3 Proteases as Process Catalysts 3488.4 Proteases in Organic Synthesis 350

XII Contents

8.5 Peptide Synthesis 3508.5.1 Chemical Synthesis of Peptides 3518.5.2 Enzymatic Synthesis of Peptides 3548.6 Conclusions 360

References 361

9 Semisynthetic Enzymes 379Usama M. Hegazy and Bengt Mannervik

9.1 Usefulness of Semisynthetic Enzymes 3799.2 Natural Protein Biosynthesis 3809.3 Sense Codon Reassignment 3819.4 Missense Suppression 3859.5 Evolving the Orthogonal aaRS/tRNA Pair 3879.6 Nonsense Suppression 3909.7 Mischarging of tRNA by Ribozyme 3959.8 Evolving the Orthogonal Ribosome/mRNA Pair 3969.9 Frame-Shift Suppression 3979.10 Noncanonical Base Pairs 3999.11 Chemical Ligation 4019.12 Inteins 4049.13 EPL 4109.14 Post-Translational Chemical Modification 4119.15 Examples of Semisynthetic Enzymes 4159.16 Conclusions 419

References 419

10 Catalysis by Peptide-Based Enzyme Models 433Giovanna Ghirlanda, Leonard J. Prins, and Paolo Scrimin

10.1 Introduction 43310.2 Peptide Models of Hydrolytic Enzymes 43410.2.1 Ester Hydrolysis and Acylation 43410.2.1.1 Catalytically Active Peptide Foldamers 43510.2.1.2 Self-Organizing Catalytic Peptide Units 43810.2.1.3 Multivalent Catalysts 44010.2.2 Cleavage of the Phosphate Bond 44410.2.2.1 DNA and DNA Models as Substrates 44610.2.2.2 RNA and RNA Models as Substrates 45010.3 Peptide Models of Heme Proteins 45610.3.1 Heme Proteins 45710.3.1.1 Early Heme-Peptide Models: Porphyrin as Template 45710.3.1.2 Bishistidine-Coordinated Models 45810.3.1.2.1 Water-Soluble Models: Heme Sandwich 45810.3.1.2.2 Water-Soluble Models: Four-Helix Bundles 46010.3.1.2.3 Membrane-Soluble Heme-Binding Systems 462

Contents XIII

10.3.2 Diiron Model Proteins: the Due-Ferri Family 46410.4 Conclusions 467

References 467

11 Substrate Recognition 473Keith Brocklehurst, Sheraz Gul, and Richard W. Pickersgill

11.1 Recognition, Specificity, Catalysis, Inhibition, and Linguistics 47311.2 Serine Proteinases 47611.3 Cysteine Proteinases 48011.4 Glycoside Hydrolases 48511.5 Protein Kinases 48811.6 aaRSs 49011.7 Lipases 49211.8 Conclusions 493

References 494

12 Protein Recognition 505Robyn E. Mansfield, Arwen J. Cross, Jacqueline M. Matthews,and Joel P. Mackay

12.1 General Introduction 50512.2 Nature of Protein Interfaces 50612.2.1 General Characteristics of Binding Sites 50612.2.2 Modularity and Promiscuity in Protein Interactions 50712.2.3 Hotspots at Interfaces 50812.3 Affinity of Protein Interactions 50912.3.1 Introduction 50912.3.2 ‘‘Irreversible’’ Interactions 51012.3.3 Regulatory Interactions 51012.3.4 Ultra-Weak Interactions 51112.4 Measuring Protein Interactions 51212.4.1 Introduction 51212.4.2 Discovering/Establishing Protein Interactions 51212.4.3 Determining Interaction Stoichiometry 51312.4.4 Measuring Affinities 51412.4.5 Modulation of Binding Affinity 51512.5 Coupled Folding and Binding 51512.5.1 Introduction 51512.5.2 Characteristics of Intrinsically Unstructured Proteins 51612.5.3 Advantages of Disorder for Protein Recognition 51612.5.4 Diversity in Coupled Folding and Binding 51812.6 Regulation of Interactions by PTMs 51912.6.1 Introduction 51912.6.2 Types of PTMs 51912.6.3 A Case Study – Histone Modifications 52012.7 Engineering and Inhibiting Protein–Protein Interactions 521

XIV Contents

12.7.1 Introduction 52112.7.2 Engineering Proteins with a Specific Binding Functionality 52112.7.3 Optimizing Protein Interactions 52312.7.4 Engineering DNA-Binding Proteins 52312.7.5 Searching for Small-Molecule Inhibitors of Protein Interactions 52412.7.6 Flexibility and Allosteric Inhibitors 52612.8 Conclusions 527

References 527

13 Mammalian Peptide Hormones: Biosynthesis and Inhibition 533Karen Brand and Annette G. Beck-Sickinger

13.1 Introduction 53313.2 Mammalian Peptide Hormones 53413.3 Biosynthesis of Peptide Hormones 53513.3.1 Production and Maturation of Prohormones before Entering the

Secretory Pathway 53513.3.2 Secretory Pathways 54013.3.3 Prohormone Cleavage 54213.3.3.1 Basic Amino Acid-Specific Members of the Proprotein

Convertase Family 54813.3.3.2 Different Biologically Active Peptides from one Precursor 55113.3.3.3 Nomenclature at the Cleavage Site 55113.3.3.4 Prediction of Cleavage Sites –Discovery of New Bioactive Peptides 55213.3.4 Further PTMs 55213.3.4.1 Removal of Basic Amino Acids 55213.3.4.2 C-Terminal Amidation 55313.3.4.3 Acylation 55413.3.4.4 Pyroglutamylation 55413.3.4.5 N-Terminal Truncation 55413.4 Inhibition of Biosynthesis 55513.4.1 Readout Systems to Investigate Cleavage by Proteases 55513.4.2 Rational Design of Inhibitors of the Angiotensin-Converting

Enzyme 55713.4.3 Proprotein Convertase Inhibitors 56113.4.3.1 Endogenous Protein Inhibitors and Derived Inhibitors 56213.4.3.2 Peptide Inhibitors 56313.4.3.3 Peptide-Derived Inhibitors 56313.4.3.4 Are there Conformational Requirements for Substrates? 56413.5 Conclusions 565

References 565

14 Insect Peptide Hormones 575R. Elwyn Isaac and Neil Audsley

14.1 Introduction 57514.2 Structure and Biosynthesis of Insect Peptide Hormones 576

Contents XV

14.3 Proctolin 57814.4 Sex Peptide 58014.5 A-Type Allatostatins 58214.6 CRF-Related Diuretic Hormones (DH) 58414.7 Insect Peptide Hormones and Insect Control 58614.8 Conclusions 589

References 590

15 Plant Peptide Signals 597Javier Narváez-Vásquez, Martha L. Orozco-Cárdenas, and Gregory Pearce

15.1 Introduction 59715.2 Defense-Related Peptides 59915.2.1 Systemin 59915.2.2 Hydroxyproline-Rich Systemin Glycopeptides 60315.2.3 Arabidopsis AtPep1-Related Peptides 60415.3 Peptides Involved in Growth and Development 60515.3.1 CLAVATA3 and the CLE Peptide Family 60515.3.1.1 CLAVATA3 (CLV3) 60515.3.1.2 CLV3-Related Peptides 60715.3.2 Rapid Alkalinization Factor Peptides 60915.3.3 Rotundifolia4 and Devil1 61015.3.4 C-Terminally Encoded Peptide 1 61115.3.5 Tyrosine-Sulfated Peptides 61115.3.5.1 Phytosulfokine 61115.3.5.2 Plant Peptides Containing Sulfated Tyrosine 1 61315.3.6 Polaris 61315.3.7 Inflorescence Deficient in Abscission 61415.3.7.1 4-kDa Peptide 61515.4 Peptides Involved in Self-Recognition 61515.4.1 S-Locus Cysteine Rich Peptides 61515.5 Methods in Plant Regulatory Peptide Research 61615.5.1 Discovery of Systemin 61715.5.2 Identification of Novel Peptide Signals using the Cell

Alkalinization Assay 61815.5.3 Isolation of Tyrosine-Sulfated Peptides 62115.5.4 Use of Peptidomics 62215.5.5 Fishing Ligands with Bait Receptors 62215.6 Conclusions 623

References 624

16 Nonribosomal Peptide Synthesis 631Sean Doyle

16.1 Introduction 63116.2 NRPs 63216.3 NRP Synthetase Domains 635

XVI Contents

16.3.1 Adenylation Domains 63516.3.2 Thiolation Domains 63816.3.3 Condensation Domains 63816.4 PPTases 63916.4.1 40PPTase Activity Determination 64016.5 Experimental Strategies for NRPS Investigations 64216.5.1 Degenerate PCR 64516.5.2 Determination of Adenylation Domain Specificity 64716.5.2.1 Protein MS 64716.5.2.2 Identification of NRP Synthetase Adenylation

Domain Specificity (Strategy I) 64816.5.2.3 Identification of NRP Synthetase Adenylation

Domain Specificity (Strategy II) 64916.6 Non-NRPS 64916.7 Conclusions 650

References 650

Index 657

Contents XVII

List of Contributors

XIX

Amino Acids, Peptides and Proteins in Organic Chemistry.Vol.2 – Modified Amino Acids, Organocatalysis and Enzymes. Edited by Andrew B. HughesCopyright � 2009 WILEY-VCH Verlag GmbH & Co. KGaA, WeinheimISBN: 978-3-527-32098-1

Neil AudsleyThe Food and EnvironmentResearch AgencySand HuttonYork YO41 1LZUK

Sonia BarberisUniversidad Nacional de San Luis,Chacabuco y PederneraFaculty of Chemistry, Biochemistry andPharmacySan LuisArgentina

Annette G. Beck-SickingerLeipzig UniversityInstitute of BiochemistryBrüderstraße 3404103 LeipzigGermany

Karen BrandLeipzig UniversityInstitute of BiochemistryBrüderstraße 3404103 LeipzigGermany

Keith BrocklehurstQueen Mary, University of LondonSchool of Biological and ChemicalSciencesFogg Building, Mile End RoadLondon E1 4NSUK

Arwen J. CrossUniversity of SydneySchool of Molecular and MicrobialBiosciencesG08 Biochemistry BuildingNSW 2006SydneyAustralia

Valery M. DembitskyThe Hebrew University of JerusalemSchool of PharmacyDepartment of Medicinal Chemistryand Natural ProductsPO Box 12065Jerusalem 91120Israel

Marc DevocelleRoyal College of Surgeons in IrelandCentre for Synthesis & ChemicalBiologyDepartment of Pharmaceutical &Medicinal Chemistry123 St. Stephens GreenDublin 2Ireland

Sean DoyleNational University of IrelandMaynoothDepartment of BiologyMaynooth, Co. KildareIreland

Nicholas GathergoodDublin City UniversitySchool of Chemical Sciences andNational Institute for CellularBiotechnologyGlasnevin, Dublin 9Ireland

Giovanna GhirlandaArizona State UniversityDepartment of Chemistry andBiochemistryTempe, AZ 85287-1604USA

Darren GriffithRoyal College of Surgeons in IrelandCentre for Synthesis & ChemicalBiologyDepartment of Pharmaceutical &Medicinal Chemistry123 St. Stephens GreenDublin 2Ireland

Sheraz GulEuropean ScreeningPort GmbHSchnackenburgallee 11422525 HamburgGermany

Fanny GuzmánPontificia Universidad Católica deValparaísoInstitute of BiologyAvenida Brasil 2950ValparaísoChile

R. Elwyn IsaacUniversity of LeedsInstitute of Integrative and ComparativeBiologyFaculty of Biological SciencesLeeds LS2 9JTUK

Thomas HayesDublin City UniversitySchool of Chemical Sciences andNational Institute for CellularBiotechnologyGlasnevinDublin 9Ireland

Usama M. HegazyUppsala UniversityBiomedical CenterDepartment of Biochemistry andOrganic ChemistryBox 576751 23 UppsalaSweden

XX List of Contributors

Andrés IllanesPontificia Universidad Católica deValparaísoSchool of Biochemical EngineeringAvenida Brasil 2147ValparaísoChile

Uli KazmaierUniversität des SaarlandesInstitut für Organische ChemieIm Stadtwald66123 SaarbrückenGermany

Valery P. KukharNational Academy of Sciences ofUkraineInstitute of Bioorganic Chemistry andPetrochemistryMurmanskaya StreetKiev 94Ukraine

Joel P. MackayUniversity of SydneySchool of Molecular and MicrobialBiosciencesG08 Biochemistry BuildingNSW 2006SydneyAustralia

Robyn E. MansfieldUniversity of SydneySchool of Molecular and MicrobialBiosciencesG08 Biochemistry BuildingNSW 2006SydneyAustralia

Bengt MannervikUppsala UniversityBiomedical CenterDepartment of Biochemistry andOrganic ChemistryBox 576751 23 UppsalaSweden

Celine J. MarmionRoyal College of Surgeons in IrelandCentre for Synthesis and ChemicalBiologyDepartment of Pharmaceutical andMedicinal Chemistry123 St. Stephens GreenDublin 2Ireland

Jacqueline M. MatthewsUniversity of SydneySchool of Molecular and MicrobialBiosciencesG08 Biochemistry BuildingNSW 2006SydneyAustralia

Javier Narváez-VásquezUniversity of California RiversideDepartment of Botany and PlantSciences3401 Watkins Dr.Riverside, CA 92521USA

Martha L. Orozco-CárdenasUniversity of California RiversideDepartment of Botany and PlantSciences3401 Watkins Dr.Riverside, CA 92521USA

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and

University of California RiversidePlant Transformation Research CenterRiverside, CA 92521USA

Gregory PearceWashington State UniversityInstitute of Biological ChemistryPullman, WA 99164USA

Richard W. PickersgillQueen Mary, University of LondonSchool of Biological and ChemicalSciencesJoseph Priestley BuildingMile End RoadLondon E1 4NSUK

Leonard J. PrinsUniversity of PadovaPadova SectionDepartment of Chemical Sciences andITM-CNRVia Marzolo 135131 PadovaItaly

Yingmei QiTemple UniversityDepartment of Chemistry1901 N. 13th StreetPhiladelphia, PA 19122USA

Vadim D. RomanenkoNational Academy of Sciences ofUkraineInstitute of Bioorganic Chemistry andPetrochemistryMurmanskaya StreetKiev 94Ukraine

Paolo ScriminUniversity of PadovaPadova SectionDepartment of Chemical Sciences andITM-CNRVia Marzolo 135131 PadovaItaly

Scott McN. SieburthTemple UniversityDepartment of Chemistry1901 N. 13th StreetPhiladelphia, PA 19122USA

Morris SrebnikThe Hebrew University of JerusalemSchool of PharmacyDepartment of Medicinal Chemistryand Natural ProductsPO Box 12065Jerusalem 91120Israel

Joëlle VidalUniversité de Rennes 1CNRS UMR 6510, Chimie etPhotonique MoléculairesCampus de Beaulieu, case 101235042 Rennes CedexFrance

Haibo XieDublin City UniversitySchool of Chemical Sciences andNational Institute for CellularBiotechnologyGlasnevin, Dublin 9Ireland

XXII List of Contributors