Practical Medicinal Chemistry with Macrocycles E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 1391

Veröffentlichungsjahr: 2017

Beschreibung

Including case studies of macrocyclic marketed drugs and macrocycles in drug development, this book helps medicinal chemists deal with the synthetic and conceptual challenges of macrocycles in drug discovery efforts. * Provides needed background to build a program in macrocycle drug discovery -design criteria, macrocycle profiles, applications, and limitations * Features chapters contributed from leading international figures involved in macrocyclic drug discovery efforts * Covers design criteria, typical profile of current macrocycles, applications, and limitations

Leseprobe

Table of Contents

Cover

Title Page

Foreword

Introduction

About the Contributors

Part I: Challenges Specific to Macrocycles

1 Contemporary Macrocyclization Technologies

1.1 Introduction

1.2 Challenges Inherent to the Synthesis of Macrocycles

1.3 Challenges in Macrocycle Characterization

1.4 Macrocyclization Methods

1.5 Cyclization on the Solid Phase

1.6 Summary

References

2 A Practical Guide to Structural Aspects of Macrocycles (NMR, X‐Ray, and Modeling)

2.1 Background

2.2 Experimental Studies of Macrocycles

2.3 Molecular Modeling of Macrocyclic Peptides

2.4 Summary

Acknowledgments

References

3 Designing Orally Bioavailable Peptide and Peptoid Macrocycles

3.1 Introduction

3.2 Improving Peptide Plasma Half‐Life

3.3 Absorption, Bioavailability, and Methods for Predicting Absorption

3.4

In Silico

Modeling

3.5 Future Directions

References

Part II: Classes of Macrocycles and Their Potential for Drug Discovery

4 Natural and Nature‐Inspired Macrocycles

4.1 Introduction to Natural Macrocycles as Drugs and Drug Leads

4.2 Biosynthetic Pathways, Natural Role, and Biotechnological Access

4.3 QSAR and Chemoinformatic Analyses of Common Features

4.4 Case Studies: Selected Natural Macrocycles of Special Relevance in Medicinal Chemistry

References

5 Bioactive and Membrane-Permeable Cyclic Peptide Natural Products

5.1 Introduction

5.2 Structural Motifs and Permeability of Cyclic Peptide Natural Products

5.3 Conformations of Passively Permeable Bioactive Cyclic Peptide Natural Products

5.4 Recently Discovered Bioactive Cyclic Peptide Natural Products

5.5 Conclusions

References

6 Chemical Approaches to Macrocycle Libraries

6.1 Introduction

6.2 Challenges Associated with Macrocyclic One‐Bead‐One‐Compound Libraries

6.3 Deconvolution of Macrocyclic Libraries

6.4 Peptide‐Encoded Macrocyclic Libraries

6.5 DNA‐Encoded Macrocyclic Libraries

6.6 Parallel Synthesis of Macrocyclic Libraries

6.7 Diversity‐Oriented Synthesis

6.8 Perspective

6.9 Conclusion

References

7 Biological and Hybrid Biological/Chemical Strategies in Diversity Generation of Peptidic Macrocycles

7.1 Introduction

7.2 Cyclic Peptide Libraries on Phage Particles

7.3 Macrocyclic Peptide Libraries via

In Vitro

Translation

7.4 Emerging Strategies for the Combinatorial Synthesis of Hybrid Macrocycles

In Vitro

and in Cells

7.5 Comparative Analysis of Technologies

7.6 Conclusions

References

8 Macrocycles for Protein–Protein Interactions

8.1 Introduction

8.2 Library Approaches to Macrocyclic PPI Inhibitors

8.3 Structural Mimicry

8.4 Multi‐Cycles for PPIs

8.5 The Future for Targeting PPIs with Macrocycles

References

Part III: The Synthetic Toolbox for Macrocycles

9 Synthetic Strategies for Macrocyclic Peptides

9.1 Introduction to Peptide Macrocyclization

9.2 One Size Does Not Fit All: Factors to Consider During Synthesis Design

9.3 Peptide Macrocyclization in Solution

9.4 Peptide Macrocyclization on Solid Support

9.5 Peptide Macrocyclization by Disulfide Bond Formation

9.6 Conclusion

References

10 Ring‐Closing Metathesis‐Based Methods in Chemical Biology

10.1 Introduction

10.2 Protein–Protein Interactions: Challenges and Opportunities

10.3 Natural Products as Modulators of Protein–Protein Interactions

10.4 Introduction to Ring‐Closing Metathesis

10.5 Selected Examples of Synthetic Macrocyclic Probes Using RCM‐Based Approaches

10.6 Summary

References

11 The Synthesis of Peptide‐Based Macrocycles by Huisgen Cycloaddition

11.1 Introduction

11.2 Dipolar Cycloaddition Reactions

11.3 Macrocyclic Peptidomimetics

11.4 Macrocyclic β‐Strand Mimetics as Cysteine Protease Inhibitors

11.5 Conclusion

References

12 Palladium‐Catalyzed Synthesis of Macrocycles

12.1 Introduction

12.2 Stille Reaction

12.3 Suzuki–Miyaura Reaction

12.4 Heck Reaction

12.5 Sonogashira Reaction

12.6 Tsuji–Trost Reaction

12.7 Other Reactions

12.8 Conclusion

References

13 Alternative Strategies for the Construction of Macrocycles

13.1 Introduction

13.2 Alternative Methods for Macrocyclization Involving Carbon–Carbon Bond Formation

13.3 Alternative Methods for Macrocyclization Involving Carbon–Carbon Bond Formation: Ring Expansion and Photochemical Methods

13.4 Alternative Methods for Macrocyclization Involving Carbon–Oxygen Bond Formation

13.5 Alternative Methods for Macrocyclization Involving Carbon–Nitrogen Bond Formation

13.6 Alternative Methods for Macrocyclization Involving Carbon–Sulfur Bond Formation

13.7 Conclusion and Summary

References

14 Macrocycles from Multicomponent Reactions

14.1 Introduction

14.2 General Aspects of Multicomponent Reactions (MCRs) in Macrocycle Syntheses

14.3 Concluding Remarks and Future Perspectives

References

15 Synthetic Approaches Used in the Scale‐Up of Macrocyclic Clinical Candidates

15.1 Introduction

15.2 Background

15.3 Literature Examples

15.4 Conclusions

References

Part IV: Macrocycles in Drug Development

16 Overview of Macrocycles in Clinical Development and Clinically Used

16.1 Introduction

16.2 Datasets Generation

16.3 Marketed Macrocyclic Drugs

16.4 Macrocycles in Clinical Studies

16.5

De Novo

Designed Macrocycles

16.6 Overview and Conclusions

Appendix 16.A

References

17 The Discovery of Macrocyclic IAP Inhibitors for the Treatment of Cancer

17.1 Introduction

17.2 DNA‐Programmed Chemistry Macrocycle Libraries

17.3 A New Macrocycle Ring Structure

17.4 Design and Profiling of Bivalent Macrocycles

17.5 Improving the Profile of the Bivalent Macrocycles

17.6 Selection of the Optimal Bivalent Macrocyclic IAP Antagonist

17.7 Summary

Acknowledgments

References

18 Discovery and Pharmacokinetic–Pharmacodynamic Evaluation of an Orally Available Novel Macrocyclic Inhibitor of Anaplastic Lymphoma Kinase and c‐Ros Oncogene 1

18.1 Introduction

18.2 Discovery and Synthesis

18.3 Evaluation of Pharmacokinetic Properties Including CNS Penetration

18.4 Evaluation of Pharmacokinetic–Pharmacodynamic (PKPD) Profiles

18.5 Conclusion

References

19 Optimization of a Macrocyclic Ghrelin Receptor Agonist (Part II)

19.1 Introduction

19.2 Advanced AA

3

and Tether SAR

19.3 Structural Studies

19.4 Conclusions

Acknowledgments

References

20 Solithromycin

20.1 Introduction

20.2 Structure–Activity Relationship (SAR) of Ketolides and Selection of Solithromycin

20.3 Mechanism of Action

20.4 Overcoming the Ketek Effect

20.5 Manufacture of Solithromycin

20.6 Polymorphism

20.7 Pharmaceutical Development

20.8 Clinical Data

20.9 Summary

References

Index

End User License Agreement

List of Tables

Chapter 01

Table 1.1 Common structural analysis techniques and their applications to macrocycles.

Chapter 02

Table 2.1 Selected classes of macrocyclic peptides with their sizes and structural features of representative examples.

Table 2.2 Online and stand‐alone tools helping generate topologies and force field parameters for nonstandard amino acids.

Chapter 04

Table 4.1 Extract of calculated descriptors of registered drugs.

Chapter 06

Table 6.1 Comparison of chemical approaches to macrocycle libraries.

Chapter 07

Table 7.1 Representative examples of disulfide‐bridged peptides isolated by M13 phage display against the indicated targets.

Table 7.2 Macrocyclic peptides isolated through the different cyclization and library screening strategies discussed in the text.

Chapter 08

Table 8.1 Sequences of Lead 1 and 2 and novel grafted cyclic β‐sheet peptides.

Chapter 09

Table 9.1 Linkers and resins used for side chain anchoring in the solid‐phase macrocyclization strategy.

Table 9.2 Side chain anchoring strategies for peptide cyclization.

Table 9.3 Conditions for disulfide bond formation in solution with solid‐supported oxidizing agents.

Table 9.4 Commonly used cysteine thiol protecting groups for disulfide bond formation on solid support.

Chapter 14

Table 14.1 Effect of macrocyclization on the biological activity of linear molecules.

Table 14.2 Number of library members available for the two diacid/diisocyanide combinations in bidirectional Ugi‐MiBs, excluding higher cyclic oligomers.

Chapter 15

Table 15.1 List of macrocyclic drugs launched between 1960 and 2015.

Chapter 16

Table A.16.1 Registered macrocyclic‐based drugs as of January 25, 2017.

Table A.16.2 Macrocyclic‐based compounds in clinical development as of January 25, 2017.

Table 16.1 Calculated physicochemical properties for oral small molecule drugs, different classes of registered macrocycle drugs, and macrocycles in clinical development.

Table 16.2 Macrocyclic drugs of the glycopeptide subclass.

Table 16.3 Pharmacokinetic parameters of glycopeptide macrocycles.

Table 16.4 Macrocyclic drugs of the ascomycin subclass.

Table 16.5 Macrocyclic drugs of the ansamycin subclass.

Table 16.6 Macrocyclic drugs of the rapamycin subclass.

Table 16.7 Macrocyclic drugs of the lactam bridge cyclic peptide subclass.

Table 16.8 Orally administered CsA analogues in clinical development.

Table 16.9 Macrocycles in the

Clostridium difficile

drug pipeline.

Table 16.10 Macrolides and ansamycins in clinical development.

Table 16.11 Macrocyclic NS3/4a and NS5B inhibitors in clinical development.

Table 16.12 Macrocyclic kinase inhibitors in clinical development.

Chapter 17

Table 17.1 Binding affinities (IC

50

values) of P2–P5‐linked macrocyclic compounds for XIAP BIR2 and BIR3.

Table 17.2 Chemical structures of P3–P5 linked macrocyclic compounds and their competitive binding affinities (IC

50

values) for XIAP BIR2 and BIR3 domains and cIAP‐1 BIR3 domain and activity in a cell‐free caspase‐3 rescue assay.

Table 17.3 Chemical structures of P3–P5 linked symmetric dimeric macrocyclic compounds and binding affinities (IC

50

values) for XIAP BIR2, BIR3 domains, and cIAP‐1 BIR3 domain.

Table 17.4 Activity of key compounds in caspase‐3 rescue and antiproliferative assays.

Table 17.5 Biological activities of P3–P5 linked asymmetric dimeric IAP antagonists.

Table 17.6 Pharmacokinetic parameters of dimeric macrocyclic compounds in mice following a 1 mg/kg i.v. dose.

Table 17.7 Biological activities of dimeric IAP antagonists.

Table 17.8 Summary of IAP biological data and ADME properties for compound

33

.

Chapter 18

Table 18.1 Potency and

in vitro

ADME properties of crizotinib (

1

).

Table 18.2 Potency and efficiency of crizotinib in ALK‐L1196M.

Table 18.3 Potency and

in vitro

ADME properties of PF‐06439015.

Table 18.4 Acyclic ALK inhibitors—potency, efficiency, and

in vitro

ADME.

Table 18.5 Early macrocyclic ALK inhibitors—potency, efficiency, and

in vitro

ADME.

Table 18.6 Amide macrocyclic ALK inhibitors—potency, efficiency, and

in vitro

ADME.

Table 18.7 Potency, ADME, and selectivity of macrocyclic analogues.

Table 18.8 PK parameters of

PF‐06463922

in rats and dogs.

Chapter 19

Table 19.1 PK–ADME and CYP 3A4 impact of

D

‐Tyr and

D

‐Leu at the AA

3

position together with initial tether variations.

Table 19.2 Additional tether SAR explorations: Reduction of aromatic content and additional conformational constraints through methyl substitution.

Table 19.3 Amide torsion angles in the X‐ray structure of TZP‐102 salt.

Chapter 20

Table 20.1 MIC data of clarithromycin analogues.

Table 20.2 MIC data of ketolides.

Table 20.3 Comparison of MIC data of ketolides and fluoroketolides.

Table 20.4 Mouse pharmacokinetics of compound

20

.

List of Illustrations

Chapter 01

Figure 1.1 Macrocycles are at the intersection of small molecules and biological drugs chemical space.

Figure 1.2 Lokey’s conformational hypothesis for passive membrane permeability of peptide macrocycles.

Scheme 1.1 Carboxylic acid activation disfavors the cyclization‐conducive conformation

3

.

Figure 1.3 The site of retrosynthetic ring disconnection can greatly affect the yield and selectivity of the forward process.

Scheme 1.2 Carboxylic acid side‐reaction pathways by way of oxazolone intermediate (a), ketene formation (b), and Curtius rearrangement of acyl azides (c).

Scheme 1.3 Cyclol formation in a peptide macrocyclization can lead to DKP formation.

Figure 1.4 Selective solubility of the activating agent by‐product simplifies isolation.

Scheme 1.4 T3P

®

proves successful in a difficult macrocyclization to cycloaspeptide E (

24

).

Scheme 1.5 Linearization of peptides by cyanogen bromide at methionine residues (a) and selective hydrolysis of weak aziridine amides (b).

Figure 1.5 QM calculations enable high predictability of macrocyclic NMR chemical shifts.

Figure 1.6 Site selection and chemistry both affect the macrocyclization efficiency toward Riccardin C.

Scheme 1.6 Macrolactonization by acid or alcohol activation.

Figure 1.7 Common carboxylate activation agents for macrolactonization.

Scheme 1.7 Configuration‐dependent mechanistic switching in the Mitsunobu reaction toward

27

, a derivative of peloruside A.

Scheme 1.8 Peptide cyclization by NCL and desulfurization to effectively ligate at an alanine residue.

Scheme 1.9 Peptide cyclization by traceless Staudinger ligation.

Scheme 1.10 Cysteine‐based macrocyclization technique for peptides.

Scheme 1.11 Macrocyclization of biosynthetic peptides with non‐proteinogenic amino acids.

Scheme 1.12 In flow CuAAC‐mediated macrocyclization and subsequent diversification by palladium‐catalyzed cross‐coupling.

Scheme 1.13 Macrocyclization by C─C bond formation with the Stille coupling (a), Diels–Alder reaction (b), and Ni‐catalyzed reductive coupling (c).

Scheme 1.14 “Self‐editing” in RCM to produce a single rearranged thermodynamic product.

Scheme 1.15 Stabilized alpha‐helical peptide derived from stapled peptides by RCM.

Scheme 1.16 Macrocyclization by Ugi MCR.

Scheme 1.17 Multiple multicomponent macrocyclizations (MiBs).

Scheme 1.18 Macrocyclization by the disrupted Ugi MCR with aziridine aldehyde dimers, peptides, and isocyanides.

Scheme 1.19 Late‐stage functionalization for peptide conjugates by aziridine ring opening.

Scheme 1.20 Immobilized coupling reagents for amide bond formation.

Scheme 1.21 Macrocyclization by the disrupted Ugi MCR on solid phase.

Scheme 1.22 Cyclative release strategies for macrocyclic peptidomimetics.

Scheme 1.23 Cyclative release by disulfide formation.

Chapter 02

Figure 2.1 Pharmaceutical, agricultural, and industrial applications of cyclotides. The range of potential applications of cyclotides is illustrated schematically by showing the relevant target organisms.

Figure 2.2 Structural information on macrocycles that can be derived from NMR experiments. The types of structural information are mapped onto the structure of SFTI‐1 (PDB: 1JBL), which is used here as an example of a macrocyclic peptide. Additional information and the NMR experiments that can be used are shown on the right. This figure is adapted from one in an article by Yudin [2].

Figure 2.3 Structure determination of macrocycles by NMR. (a) Flowchart of the general process of structure determination, which can vary depending on the size of the macrocycle. Specific features of structure determination for macrocyclic peptides compared with linear peptides are highlighted in the gray box on the bottom right of the figure. (b) Overlay of the 20 lowest energy structures of kalata B1 (PDB: 1NB1).

Figure 2.4 Analysis of dynamics by NMR relaxation. The general process involves acquisition of relaxation parameters such as

T

1

(longitudinal relaxation time),

T

2

(transverse relaxation time), and hNOE (heteronuclear NOE), followed by fitting of the relaxation parameters to motional parameters such as

T

o

(overall correlation time),

T

i

(internal correlation time), and

S

2

(square of the generalized order parameter). Experimental data and the fitted

S

2

values mapped onto the structure of cyclic Vc1.1 are shown as an example of the process.

Figure 2.5 Racemic and quasi‐racemic structures of kalata B1. (a) Packing of the

L

‐ and

D

‐enantiomers of kalata B1 in the unit cell. The

L

‐ and

D

‐enantiomers are labeled with

L

and

D

, respectively. (b, c) quasi‐racemic structures of kalata B1 composed of a mutant of

L

‐kalata B1 (i.e., [G6A]kalata B1 and [V25A]kalata B1) colored in dark gray and

D

‐kalata B1 colored in light gray. The side chains and the positions of the Cys residues for the

L

‐enantiomer are labeled with Roman numerals.

Figure 2.6 Examples of complex structures involving macrocyclic peptides. (a) NMR complex structure of a PEM with HIV‐1 TAR RNA. (b) NMR complex structure of a grafted MCoTI‐I with the p53‐binding domain of HDM2. (c and d) Complex structures of a bicyclic peptide and a thioester cyclized peptide to their protein targets solved by X‐ray crystallography.

Figure 2.7 Molecular modeling methods used to study cyclic peptides. The methods are in black boxes and are linked by dashed lines to their applications, which are in white boxes. As apparent from this diagram, molecular dynamics (MD) methods are the most versatile. All the methods are described in the text. MM, molecular mechanics; MMPBSA, molecular mechanics/Poisson–Boltzmann surface area; QM, quantum mechanics; REMD, replica‐exchange molecular dynamics.

Figure 2.8 Timescales of protein motion types, MD simulations, and nuclear magnetic resonance (NMR) experiments. All MD simulation methods have a time step of a few femtoseconds (fs), and the figure shows for each of them the timescale of the process that typically simulate. ns, nanosecond; ps, picosecond; REMD, replica‐exchange molecular dynamics; RDC, residual dipolar coupling.

Chapter 03

Figure 3.1 Desmopressin

1

and SNAC

2

.

Figure 3.2 BL3020‐1 (

3

) and Veber–Hirschman peptide (

4

).

Figure 3.3 Pentaleucine

5

, hexaleucine

6

, and HIF inhibitor

7

.

Figure 3.4 Cyclosporin A (CSA,

8

) conformations.

Figure 3.5 The Lokey peptide 1NMe3

9

and lysine variant

10

.

Figure 3.6 Sanguinamide A

11

, danamide D

12

, and danamide F

13

.

Figure 3.7 An example of a synthetic depsipeptide with favorable cell permeability based on the RRCK assay (3.3 × 10

−6

 cm/s).

Figure 3.8 Ulimorelin (TZP‐101,

14

).

Chapter 04

Figure 4.1 Distribution of principal classes of natural products within macrocycles (Bartelt, R., Brandt, W., Haupt, H., and Wessjohann, L. A. Statistical analysis of macrocycles. To be submitted).

Figure 4.2 Proportional areas of medicinal applications described for macrocyclic drugs (Bartelt, R., Brandt, W., Haupt, H., and Wessjohann, L. A. Statistical analysis of macrocycles. To be submitted).

Scheme 4.1 Principal of polyketide synthesis with subsequent macrocyclization. During its biosynthesis the linear precursor is connected via a thioester bond to acyl carrier proteins (ACP, bound to the sulfur – only the bond is shown in the scheme). Modifications and transfer to the next monomer are catalyzed by additional domains of the respective module. The starter unit is gray.

Figure 4.3 Examples for macrocyclic polyketides. In erythromycin A, ring closure is achieved via lactone formation. In ansamycins/geldanamycins, the macrocycle is formed by amide formation. In both examples, the carboxyl‐terminus of the linear precursor is activated as thioester and condensed with an amine or hydroxyl group of the same molecule. Below: Pristinamycin, which is a mixture of pristinamycin I, a cyclodepsipeptide, and pristinamycin II, a hybrid polyketide–peptide macrocycle. Backbone bonds derived from the same building block are marked in bold. The starter substrate is colored gray.

Scheme 4.2 Biosynthesis of cyclic terpenoids. Starting from the isomers isopentenyl diphosphate and dimethylallyl diphosphate, geranylgeranyl diphosphate (GGPP) synthase produces GGPP, which is the substrate of the cembrene and taxadiene synthases. Electrophilic attack of the allylic cation at C‐1/C‐3 on the double bond at C‐14 results in a common intermediate, the macrocyclic cembrenyl cation. Deprotonation leads to cembrene, while within taxadiene synthase, further rearrangements lead to taxadiene, which is modified to taxol later on. Note: Numbering of carbon atoms are according to IUPAC numbering of GGPP; established numberings of cyclic terpenoids may differ.

Figure 4.4 Statistical analysis of the abundance of described natural macrocycles with respect to ring size. As expected, the larger the ring, the lower the abundance as a trend. However, with some relevant oscillations, disfavoring, for example, uneven smaller macrocycles (13, 15, 17 members). See text for a detailed discussion [3, 4].

Figure 4.5 (a) Carbon‐only rings correlate with abundance of terpenoids, (b) non‐lactam nitrogens are predominantly located in smaller macrocycles, (c) analysis of non‐lactone oxygens: these are mostly phenol ethers with a dominance of 14‐membered cyclopeptide alkaloids [3, 4].

Figure 4.6 Ring size distribution of macrocycles depends on their biosynthetic origin [3, 4].

Figure 4.7 Conformational changes and changes in hydrogen bonding of “chameleon macrocycles” can overcome the rule of five to some extent.

Figure 4.8 Synthesized and tested erythromycin derivatives with lipophilic and polar substituents (R) investigated by Shaw

et al

.

Figure 4.9 Macrocyclic hepatitis C virus NS3/4A protease inhibitors used for SAR studies.

Figure 4.10 Based on natural product lactones, (a) apicularen A, (b) pinolidoxin, (c) decarestrictine D, and (d) related artificial macrocycles were synthesized by Kopp

et al

.

Figure 4.11 Structures of macrocycle

1

in comparison to a linear analog

2

according to Dinsmore

et al

.

Figure 4.12 Structure of the autoinducer peptide (AIP). The macrocycle was constrained by F6P and I7P substitutions, enlarged by hβ‐Met, hβ‐Ile, hβ‐Phe, hβ‐Asp, and others, and reduced by ΔF6 and ΔI7.

Figure 4.13 Macrocyclic synthetic peptoids (

R

 = 17 different amine side chains) with ring sizes 17 (

n

 = 0), 20 (

n

 = 1), and 23 (

n

 = 2) atoms [134].

Figure 4.14 Macrocycles (B

, 4

) designed on the basis of linear peptides (A,

2

) as inhibitors for the hepatitis C virus NS3 protease. u. = unsaturated, s. = saturated bridge. IC

50

values (μM) = 

2a

>1000,

2b

 = 1.4,

2c

 = 0.047,

4a

 = 400,

4b

 = 0.024,

4c

 = 0.011,

4d

 = 0.028.

Figure 4.15 (a) Structure of natural bryostatin (

1

) and (b) a simplified active analog derived by computer‐guided design (). The upper part of the compounds represents the spacer domain, while the lower one, the little changed recognition site.

Figure 4.16 Structures of (a) epothilone A (R = H), B (R = Me) and (b) basic structure of epothilone derivatives with 68 different substituents R

1

and R

2

used for CoMFA by Yuan

et al

.

Figure 4.17 (a) Example of a synthetic macrocycle complexing cadmium (and zinc ions) with antibacterial activity. (b) Example of a macrocycle able to complex iron or manganese ions tested for potential use in diagnostics and for antimicrobial activity.

Chapter 05

Figure 5.1 Synthetic peptides 1NMe3 (Lokey peptide,

1

) and Rezai 42 (

2

) have inspired numerous studies on cyclic peptide passive permeation. The proteasome inhibitor baceridin (

3

) and three recently discovered cyclic peptides with unknown bioactivity (

4–6

) closely resemble the structures of the Lokey peptides.

Figure 5.2 Structure of kalata B1. Roman numerals refer to cysteine residues involved in disulfide bonds.

Figure 5.3 Solution structure of cyclosporine A in chloroform.

Figure 5.4 Conformations of patellamide.

Figure 5.5 Conformations of valinomycin.

Figure 5.6 Scytalidamide A.

Figure 5.7 Guangomide A and B.

Figure 5.8 Rakicidin A.

Figure 5.9 Didemnin A and B.

Figure 5.10 Structures and IMHB patterns of the destruxins.

Figure 5.11 Sanguinamide A.

Figure 5.12 Structures and IMHB patterns of cyclic peptides with unknown, but likely, passive permeability.

Figure 5.13 Structures of apratoxin A and B.

Figure 5.14 Cytotoxic cyclic peptides I.

Figure 5.15 Cytotoxic cyclic peptides II.

Figure 5.16 Cytotoxic cyclic peptides III.

Figure 5.17 Cytotoxic cyclic peptides IV.

Figure 5.18 Cytotoxic cyclic peptides V.

Figure 5.19 Antibacterial cyclic peptides I.

Figure 5.20 Antibacterial cyclic peptides II.

Figure 5.21 Antibacterial cyclic peptides III.

Figure 5.22 Antiviral cyclic peptides.

Figure 5.23 Antiparasitic cyclic peptides.

Figure 5.24 Antifungal cyclic peptides.

Figure 5.25 Protease‐inhibiting cyclic peptides.

Figure 5.26 Midsized cyclic peptides with various bioactivities I.

Figure 5.27 Midsized cyclic peptides with various bioactivities II.

Figure 5.28 Midsized cyclic peptides with various bioactivities III.

Figure 5.29 Cystine knot peptides.

Figure 5.30 Cyclotides from

Hedyotis diffusa

.

Figure 5.31 Cyclotides from

Violaceae ignobilis

.

Figure 5.32 Knottins.

Figure 5.33 Peptide sequences of ribosomally synthesized likely cyclic bioactives.

Chapter 06

Figure 6.1 (a) Hit identification from a combinatorial library by iterative deconvolution; (b) hit identification from a combinatorial library by positional scanning; (c) two representative macrocyclic ligands discovered by the positional scanning method.

Figure 6.2 Design of a peptide‐encoded OBTC cyclic peptide Library. B, β‐alanine.

Figure 6.3 Structures of representative monocyclic and bicyclic peptide ligands discovered from peptide‐encoded OBTC libraries.

Figure 6.4 Design, synthesis, and screening a second‐generation OBTC library against K‐Ras G12V. The residues modified during library synthesis and optimization are colored in gray.

Figure 6.5 (a) Design of an OBTC bicyclic peptide library, in which the macrocycles are attached to the solid support through a releasable linker (e.g., ester, which can be cleaved by base hydrolysis), whereas the linear‐encoding peptides are linked to the support through stable amide bonds. (b) TNFα antagonist identified from the bicyclic peptide library. (c) K‐Ras inhibitor discovered from the bicyclic peptide library.

Figure 6.6 Selective on‐bead labeling and release of a macrocyclic compound from a single bead, while the linear‐encoding peptide is retained on the bead for later hit identification by PED–MS. TMR, tetramethyl rhodamine; Pra,

L

‐propargylglycine.

Figure 6.7 Various strategies for ring opening of macrocyclic compounds for MS/MS decoding. CNBr, cyanogen bromide; mCPBA, meta‐chloroperoxybenzoic acid.

Figure 6.8 Steps involved in the synthesis of DNA‐encoded macrocyclic libraries.

Figure 6.9 Structures of representative macrocyclic ligands discovered from DNA‐encoded libraries.

Figure 6.10 Synthesis and screening of peptide libraries by the SPOT method.

Figure 6.11 An example of photolithographic synthesis of macrocyclic peptide libraries using sequential NPPOC deprotection and coupling.

Figure 6.12 Structures of representative macrocyclic ligands discovered from DOS libraries.

Figure 6.13 (a) Example of the build/couple/pair strategy using unique build fragments. (b) Build/couple/pair example using divergent pair steps to generate conformationally diverse macrocycles.

Chapter 07

Figure 7.1 Schematic diagram for naïve selection and affinity maturation of disulfide‐bridged cyclic peptide ligands via M13 phage display. A naïve library is first displayed on a high‐valency format through fusion to the pVIII coat protein. Positive hits are validated via a phage ELISA assay and sequenced to identify consensus motifs. Affinity maturation of the ligand is achieved via a second‐generation library designed based on the consensus motifs, followed by display on a low‐valency format (pIII fusion) and affinity selection.

Figure 7.2 Three‐dimensional structure representations of disulfide‐bridged cyclic peptides isolated by phage display. The target proteins against which these peptides were selected are indicated: Fc region of human immunoglobulin G (IgG Fc; pdb 1DN2) [34]; FcεRIα (pdb 1JBF) [26]; erythropoietin hormone receptor (EPOR; pdb 1EBP) [44]; vascular epithelial growth factor (VEGF; v108 peptide, pdb 1VPP) [46]; glycoprotein 41 subunit of HIV‐1 envelope (gp41, pdb 1CZQ) [28]; insulin‐like growth factor 1 (IGF‐1, pdb 1LB7) [17]; FcεRIα (pdb 1KCO) [27]; coagulation factor FVIIa (pdb 1DVA) [24]; insulin‐like growth factor binding protein 1 (IGFBP‐1, pdb 1GJE) [47]; VEGF (v107 peptide, pdb 1KAT) [46].

Figure 7.3 Non‐phosphorylated cyclic peptide inhibitors of the Grb2 SH2 domain. Phage display‐derived

G1

peptide and its non‐reducible cyclic and bicyclic analogues.

Figure 7.4 Macrocyclic peptide binders of human IgG Fc fragment. (a) View of

Fc‐III

peptide (D

C

AWHLGELVW

C

T; green; stick models) bound to the surface of human IgG Fc domain (pdb 1DN2); (b) Computer models of

FcBP‐1

and

FcBP‐2

mimetics as prepared by transplanting 9 or 13 residues, respectively, from

Fc‐III

onto the

D

Pro‐

L

Pro template.

Figure 7.5 Bicyclic peptides on phages. (a) Overview of chemical cross‐linking strategy for generating bicyclic peptides displayed on the surface of M13 phage particles. (b) Chemical structures of cysteine cross‐linking agents. TATA, 1,3,5‐triacryloyl‐1,3,5‐triazinane; TBAB,

N

,

N

′,

N

″‐(benzene‐1,3,5‐triyl)tris(2‐bromoacetamide); TBMB, 1,3,5‐tris‐(bromomethyl)benzene. (c) Structure of bicyclic peptide inhibitor (

UK18

) of human uPa isolated by phage display. The

TBMB

‐derived linker is highlighted by the box.

Figure 7.6 Crystal structure of human uPA in complex with monocyclic and bicyclic peptide inhibitors. (a) Disulfide‐bridged peptide upain‐1 (pdb 2NWN); (b) TBMB‐linked bicyclic peptide UK18 (pdb 3QN7); (c) TBAB‐linked bicyclic peptide UK903 (pdb 4MNY); and (d) bicyclic disulfide‐bridged peptide UK504 (pdb 4GLY). The TBMB and TBAB linkers are colored in magenta. Key amino acid residues involved in the interaction with uPA are showed as sphere models. For each complex, a schematic representation of the corresponding peptide ligand is provided.

Figure 7.7 Overview of mRNA display system for the selection of functional peptides. A template DNA library is first transcribed

in vitro

to generate a randomized mRNA library (i). After conjugation with puromycin (ii) and translation of the mRNA‐encoded polypeptide (iii), a peptide–mRNA conjugate is formed. A double‐stranded DNA/RNA hybrid is then generated via reverse transcription, followed by panning of the RNA/DNA‐conjugated peptide library against an immobilized target protein. The protein‐bound peptide–RNA/DNA molecules are then recovered and amplified by polymerase chain reaction (PCR), followed by transcription and translation. Iterative rounds of affinity selection and amplification enrich the library with peptide with high affinity for the target protein, whose sequence can be determined by DNA sequencing.

Figure 7.8 Strategies for macrocyclization of

in vitro

translated peptides. (a) DSG‐mediated cyclization. (b) Cyclization via cysteine cross‐linking with 1,3‐dibromomethylbenzene. (c) Formation of lanthipeptide‐like macrocycles via oxidation of 4‐selenalysine to dehydroalanine, followed by cyclization via a Michael addition reaction.

Figure 7.9 Screening of

in vitro

translated cyclic peptide libraries via the FIT and RaPID system. (a) Flexizyme‐catalyzed tRNA aminoacylation. Initiator tRNA

CAU

is loaded with

N

‐chloroacetyl‐

D

Trp, and other selected tRNAs are loaded with N‐methylated amino acids (MeF, MeS, MeG, MeA). (b) Reprogrammed genetic code used for mRNA display peptide library against the HECT domain of ubiquitin ligase E6AP. Selected codons are made “vacant” via removal of the corresponding tRNA and AARS from the

in vitro

translation system. These codons are reprogrammed using the aminoacylated tRNAs prepared in (a). (c) Overview of the RaPID system for the selection of macrocyclic

N

‐methylated peptides against E6AP. Messenger RNA libraries containing a randomized sequence, (NNU)

8–15

, are transcribed from the corresponding cDNA library and conjugated with an oligonucleotide bearing a puromycin residue. The resulting mRNAs are translated by the FIT system in the presence of the appropriate aminoacylated tRNAs as in (a). The mRNA‐displayed linear peptides are cyclized via a reaction between the cysteine residue and the N‐terminal α‐chloroacetyl group. After affinity selection against immobilized E6AP, the cDNAs of the protein‐bound mRNA–peptide fusions are recovered and amplified by PCR. After multiple rounds of affinity selection/amplification (typically 6–10), the identity of the “hits” is determined by DNA sequencing.

Figure 7.10 Strategies for the synthesis of macrocyclic organo‐peptide hybrids (MOrPHs). (a) CuAAC/hydrazide‐mediated ligation method. (b) Oxime/AMA‐mediated ligation method. AMA, 2‐amino‐mercaptomethyl‐aryl moiety; CuAAC, copper‐catalyzed alkyne/azide cycloaddition.

Figure 7.11 Strategies for the production of macrocyclic peptide libraries in living cells. (a) Overview of SICLOPPS method for production of head‐to‐tail cyclic peptides (see Chapter 8 for further details). (b) Overview of biomimetic method for intracellular synthesis of cyclic peptides constrained by an inter‐side‐chain thioether linkage. O2beY is incorporated into the precursor polypeptide via amber stop codon suppression using an engineered aminoacyl‐tRNA synthetase and a cognate TAG suppressor tRNA. Upon expression of the polypeptide, spontaneous peptide cyclization occurs via reaction of O2beY with a neighboring cysteine (2–10 residues apart). Aspartate‐mediated hydrolysis of the peptide–intein thioester linkage releases the cyclic peptide from the intein moiety. (c) Overview of MeaF‐based method for directing the intracellular synthesis of side chain‐to‐tail cyclic peptides. The unnatural amino acid MeaF is incorporated into the precursor polypeptide via amber stop codon suppression. After ribosomal synthesis of the polypeptide, the macrocyclic peptide is formed via an intramolecular transthioesterification reaction involving MeaF side‐chain aminothiol group and the C‐terminal intein moiety, followed by an S,N‐acyl rearrangement.

Chapter 08

Figure 8.1 Split‐intein circular ligation of peptides and proteins (SICLOPPS) and the reverse two‐hybrid system (RTHS). (a) The expressed SICLOPPS intein (I

C

 : target peptide : I

N

) folds to form an active intein. An

N

‐to‐

S

acyl shift occurs at the target N‐terminal intein junction to produce a thioester, which upon transesterification with a side chain nucleophile (serine or cysteine, X = O or S, respectively) at the C‐terminal intein junction forms a lariat intermediate. An asparagine side chain liberates the cyclic peptide as a lactone, which then undergoes rearrangement to generate the desired cyclic peptide as a lactam. (b) RTHS: Interacting proteins X and Y are expressed as N‐terminal fusions with the 434 and p22 repressor proteins, respectively, under the control of the IPTG promoter. Dimerization of X and Y forms an active repressor construct, with 434 and p22 binding to their respective deoxyribonucleic acid (DNA) response elements and inhibiting downstream expression of the reporter cassette. When a cyclic peptide inhibits the interaction between X and Y, the repressor construct is not formed, therefore allowing for cell survival on selective media. For identification of inhibitors of homodimeric PPIs, a homodimeric system composed of only the 434 repressors can be used.

Figure 8.2 Cyclic peptide inhibitors of PPIs identified through SICLOPPS. (

1–4

) Ribonucleotide reductase inhibitors. (

5

)

Cyclo

‐CRYFNV, ATIC homodimerization inhibitor. (

6

) Cyclo‐SGWTVVRMY, C‐terminal binding protein (CtBP) inhibitor. (

7

)

Cyclo

‐CLLFVY, HIF‐1 inhibitor.

Figure 8.3 Random nonstandard peptide integrated discovery (RaPID) system. A complementary deoxyribonucleic acid (cDNA) library is generated via polymerase chain reaction (PCR), containing random sequences, which is transcribed to form an mRNA library (1). A puromycin linker is ligated to the 3′‐end of each mRNA species (2). The mRNA is translated to a nonstandard peptide using the flexible

in vitro

translation (FIT) system, (3) forming a library of peptide–puromycin linker–mRNA species. These undergo reverse transcription (4) to prevent nonspecific binding during selection. The target protein is immobilized with a magnetic bead and the resultant peptide–mRNA–cDNA library is then screened for target binding (5). Library enrichment is performed through PCR amplification of those sequences found to contain target binders (6).

Figure 8.4 (a) Macrocyclization utilizing glycolic acid. Diketopiperazine‐thioester formation facilitates macrocyclization through the free amino group at the N‐terminus of the peptide construct. (b) Structure of CM

11

‐1, the E6AP inhibitor identified from a library of N‐methylated thioether macrocyclic peptides. CM

11

‐1 exhibits an IC

50

of 3.2 nM against E6AP. (c) Pakti‐L1, an AKT2‐selective inhibitor with an IC

50

of 110 nM. (d) S1iL8, a SIRT‐2 selective inhibitory cyclic peptide armed with the warhead trifluoroacetyl lysine (K

Tfa

). S1iL8 has an IC

50

of 3.2 nM.

Figure 8.5 β‐strand mimetic cyclic peptide inhibitors of human immunodeficiency virus (HIV) protease.

Figure 8.6 Examples of covalent macrocyclization techniques for α‐helix stabilization.

Figure 8.7 Interaction of PERM‐1 with the surface of ERα. The surface of ERα (yellow) provides a good fit for the residues of PERM‐1 (cyan). The N‐terminal Lys and C‐terminal Gln residues of PERM‐1 are labeled. Protein data bank (PDB) code: 1PCG.

Figure 8.8 Synthesis and sequences of SAH‐p53 peptides. (a) Nonnatural olefinic amino acid derivatives were incorporated into the sequence at positions avoiding critical HDM2‐binding residues and cross‐linked at the

i

,

i +

 7 positions by ruthenium catalyzed ring‐closing olefin metathesis. (b) The series of SAH‐p53 peptides were generated by stapling the p53

14–29

sequence at the indicated positions within the sequences shown. Charge, α‐helicity, HDM2 binding affinity, cell permeability, and impact on cell viability are all indicated.

Figure 8.9 Structure of ATSP‐7041, a potent stapled inhibitor of the p53–MDM2/MDMX interaction, derived from the native p53 α‐helix.

Figure 8.10 Generation of phage‐encoded library of bicyclic peptides and an isolated active example. (a) A phage‐encoded peptide, containing three cysteine residues is scaffolded by the trifunctional mesitylene TBMB. The library is screened for selectivity against the target protein. (b) Structure of PK15, a bicyclic inhibitor of plasma kallikrein (

K

i

 = 1.5 nM), isolated through phage display.

Figure 8.11 Hot loops are defined by meeting one or more of the following three criteria: (i) the average ∆∆

G

residue

over the entire loop must be greater than 1 kcal mol

−1

, (ii) the loop contains greater than or equal to three hot spot residues (∆∆

G

residue

 > 1 kcal mol

−1

), and (iii) the loop contains greater than or equal to two consecutive hot spot residues. Loops representing each category are represented in the yellow, blue, and red circles. Some hot loops satisfy two of these criteria, and representative loops in green, purple, and boxes. There are 67 hot loops that fulfill all three criteria with one example depicted in the gray box. All structures, rendered in PyMOL (PDB codes depicted in boxes), show the interfacial chain in blue, binding partner in gray, hot loop in green, and hot spot residues in orange (∆∆

G

residue

 > 1 kcal mol

−1

) and yellow (∆∆

G

residue

 > 2 kcal mol

−1

).

Chapter 09

Figure 9.1 Four possibilities for peptide macrocyclization.

Figure 9.2 Solution‐ versus solid‐phase macrocyclization for head‐to‐tail cyclic peptides.

Figure 9.3 Turn‐inducing residues to promote

cis

‐amide bond and folded conformations.

Figure 9.4 Structure of different coupling reagents used for peptide synthesis and macrolactamization.

Figure 9.5 Ring disconnection sites and yields obtained in the synthesis of (a) cyclo[Pro‐Ala‐Ala‐Phe‐Leu]

22

and (b) cyclo[

N

Me‐Phe‐Pro‐Phe‐

N

Me‐

D

‐Trp‐

N

Me‐Lys‐Thr]

23

.

Figure 9.6 General synthetic route for head‐to‐tail macrocyclization in solution through activated ester formation (PG, side chain protecting group).

Figure 9.7 Synthesis of head‐to‐tail cyclic peptides via

O

‐to‐

N

acyl migration.

Figure 9.8 Head‐to‐tail macrocyclization through a ring contraction strategy using a hydroxylated photolabile auxiliary.

Figure 9.9 Head‐to‐tail macrocyclization via a ring contraction strategy using the (

E

)‐2‐(2‐nitrovinyl)phenol auxiliary

24

.

Figure 9.10 Ring contraction strategy by Ser/Thr ligation. Preparation of peptide salicylaldehyde esters by (a) Fmoc‐SPPS and (b) Boc‐SPPS. (c) Macrocyclization by intramolecular imine‐induced

O

‐to‐

N

acyl migration (PG, side chain protecting group).

Figure 9.11 Head‐to‐tail cyclization of peptide thioesters catalyzed by imidazole.

Figure 9.12 Head‐to‐tail macrocyclization of peptide thioacids using Sanger’s reagent.

Figure 9.13 Head‐to‐tail macrocyclization of peptide thioesters by native chemical ligation.

Figure 9.14 Head‐to‐tail macrocyclization of unprotected peptide thioesters with removable N‐terminal oxyethanethiol by native chemical ligation (Gnd, guanidine).

Figure 9.15 Solid supports for the synthesis of peptide thioesters by Fmoc‐SPPS. (a) Dbz linker on Rink amide resin to prepare peptide

N

‐acyl‐benzimidazolinones; (b) hydrazine resin for the synthesis of peptide hydrazides as thioester surrogates; (c) SEA–Trt resin for the synthesis of SEA

on/off

peptide precursors.

Figure 9.16 Head‐to‐tail macrocyclization by traceless Staudinger ligation.

Figure 9.17 Solid‐phase peptide macrocyclization via backbone anchoring strategy (PG, side chain protecting group; Y, carboxyl protecting group).

Figure 9.18 Different backbone amide linker derivatives.

Figure 9.19 Safety‐catch linkers for cyclative cleavage strategy; (a) sulfonamide safety‐catch linker and (b)

O‐tert

‐butyl‐protected catechol safety‐catch linker.

Figure 9.20 General synthetic solution‐ and solid‐phase approaches for macrocyclization by disulfide bond formation.

Figure 9.21 Solid‐supported oxidizing reagents for disulfide bond formation.

Chapter 10

Figure 10.1 (a) An illustration of a small‐molecule binding to an enzyme active site. (b) Small‐molecule modulators of protein–protein interactions via interface or an allosteric site.

Figure 10.2 Examples of bioactive macrocyclic natural products as modulators of protein–protein interactions.

Figure 10.3 Different types of metathesis reactions.

Figure 10.4 (a) Commonly employed catalyst for RCM. (b) General mechanism for RCM. (c) Examples for RCM in total synthesis.

Figure 10.5 (a)

Z

‐selective catalyst for RCM. (b) Examples for

Z

‐selective RCM. (c) Favored and disfavored transition states for Mo‐ and Ru‐based

Z

‐selective catalysis.

Figure 10.6 (a) Vinyl siloxane‐based RCM for

Z

‐olefin synthesis. (b) Selective synthesis of

E

and

Z

macrocycles using RCM.

Figure 10.7 Synthesis of macrocyclic library using RCM‐based approach.

Figure 10.8 Hit from the RCM library of compounds and optimized SAR compound.

Figure 10.9 Synthesis of compound

44

using RCM approach.

Figure 10.10 General approach for building the DOS library; (a) proposed B/C/P strategy and (b) building blocks with pluripotent and orthogonal functional group.

Figure 10.11 Few examples of macrocycles from DOS library by David Spring.

Figure 10.12 First‐ and second‐generation functionalized indoline scaffolds.

Figure 10.13 Building a diverse set of macrocyclic toolbox from enantiopure scaffold

5.1

.

Figure 10.14 A stereocontrolled aza‐Michael approach to obtain enantiopure tetrahydroquinoline‐based scaffolds

81

and

82

.

Figure 10.15 A diverse set of tetrahydroquinoline‐based macrocyclic derivatives.

Figure 10.16 Building a diverse set of macrocyclic toolbox from an enantiopure benzofuran‐based

trans‐

β‐amino acid.

Figure 10.17 An example of the synthesis of a tricyclic derivative,

98

, from the bicyclic scaffold

95

.

Figure 10.18 Examples of bioactive natural products having a 14‐membered ring.

Figure 10.19 A strategy to build a diverse 14‐membered ring‐derived small‐molecule toolbox.

Figure 10.20 Our approach to obtain two different sets of 14‐membered ring macrocyclic scaffolds for a diversity‐based small‐molecule toolbox.

Figure 10.21 A general approach to building 14‐membered glycohybrids from carbohydrates.

Figure 10.22 Our synthetic pathway to building 14‐membered glycohybrid‐based macrocyclic toolbox.

Figure 10.23 A general approach to building macrocyclic diversity from C‐linked carbohydrates.

Figure 10.24 An example of the synthesis of two different macrocycles from

C

‐linked carbohydrates.

Figure 10.25 The discovery of several macrocyclic compounds functioning as anti‐angiogenesis agents in an embryonic zebrafish study; (a) zoom section; (b) with DMSO as a control; and (c) the effect of a small molecule.

Figure 10.26 The discovery of macrocyclic small molecules functioning as correctors of the damage induced in the pore formation caused by thapsigargin, resulting in the rescue of cell death in pancreatic β‐cells: (a) our proposed working model for the dynamic regulation of protein–protein interactions; (b) mitochondrial images with thapsigargin‐induced damage and subsequent reorganization of mitochondria in the presence of

139

; (c) two sets of macrocyclic compounds and their acyclic precursors.

Chapter 11

Figure 11.1 Representative macrocycles: (a) erythromycin, (b) vancomycin, and (c) simeprevir.

Figure 11.2 Different examples of peptide cyclization. (a) Side chain‐to‐side chain cyclization, (b) “head‐to‐tail” cyclization, and (c) side chain‐to‐N‐terminus cyclization.

Scheme 11.1 [3+2] Azide–alkyne cycloaddition [50].

Figure 11.3 Putative mechanism of the Cu‐mediated azide–alkyne Huisgen cycloaddition.

Figure 11.4 Generic structure of macrocycles used in the DPC‐generated ELC library.

Figure 11.5 Macrocyclic XIAP antagonists with X‐ray structure bound to the isolated XIAP‐BIR2 domain depicted right.

Scheme 11.2 Macrocycle antagonists of XIAP BIR2 and BIR3 domains.

Scheme 11.3 Macrocyclic IAP antagonists.

Scheme 11.4 Macrocyclic Grb2 SH2 domain inhibitors.

Scheme 11.5 Macrocyclic STAT3 inhibitors.

Scheme 11.6 Macrocyclic HDAC inhibitors and somatostatin modulators.

Figure 11.6 (a) Peptide β‐strand backbone with torsional angles

φ

, Ψ, and

ω

; (b) Interactions between a peptide substrate (with residues Px) and a protease (binding subsites Sx) using the nomenclature of Schechter and Berger.

Scheme 11.7 Macrocyclic protease inhibitors.

Scheme 11.8 Additional macrocyclic protease inhibitors.

Figure 11.7 (a) A view of the intermolecular hydrogen bonding observed between two macrocycles of

41

with the hydrogen atoms of the side chains omitted for clarity. Peptide backbone hydrogen bonds are shown as yellow dashed bonds and the triazole hydrogen bonds as dashed red lines. (b) A representation of the structure of

41

showing the nanotubular structure. The structure of

41

showing extended β‐sheet conformation, with the triazole‐containing macrocyclic linkage omitted for clarity. Side view of the dimerization of the nanotubular structures in the crystal. Top view of the dimerized nanotubes in a space‐filling representation. (c) ESI spectrum of compound

41

showing the formation of oligomeric assemblies in the gas phase [M + Na] and an SEM image of the rod‐like assemblies of

41

. (d) Superimposition of the crystallographic structure of

41

(green) with

43

(black) docked into cathepsin S.

Chapter 12

Figure 12.1 Representative examples of natural products synthesized using a Stille macrocyclization step (bond(s) formed in this step shaded in grey).

Scheme 12.1 Examples of the Stille macrocyclization reaction in natural product total synthesis.

Scheme 12.2 Examples of Suzuki–Miyaura macrocyclizations in natural product total synthesis.

Scheme 12.3 Examples of Suzuki–Miyaura macrocyclizations for peptidomimetics, hemispherands, and SPMs.

Scheme 12.4 Examples of the use of the Heck macrocyclization in various applications.

Scheme 12.5 Sonogashira reactions in the synthesis of macrocyclic natural products.

Scheme 12.6 Examples of the Sonogashira macrocyclization in the synthesis of cyclic peptides and other systems.

Scheme 12.7 Examples of Tsuji–Trost macrocyclizations in natural product total synthesis.

Scheme 12.8 Examples of the use of solid‐supported Pd catalysts in Tsuji–Trost macrocyclizations.

Scheme 12.9 Miscellaneous Pd‐catalyzed macrocyclizations in natural product synthesis.

Scheme 12.10 Other Pd‐catalyzed reactions in the formation of macrocyclic peptides and peptidomimetic compounds.

Chapter 13

Scheme 13.1 LDA‐promoted Dieckmann condensation in the synthesis of diazonamide A.

Scheme 13.2 Macroaldolization

versus

macrolactonization in the total synthesis of epothilone A.

Scheme 13.3 Manganese‐catalyzed macrocyclization of oligomethylene‐tethered diene

7

and bis(3‐oxobutanoate)

8

.

Scheme 13.4 Macrocyclization of β‐ketoesters onto furans.

Scheme 13.5 Metal‐free Friedel–Crafts‐type alkylations on functionalized peptides.

Scheme 13.6 Synthesis of a rigidified polyether macrocycle under oxidative copper catalysis.

Scheme 13.7 Efficient synthesis of a rigidified cyclophane structure.

Scheme 13.8 Synthesis of a macrocycle capable of carbohydrate recognition.

Scheme 13.9 Synthesis of a macrocycle at high concentration using Glaser–Hay coupling.

Scheme 13.10 Glaser–Hay macrocyclization of a macrocyclic lipid under continuous flow conditions.

Scheme 13.11 Nickel‐catalyzed macrocyclization of an aldehyde and internal alkyne.

Scheme 13.12 Ligand control in nickel‐catalyzed macrocyclizations.

Scheme 13.13 Influence of NHC structure on nickel‐catalyzed macrocyclizations.

Scheme 13.14 Nickel‐catalyzed exo‐selective macrocyclization.

Scheme 13.15 Enantioselective nickel‐catalyzed macrocyclization of an aldehyde and internal alkyne.

Scheme 13.16 Macrocyclic cycloisomerization toward amphidinolide A.

Scheme 13.17 Macrolactonization toward amphidinolide A.

Scheme 13.18 Copper‐catalyzed Sonogashira‐type cross‐coupling toward (

S

)‐zearalane.

Scheme 13.19 Copper‐catalyzed Sonogashira‐type cross‐coupling with

in situ

reduction to form 1,3‐dienes.

Scheme 13.20 Macrocyclization toward the trienomycins.

Scheme 13.21 Macrocyclization via Horner–Wadsworth–Emmons or Masamune–Roush reactions.

Scheme 13.22 Macrocyclization toward (+)‐dactylolide and lactimidomycin.

Scheme 13.23 Macrocyclization toward (+)‐phorboxazole A.

Scheme 13.24 Rhodium‐catalyzed intramolecular cyclopropanation by diazoacetates to form macrolactones.

Scheme 13.25 Chiral linkers in rhodium‐ and copper‐catalyzed intramolecular cyclopropanation.

Scheme 13.26 Nickel‐mediated oxidative coupling macrocyclization.

Scheme 13.27 Macrocyclization by organocuprate oxidation.

Scheme 13.28 Horseradish peroxidase (HRP)‐catalyzed macrocyclization toward dihydrolyfoline.

Scheme 13.29 Oxidative macrocyclization of a pentapyrrane bearing two terminal β‐linked pyrroles.

Scheme 13.30 Gold‐catalyzed macrocyclization to form cyclobutenes.

Scheme 13.31 Gold‐catalyzed olefination.

Scheme 13.32 Aza‐Claisen ring expansion in the total synthesis of isohaliclorensin.

Scheme 13.33 Comparison between ring expansion and lactonization routes for the synthesis of macrolactones.

Scheme 13.34 Story’s synthesis of Exaltolide®.

Scheme 13.35 Ring expansion via opening of cyclopropane moiety.

Scheme 13.36 Trans‐lactonization ring expansion reaction.

Scheme 13.37 Ring expansion via Grob fragmentation.

Scheme 13.38 Ring expansion via olefin metathesis.

Scheme 13.39 Photochemical decarboxylation and subsequent macrocyclization.

Scheme 13.40 Photochemical synthesis of a macrolactone from

N

‐alkenylphthalimide.

Scheme 13.41 Photochemical reaction of an aryl halide to form a macrocyclic biaryl.

Scheme 13.42 Chan–Lam–Evans coupling to MMP derivatives.

Scheme 13.43 Chan–Lam–Evans macrocyclization in the synthesis of chloropeptin I.

Scheme 13.44 Macrocyclic Williamson etherification of an ω‐bromophenolate.

Scheme 13.45 Mitsunobu reaction in the total synthesis of xestodecalactone A.

Scheme 13.46 Macrocyclization via S

N

Ar for the synthesis of models of vancomycin.

Scheme 13.47 S

N

Ar macrocyclization facilitated by Ru‐π complexes.

Scheme 13.48 S

N

Ar macrocyclization forming a quaternary stereocenter.

Scheme 13.49 On‐resin S

N

Ar macrocyclization toward peptidomimetics.

Scheme 13.50 Ullmann coupling applied to the synthesis of a model of deoxybouvardin.

Scheme 13.51 Macrocyclic Ullmann coupling using an aliphatic secondary alcohol.

Scheme 13.52 Macrocyclic Ullmann coupling using microwave irradiation.

Scheme 13.53 Macrocyclization via allylic C–H activation.

Scheme 13.54 Macrocyclization via propargylic C–H activation.

Scheme 13.55 Macrocyclization via alkylation of 2‐nitrobenzenesulfonamide.

Scheme 13.56 Macrocyclization via double alkylation.

Scheme 13.57 Macrocyclic Mitsunobu reaction for the formation of a C–N bond.

Scheme 13.58 Macrocyclic S

N

Ar reaction for the formation of a C–N bond.

Scheme 13.59 Macrocyclic enamide via Ullmann coupling.

Scheme 13.60 Macrocyclic Ullmann coupling.

Scheme 13.61 Ramberg–Bäcklund approach to a macrocyclic amine.

Scheme 13.62 Synthesis of a macrocyclic peptide via thioalkylation.

Scheme 13.63 Ramberg–Bäcklund reaction within a macrocyclic framework.

Scheme 13.64 Thiol–ene macrocyclization of a peptide on solid support.

Scheme 13.65 Bis‐thiol–ene macrocyclization of a peptide.

Chapter 14

Figure 14.1 Selected naturally occurring macrocyclic drugs or simple derivatives derived from a natural product lead.

Figure 14.2 (a) Schematic sketch of solvated cyclosporine A conformation in polar medium (water), highlighting possible hydrogen interactions with the solvent. (b) Schematic sketch of cyclosporine A conformation in nonpolar medium (chloroform), showing the macrocycle “hiding” some of its hydrogen donors and acceptors through intramolecular interactions.

Figure 14.3 Synthetic macrocyclic drug candidates. (a) JAK2/FLT3 inhibitor pacritinib (Phase II). (b) Anti‐angiogenic RGD‐cyclopeptide (v.i.) cilengitide (Phase III).

Figure 14.4 Some significant parameters in macrocyclization [29]. (a) All possible macrocyclization sites toward

cyclo

‐[Pro‐Ala‐Ala‐Phe‐Leu] and associated yields. (b) pH‐dependent Ag‐ion‐catalyzed macrocyclization of heptapeptide thioester. (c) Influence of coupling reagent on the macrolactonization of hemiswinholide A precursor.

Scheme 14.1 (a) General scheme of a single‐component macrocyclization approach (SCR). (b) SCR‐macrolactamization of a hypothetical peptide and the effect of different coupling reagents on the atom economy of the entire process.

Scheme 14.2 (a) The Passerini three‐component reaction (P3CR). (b) The Ugi four‐component reaction (U4CR). (c) General scheme of a multicomponent macrocyclization approach (MiB). The macrocycle carries the diversity delivered by the additional component FG

3

[22]. (d) Multicomponent reaction‐based macrocyclization of a hypothetical peptide highlighting the atom economy of the entire process.

Scheme 14.3 Peptide N → C directionality in Ugi‐MiB reactions. (a) MiBs involving one bifunctional building block. (b) Unidirectional Ugi‐MiB involving two bifunctional building blocks. (c) Bidirectional Ugi‐MiB with equally bifunctionalized building blocks lead to bidirectional products (N → C‐terminus directions of peptide moieties run in counter‐orientation) [22].

Scheme 14.4 Ugi‐4CR‐based macrocyclizations of single bifunctional building blocks. The monofunctional building blocks define the side chain functionality.

Scheme 14.5 The first Ugi‐4CR macrocyclizations reported utilized linear oligoglycines. (a) Unidirectional MiB reaction involving triglycine; (b) Unidirectional MiB reaction involving hexaglycine; (c) Synthesis of an eledoisin cyclic analogue (

6

).

Scheme 14.6 (a) MiB approach to RGD mimetic cyclopeptoid

7

. (b) MiB approach to cyclodepsipeptoid analogues of Sansalvamide A.

Scheme 14.7 Ugi‐4CR‐based macrocyclizations of peptides involving amphoteric aziridine carboxaldehydes (a) Proposed mechanism. (b) Examples of synthesized macrocycles

8–10

. (c) Application in the macrocyclization of rigid homochiral oligoprolines and comparison with standard procedures. (d) On‐resin Ugi‐4CR macrocyclization of peptides with aziridine carboxaldehyde and

tert

‐butyl isonitrile.

Scheme 14.8 Synchronized synthesis of macrocycles with a droplet‐based microfluidic technique.

Scheme 14.9 Application of Ugi‐4CR‐based macrocyclizations in the synthesis of medicinally significant macrocycles. (a) Synthesis of cell‐penetrating fluorescently labeled macrocycle

12

. (b) Fluorescein‐labeled RGD‐containing α

V

β

3

integrin receptor targeting macrocycle

13

. (c) Ugi‐4CR/peptide native ligation toward synthesis of cyclo‐tail peptides

14

.

Scheme 14.10 Synthesis of the disulfide‐bridged peptidomimetic macrocycle

19

.

Scheme 14.11 (a) Extended possibilities for Ugi‐4CR macrocyclizations of peptides (b) Side chain‐to‐side chain MiB. (c) Side chain‐to‐head MiB.

Scheme 14.12 Formation of 5‐aminooxazoles by MCR between aldehydes, amines, and α‐isocyanoacetamides (Zhu‐3CR).

Scheme 14.13 Zhu‐3CR/traceless activation/macrocyclization cascade. (a) Proposed mechanism. (b) Examples of synthesized depsicyclopeptides

26a–f

. (c) Application in the synthesis of endoglycodepsipeptides

27

.

Scheme 14.14 Synthesis of heterocycles (a) and thioaza macrocycles (b).

Scheme 14.15 Synthesis of triazole‐containing macrocycle compounds by tandem MCRs and intramolecular Sonogashira cross‐coupling.

Scheme 14.16 Zhu‐3CR‐based approach for the synthesis of

m

‐cyclophanes. (a) Reaction conditions. (b) Examples and yields of synthesized macrocycles.

Scheme 14.17 Synthesis of steroid–peptoid hybrid macrocycles by bidirectional Ugi‐4CRs involving two bifunctional building blocks. Head‐to‐head (H–H) and head‐to‐tail (H–T) regioisomers are formed in almost equal amounts. Yields refer to the mixture, but, for clarity, only the H–T isomers are shown.

Scheme 14.18 Steroid–peptoid hybrid macrocycles enhanced with higher hydrophilicity or lipophilicity. (a) Installation of the lipophilic diphenyl ether moiety common in natural antibiotics in syntheses of steroid–peptoid macrocyclic hybrids

39

. (b) Installation of hydrophilic motifs toward the synthesis of secocholane hybrid macrocycle

40

.

Scheme 14.19 Application of biaryl ether bis‐isonitriles in Ugi‐MiBs. (a) and (b) Synthesis of natural product‐inspired biaryl ether‐cyclopeptoid macrocycles

45

and

47

(note: these reactions were run without using (pseudo)dilution). (c) Synthesis of glycosylated macrocycle

50

(protected form) integrating macrocyclization and introduction of the glycosyl building block. (d) Side chain‐to‐backbone and backbone‐to‐backbone bidirectional macrocyclizations of peptides by double Ugi‐4CR. (e) Synthesis of cyclopeptoid

53

containing a photoswitchable unit. Note: Macrocyclization is usually performed using pseudo‐dilution by slow addition of diisocyanide and acid/diacid building blocks to the preformed imines.

Scheme 14.20 Passerini‐3CR‐MiB approach toward macrolactones. (a) Diacid/diisocyanide combination. (b) Diacid/diol combination. (c) Diisonitrile/diol combination with exocyclic ester formation.

Scheme 14.21 (a) Combinatorial library of macrocycles by MiB approach. (b) MiB‐combinatorial synthesis of cholane–peptoid hybrid macrocycles.

Scheme 14.22 Ugi‐MiB‐based quenching approach of macrocyclic oligoimine‐based DCLs generated from

61

and

62

.

Scheme 14.23 Synthesis of three‐dimensional multi‐macrocycles by threefold Ugi‐4CR‐based macrocyclizations, including trifunctional building blocks.

Scheme 14.24 Synthesis of a mixed library of cryptands by a threefold combinatorial MiB.

Scheme 14.25 Sequential MiBs applied to the synthesis of multi‐macrocycles. (a) Clam‐shaped macrobicycles and (b) igloo‐shaped macrotetracycles.

Chapter 15

Scheme 15.1 Structures of sagopilone and epothilone B.

Scheme 15.2 Synthesis of sagopilone (ZK‐EOP).

Scheme 15.3 Structures of desoxy‐biphenomycin B and biphenomycin B.

Scheme 15.4 Scalable synthesis of desoxy‐biphenomycin B Core.

Scheme 15.5 Structures of pasireotide and somatostatin.

Scheme 15.6 Scalable synthesis of pasireotide.

Scheme 15.7 Synthesis of ulimorelin (TZP‐101).

Scheme 15.8 Structures of vaniprevir and grazoprevir.

Scheme 15.9 Synthesis of the linear precursor

31

for vaniprevir.

Scheme 15.10 Scalable synthesis of vaniprevir.

Scheme 15.11 Scalable synthesis of grazoprevir.

Scheme 15.12 Retrosynthetic analysis of ciluprevir.

Scheme 15.13 Initial RCM of linear diene

42

toward ciluprevir.

Scheme 15.14 First‐generation RCM process for ciluprevir.

Scheme 15.15 Second‐generation RCM process for ciluprevir.

Scheme 15.16 RCM process for simeprevir.

Scheme 15.17 Structures of IDX316 and IDX320.

Scheme 15.18 Discovery route to IDX316.

Scheme 15.19 RCM approach to IDX316.

Scheme 15.20 RCM approach of IDX320.

Scheme 15.21 Potential RCM options for vaniprevir.

Scheme 15.22 RCM‐2 option toward vaniprevir.

Scheme 15.23 First‐generation RCM route toward vaniprevir.

Scheme 15.24 Second‐generation RCM route toward vaniprevir.

Scheme 15.25 RCM route toward SB1317.

Scheme 15.26 Structures of eribulin and halichondrin B.

Scheme 15.27 Retrosynthetic analysis of eribulin.

Scheme 15.28 First‐generation eribulin process.

Scheme 15.29 Second‐generation eribulin process.

Scheme 15.30 Retrosynthetic analysis of MK‐6325.

Scheme 15.31 Scalable synthesis of MK‐6325.

Scheme 15.32 Structures of octreotide and somatostatin.

Scheme 15.33 Sandoz process for octreotide.

Scheme 15.34 Wockhardt process for octreotide.

Scheme 15.35 Other examples of macrocyclic peptides constructed by disulfide bond formation.

Scheme 15.36 Structures of DZ‐2384 and (−)‐diazonamide A.

Scheme 15.37 Macrocyclization via Kita oxidation.

Scheme 15.38 Electrolytic macrocyclization.

Scheme 15.39 Structures of icotinib and erlotinib.

Scheme 15.40 Scalable synthesis of icotinib.

Chapter 16

Figure 16.1 (a) Therapeutic indications and (b) chemical classes for oral (gray bars,

N

 = 22) and parenteral (black bars,

N

 = 52) approved macrocycles.

Figure 16.2 Subclass distribution of oral (gray bar,

N

 = 1) and parenteral (black bars,

N

 = 31) macrocyclic peptide drugs.

Figure 16.3 Subclass distribution of oral (black bars,

N

 = 18) and parenteral (gray bars,

N

 = 11) ansamycin and macrolide drugs.

Figure 16.4 (a) Therapeutic indications and (b) chemical classes for oral (gray bars,

N

 = 22) and parenteral (black bars,

N

 = 31) macrocycles in clinical trials.

Figure 16.5 Subclass distribution of oral (gray bars,

N

 = 6) and parenteral (black bars,

N

 = 17) macrocyclic peptides drugs.

Chapter 17

Figure 17.1 Generic structure of macrocyclic compounds in the DPC‐generated ELC library.

Figure 17.2 X‐ray co‐crystal structural information indicated a superior macrocyclic ring closure, resulting in a series of compounds with greater binding affinity for the XIAP BIR2 binding site (a) X‐ray co‐crystal structure of the P2–P5‐linked macrocyclic compound

5

(yellow) bound to the BIR2 domain (PDB accession number 4WVT). The compound makes a number of hydrogen‐bond interactions (indicated as yellow broken lines) and lipophilic interactions from the P1, P3, and P4 side chains. (b) Structure of compound

7

, linear precursor to macrocycle

1

, a P2–P5‐linked macrocycle. (c) Overlap of the co‐crystal structures of the BIR2 domain with the linear compound

7

(green) (PDB accession number 4WVS) and P3–P5‐linked macrocyclic compound

8

(orange) (PDB accession number 4WVU), showing that the backbone of the open chain overlaps almost exactly with the P3–P5‐linked macrocyclic compound

8

.

Figure 17.3 Examples of bivalent IAP antagonists

13

(birinapant),

14

,

15

, and

16

.

Figure 17.4 Plasma levels and pharmacokinetic parameters for macrocycles

21–23

following intravenous administration to mice (

21

at 0.2 mg/kg,

22–23

both at 1 mg/kg).

Figure 17.5 (a) Antitumor activity of compound

22

against established MDA‐MB‐231 human breast carcinoma xenografts implanted subcutaneously in athymic mice. (Arrowheads indicate time of dosing (q3d × 5)). (b) Antitumor activity of compound

22

against established A875 human melanoma xenografts implanted subcutaneously in athymic mice. (Arrowheads indicate time of dosing (q3d × 5)).

Figure 17.6 Model of compound

22

bound to the BIR2‐3 domains of XIAP protein. Carbon atoms of

22

are shown in green, and oxygen and nitrogen atoms are highlighted in red and blue, respectively. The protein surface is colored by electrostatic potential, with regions of negative potential shown in red hues, positive potential in blue, and neutral (hydrophobic) regions in white.

Scheme 17.1 (a) EDCI, HOAt, NMM, DMF; (b) TFA, DCM; (c) Boc‐

L

‐Leu, EDCI, HOAt,

N

‐methylmorpholine, DMF; (d) TFA, DCM; (e) Boc‐

N

‐Me‐

L

‐Ala, EDCI, HOAt,

N

‐methylmorpholine, DMF; (f) aq. LiOH, THF; (g)

39

or

40

, HATU,

N

‐methylmorpholine, DMF; (h) CuSO

4

, sodium ascorbic acid, THF/

t

BuOH/H

2

O; (i) Hoveyda–Grubbs II catalyst, DCE, 70°C; (j) TFA, DCM; (k) Pd/C, H

2

, MeOH.

Figure 17.7 Antitumor activity of

33

in the A875 xenograft model in mice. Compounds were administered intraperitoneally (i.p.) every 3 days for six doses or weekly for two doses beginning on day 10.

Chapter 18

Figure 18.1 Left panel: Crizotinib (

1

) co‐crystal structure in ALK‐L1196M kinase domain (PDB 2YFX, 1.7 Å). Right panel: PF‐06439015 (

2

) bound to ALK‐L1196M KD (PDB 4CD0, 2.2 Å).

Figure 18.2 Internal clash of amide and pyrazole in preferred conformation of

3e

causes rotation of the amide into a less productive binding conformation.

3e

co‐crystallized with ALK KD (PDB 5KZ0).

Figure 18.3 Left panel: Acyclic amide

3e

co‐crystal structure in ALK (cyan, PDB 5KZ0) overlaid with modeled macrocycle

4g

(purple) in ALK. Right panel:

4g

co‐crystal structure in ALK‐kinase domain (green, PDB 4CMU) overlaid with modeled ligand (purple).

Figure 18.4 Structure of

4g

bound in ALK (green, PDB 4CMU) and TrkB (purple, PDB 4AT3) with selectivity residues and vector highlighted.

Figure 18.5

PF‐06463922

(

4q

) co‐crystal structure in ALK‐L1196M kinase domain (PDB 4CLJ, 1.7 Å) overlaid with crizotinib (

1

) in complex with ALK‐L1196M from Figure 18.1, left panel.

Figure 18.6 Crizotinib (

1

) and

PF‐06463922

(

4q

) NIH3T3 phospho‐ALK IC

50

values across an engineered panel of patient‐reported crizotinib‐resistant mutations.

Scheme 18.1 Synthesis of

PF‐06463922

(

4q

) by an unprecedented directed arylation.

Reagents and conditions

: (a) 5 mol% Pd(P

t

Bu

3

)

2

, 3 eq DIPEA, 1.1 eq

6

, toluene, 80°C, 4 bar CO, 18 h, 70%; (b) 1.1 eq NBS, THF, −10°C, 2 h, 86%; (c) acetic anhydride, 100°C, 8 h, quant.; (d) 20 mol% cataCXium A, 10 mol% Pd(OAc)

2

, 5 eq KOAc,

t

‐AmOH, 130°C, 14 h; (e) 10 eq 4N HCl in dioxane, MeOH, 60°C, 14 h, 42% over two steps.

Figure 18.7 Concentration–time profile of

PF‐06463922

in rats (a) and dogs (b),

n

 = 2. Rats were administered 1 mg/kg (i.v.) and 5 mg/kg (oral gavage) in solution formulation. Dogs were administered 1 mg/kg (i.v.) and 2 mg/kg (oral gavage) in solution formulation.

Figure 18.8 Total (a) and unbound (b) concentrations of

PF‐06463922

in brain homogenate, CSF, and plasma (

n

 = 2).

Figure 18.9 Quantitative whole‐body autoradiograph of a male animal 1 h following a single oral dose of [

14

C]

PF‐06463922

.

Figure 18.10 H&E stains (a, c, and e) and MALDI‐MS images (b, d and f) of mouse brain slices. (a) and (b) are from a tumor‐naïve mouse dosed at 400 mg/kg. (c) and (d) are from a tumor‐bearing mouse dosed at 200 mg/kg. (e) and (f) are from a tumor‐bearing mouse dosed at 100 mg/kg. All animals were orally dosed once. MS images were acquired at 75 × 75 µm pixel resolution.

Figure 18.11

PF‐06463922

antitumor efficacy in ALK fusion‐driven intracranial tumor models. (a) Representative magnetic resonance images showing regression of large established H3122 EML4‐ALKWT intracranial tumors in mice following

PF‐06463922

infusion. (b) Quantitation of brain tumor sizes following

PF‐06463922

treatment in the H3122 EML4‐ALKWT intracranial model shown in (a). Values are presented as mean ± SEM.

Figure 18.12 Main workstream of a two‐step approach to characterize

in vivo

exposure–response relationships of MTAs between drug exposures, biomarker response, and antitumor efficacy. MTAs, molecularly targeted agents; PKDZ, pharmacokinetics‐disease; PKPD, pharmacokinetics–pharmacodynamics.

Figure 18.13 PKPD model‐fitted and observed ALK inhibition by

PF‐06463922

in athymic mice implanted with H3122 non‐small cell lung cancer (NSCLC) cells expressing the EML4‐ALKL1196M following repeated oral administration. ALK OBS, the observed ALK response (ratio to the vehicle control animal data); ALK PRED, the model‐fitted ALK responses; CP PRED, the one‐compartment‐fitted plasma concentrations of

PF‐06463922

, S1, study 1; S2, study 2.

Figure 18.14 Observed tumor volumes and model‐fitted tumor growth inhibition curves in athymic mice implanted with H3122 NSCLC cells expressing the EML4‐ALKL1196M (a) or NIH3T3 cells expressing the CD74‐ROS1 (b) following repeated oral administration of

PF‐06463922

. IPRED, the model‐fitted individual tumor growth curves; OBS, the observed individual tumor volumes.

Figure 18.15 Comparison of

PF‐06463922

concentration–response curves for target modulation and tumor growth inhibition in nonclinical tumor models. Concentration–response curves for ALK inhibition and tumor growth inhibition were simulated at the concentration range of 0.01–10 000 ng/ml using the parameters estimated from nonclinical tumor models with H3122 NSCLC cells expressing the EML4‐ALK

L1196M

(a) and NIH3T3 cells expressing the CD74‐ROS1 (b). The dotted lines to the axes indicate the estimated tumor stasis concentration (Tsc), the EC

60

estimate for ALK inhibition (EC

60

), and the proposed minimum target efficacious concentration (

C

eff

).

Figure 18.16 M&S summary for evaluation of pharmacokinetic‐pharmacodynamic‐disease (PK‐PDDZ) relationships of

PF‐06463922

in nonclinical tumor models.

Chapter 19

Figure 19.1 Lead progression: HTS hit structure (

1

), initial clinical candidate (

2

, TZP‐101 or ulimorelin), and optimized oral clinical candidate (

3

, TZP‐102). (The nomenclature and the tether backbone numbering shown are used throughout the text.)

Figure 19.2 Panels a and b: The open (a) and closed (b) conformation of TZP‐101 macrocyclic structure showing the molecular fields and solvent‐accessible molecular surface using Forge™ software (v10, Cresset, United Kingdom). Panel c: X‐ray crystal structure of TZP‐101 showing the IHB network (solvent and counterion omitted for clarity). Panel d: Solution NMR consensus structure and molecular dynamics simulation also demonstrating hydrophobic collapse possibility. Panel e: Variable temperature NMR data indicating that the tether amide N–H (cf. Figure 19.1) is not solvent exposed, likely due to IHB.

Figure 19.3 Lead optimization strategies discussed herein.

Figure 19.4 Correlation plots based on data presented in Table 19.1.

Figure 19.5 Rat gastric emptying data (oral administration, metoclopramide as positive control).

Figure 19.6 X‐ray crystal structures of

2

(TZP‐101) and

3

(TZP‐102) (counterions omitted for clarity).

Chapter 20

Figure 20.1 Structures of macrolides and ketolides.

Figure 20.2 Schematic representation of bacterial ribosome and antibiotic sites of interaction.

Figure 20.3 Crystallographic structure of clarithromycin bound to the

Deinococcus radiodurans

ribosome from PDB code 1J5A. The purple‐colored lines and numbers are the interaction distances (values are in angstroms) between clarithromycin (yellow) and ribosome in the active site. The interacting residues and clarithromycin are presented in capped sticks with their atom types. Remaining residues are presented as stick model in beige color. All residues are labeled with their residue names in red color. Hydrogen atoms are omitted.

Figure 20.4 Crystallographic structure of solithromycin bound to the

Escherichia coli

ribosome from PDB code 4WWW. (a) Position of solithromycin (yellow) within the ribosomal binding site. The neighboring 23S rRNA residues and amino acid residues of protein L22 are labeled. Only polar hydrogens are shown. Interacting residues and solithromycin are shown in capped sticks. (b) Interactions involving the triazolyl‐aminophenyl side chain of solithromycin. (c) Interactions of 2‐fluorine of solithromycin and desosamine to 23S rRNA in the drug binding site.

Figure 20.5 Large‐scale synthesis of solithromycin. (a) Bz

2