Nucleic Acids in Medicinal Chemistry and Chemical Biology E-Book

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Wiley series in drug discovery and development
• Sprache: Englisch

Seitenzahl: 952

Veröffentlichungsjahr: 2022

Beschreibung

Nucleic Acids in Medicinal Chemistry and Chemical Biology An up-to-date and comprehensive exploration of nucleic acid medicinal chemistry and its applications In Nucleic Acids in Medicinal Chemistry and Chemical Biology: Drug Development and Clinical Applications, a team of distinguished researchers delivers a comprehensive overview of the chemistry and biology of nucleic acids and their therapeutic applications. The book emphasizes the latest research in the field, including new technologies like CRISPR that create novel possibilities to edit mutated genes at the genomic DNA level and to treat inherited diseases and cancers. The authors explore the application of modified nucleosides and nucleotides in medicinal chemistry, a variety of current topics on nucleic acid chemistry and biology, nucleic acid drugs used to treat disease, and more. They also probe new domains of pharmaceutical research, offering the reader a wealth of new drug discovery opportunities emerging in this dynamic field. Readers will also find: * A thorough introduction to the basic terminology and knowledge of the field of nucleic acid medicinal chemistry * Comprehensive explorations of the methods used to determine the development of nucleic acid drugs * Practical discussions of new technologies, like CRISPR, nanotechnology-based delivery systems, synthetic biology, and DNA-encoded chemical libraries * In-depth examinations of the latest, cutting-edge developments in nucleic acid medicinal chemistry Perfect for medicinal and nucleic acid chemists, Nucleic Acids in Medicinal Chemistry and Chemical Biology will also earn a place in the libraries of biochemists, chemical biologists, and pharmaceutical researchers.

Leseprobe

Table of Contents

Cover

Series Page

Title Page

Copyright Page

PREFACE

CONTRIBUTORS

FOREWORD

NUCLEIC ACID‐BASED THERAPEUTICS: A TOUR DE FORCE

INTRODUCTION

REFERENCES

CHAPTER 1: DESIGN, SYNTHESIS, AND APPLICATIONS OF NUCLEOSIDE PHOSPHATE AND PHOSPHONATE PRODRUGS

1.1. INTRODUCTION

1.2. NUCLEOSIDE PHOSPH(ON)ATE PRODRUGS

1.3. SYNTHESIS OF NUCLEOSIDE PHOSPH(ON)ATE PRODRUGS

1.4. CONCLUSION

ABBREVIATIONS

ACKNOWLEDGMENT

REFERENCES

CHAPTER 2: CYCLIC DINUCLEOTIDES: A NEW‐GENERATION DRUG FOR IMMUNE THERAPY

2.1. STRUCTURE OF CDNs

2.2. cGAS‐cGAMP‐STING PATHWAY

2.3. DEGRADATION OF CDNs IN ENPP1 AND SERUM

2.4. CDN‐BASED THERAPY FOR ANTI‐INFECTION TREATMENT

2.5. CDN‐BASED THERAPY FOR ANTI‐TUMOR TREATMENT

2.6. CDN‐BASED THERAPY FOR AUTOIMMUNE TREATMENT

2.7. CDNs DELIVERY

2.8. CDNs SYNTHESIS

2.9. CONCLUSION AND PERSPECTIVE

REFERENCES

CHAPTER 3: ENZYMATIC AND ENDOGENOUS SYNTHESIS OF NAD(P)‐DERIVED CALCIUM‐MOBILIZING MESSENGERS

3.1. INTRODUCTION

3.2. CYCLIC ADP‐RIBOSE AND NAADP

3.3. ENZYMATIC SYNTHESIS

3.4. ENDOGENOUS SYNTHESIS

3.5. SARM1 – A NEW ENZYME FOR BIOGENESIS OF cADPR AND NAADP

3.6. ADPR: A CA

2+

‐MOBILIZING SECOND MESSENGER?

REFERENCES

CHAPTER 4: SELENIUM ATOM‐MODIFIED NUCLEIC ACIDS FOR STRUCTURAL, FUNCTIONAL, AND DIAGNOSTIC STUDIES

4.1. BACKGROUND

4.2. SeNA ADVANTAGES FOR CRYSTALLIZATION AND PHASING IN NUCLEIC ACID CRYSTALLOGRAPHY

4.3. RECENT SeNA MODIFICATIONS

4.4. SeNA‐FACILITATED STRUCTURAL AND FUNCTIONAL STUDIES VIA X‐RAY AND NEUTRON DIFFRACTION CRYSTALLOGRAPHY

4.5. SeNA POTENTIALS IN THERAPEUTIC AND DIAGNOSTIC DEVELOPMENT

4.6. CONCLUSIONS AND PERSPECTIVES

REFERENCES

CHAPTER 5: SEQUENCE‐SPECIFIC CHROMOSOMAL DNA BINDERS

5.1. INTRODUCTION

5.2. COMPARISON OF PROTEIN‐BASED AND SYNTHETIC DNA TARGETING SYSTEMS

5.3. TFOs STRUCTURE VIA HOOGSTEEN BOND INTERACTION

5.4. PNA AS dsDNA INVASION AGENT

5.5. PYRROLE‐IMIDAZOLE POLYAMIDES (PIPs)

5.6. PERSPECTIVES

ACKNOWLEDGMENT

REFERENCES

CHAPTER 6: DNA SYNTHESIS AND SYNTHETIC GENOME

6.1. INTRODUCTION

6.2. DESIGN A SYNTHETIC GENOME

6.3. SYNTHESIZE AND ASSEMBLE A GENOME FROM SCRATCH

6.4. GENOME TRANSPLANTATION

6.5. BUG MAPPING AND DEBUGGING

ACKNOWLEDGMENTS

REFERENCES

CHAPTER 7: METHODS FOR MAPPING OF NUCLEIC ACIDS EPIGENETIC MODIFICATIONS AND ITS CLINIC APPLICATIONS

7.1. INTRODUCTION

7.2. METHODS FOR MAPPING OF EPIGENETIC MODIFICATIONS IN DNA

7.3. METHODS FOR MAPPING OF EPIGENETIC MODIFICATIONS IN RNA

7.4. THE CLINIC APPLICATIONS OF DETECTION OF NUCLEIC ACIDS EPIGENETIC MODIFICATIONS

7.5. CONCLUSION AND FUTURE PROSPECT

REFERENCES

CHAPTER 8: DNA‐ENCODED CHEMICAL LIBRARIES USED FOR DRUG DISCOVERY

8.1. INTRODUCTION

8.2. ENCODING METHODS OF DELs

8.3. CHEMICAL DIVERISTY OF DELs

8.4. SELECTION METHODS OF DELs

8.5. APPLICATIONS OF DELS FOR HIT DISCOVERY

8.6. SUMMARY AND OUTLOOK

ACKNOWLEDGMENT

REFERENCES

CHAPTER 9: NUCLEIC ACID–BASED NANOCARRIERS AS DRUG DELIVERY SYSTEM

9.1. INTRODUCTION

9.2. DESIGN OF NUCLEIC ACID–BASED NANOSTRUCTURES FOR DRUG DELIVERY SYSTEM

9.3. STRATEGIES FOR EFFICIENT DRUG DELIVERY WITH NUCLEIC ACID NANOSTRUCTURES

9.4. APPLICATIONS OF DNA/RNA NANOSTRUCTURES FOR DRUG DELIVERY

9.5. CONCLUSION AND FUTURE PERSPECTIVES

REFERENCES

CHAPTER 10: FLUORESCENCE HYBRIDIZATION IMAGING OF NEUROLOGICAL DISEASE MESSENGER RNAs

ABBREVIATIONS

10.1. INTRODUCTION

10.2. STRATEGY

10.3. METHODS

10.4. RESULTS

10.5. DISCUSSION

ACKNOWLEDGMENTS

REFERENCES

CHAPTER 11: PROGRESS OF OLIGONUCLEOTIDE THERAPEUTICS TARGET TO RNA

11.1. BACKGROUND

11.2. VARIETIES AND PROGRESS OF OLIGONUCLEOTIDE DRUGS IN CLINICAL TRIALS

11.3. SAFETY AND SPECIFICITY OF OLIGONUCLEOTIDE DRUGS

11.4. BARRIERS FOR ONs DELIVERY

11.5. DELIVERY OF OLIGONUCLEOTIDE DRUGS

11.6. CHEMICAL MODIFICATION OF OLIGONUCLEOTIDE DRUGS

11.7. EPILOGUE

REFERENCES

CHAPTER 12: CRISPR/CAS9

12.1. INTRODUCTION

12.2. BASICS OF CRISPR/Cas9 FOR GENE THERAPY

12.3. CLINICAL TRIAL I, EDITING THE CCR5 GENE IN HUMAN STEM CELLS

12.4. CLINICAL TRIAL II FOR SCD, B‐THALASSEMIA, AND CANCER

12.5. CHALLENGES AND OPPORTUNITIES

REFERENCES

CHAPTER 13: APTAMER PROPERTIES, FUNCTIONS, AND APPLICATIONS

13.1. INTRODUCTION

13.2. SELEX TECHNOLOGY

13.3. PROPERTIES OF APTAMERS

13.4. APTAMER FUNCTIONS

13.5. APTAMER‐BASED ANALYSIS METHOD

13.6. APTAMER‐BASED BIOMARKER DISCOVERY

13.7. APTAMER–BASED TARGETED THERAPY

13.8. APTAMER/APTAZYME‐BASED RIBOSWITCHES

13.9. CHALLENGES AND SOLUTIONS

13.10. CONCLUSION

REFERENCES

CHAPTER 14: G‐QUADRUPLEX AS A PLATFORM FOR NEW PERSPECTIVES IN NUCLEIC ACID TARGETING FOR THERAPEUTIC APPLICATIONS

14.1. INTRODUCTION

14.2. IS THE LIGAND DESIGN CHANGING?

14.3. THERAPEUTIC EFFICIENCY: SELECTIVE vs NOT SELECTIVE?

14.4. PROTEIN‐BASED LIGANDS FOR G‐QUADRUPLEXES

14.5. METHODS FOR G4 IDENTIFICATION AND CHARACTERIZATION

14.6. CONCLUDING REMARKS

ACKNOWLEDGMENTS

REFERENCES

INDEX

Wiley Series in Drug Discovery and Development

End User License Agreement

List of Tables

Chapter 2

TABLE 2.1

Combinational therapies based on CDNs for antitumor treatment

TABLE 2.2

Pipeline of STING targeted drugs

Chapter 3

TABLE 3.1

Literature summary of the biological functions regulated by cADPR

...

Chapter 5

TABLE 5.1

Comparison of protein‐based and synthetic DNA targeting systems

...

TABLE 5.2

The limitations and strategies of improvement of TFOs

TABLE 5.3

Biological functions of sequence‐specific Epi‐drugs

TABLE 5.4

Summary of representative non‐covalent DNA binding systems

Chapter 7

TABLE 7.1

Diagnostic and prognostic of DNA methylation from liquid biopsy/t

...

TABLE 7.2

Diagnostic and prognostic of 5hmc from liquid biopsy/tissues biop

...

Chapter 8

TABLE 8.1

Summary and comparison of DEL encoding methods

TABLE 8.2

Summary and comparison of DEL selection methods

TABLE 8.3

DEL‐compatible reactions

TABLE 8.4

A summary of identified hit compounds from recent DEL

Chapter 10

TABLE 10.1

Fluorophore‐PNA‐peptide sequences

TABLE 10.2

Fluorophore‐PNA‐peptide sequences

TABLE 10.3

Unique to human

HTT

siRNA 27mer duplexes

Chapter 11

TABLE 11.1

Commercialized ONs approved by FDA/EMA (until January 2021)

TABLE 11.2

The ON drugs in phase III clinical trial

TABLE 11.3

The siRNA drug using lipid‐based delivery system in the clinical

...

TABLE 11.4

The modification details and sequences of siRNA‐GalNAc drugs

...

Chapter 12

TABLE 12.1

Ongoing clinical trials with

ex vivo

CRISPR gene editing

Chapter 13

TABLE 13.1

Comparison between aptamers and antibodies

TABLE 13.2

The biomarkers have been identified by DNA aptamers

List of Illustrations

Introduction

Figure 1 Structures of entecavir, tenofovir (TFV), and its derivatives TDV a...

Figure 2 Structure of Sofosbuvir.

Chapter 1

Figure 1.1 Formation

in vivo

of the active triphosphate (TP) of FNC.

Figure 1.2 Design and mechanism of action of nucleoside phosph(on)ate prodru...

Figure 1.3 Nucleoside phosph(on)ate prodrugs in clinical use.

Figure 1.4 Activation of carbonyloxymethyl ester prodrugs.

Figure 1.5 Structure of adefovir dipivoxil.

Figure 1.6 Structure of tenofovir disoproxil fumarate (TDF).

Figure 1.7 Structure of besifovir (LB80380).

Figure 1.8 Structure of non‐nucleoside prodrugs BMS‐188494 and ER‐2785...

Figure 1.9 Design and activation of alkoxyalkyl monoester prodrugs.

Figure 1.10 Structure of brincidofovir (CMX‐001).

Figure 1.11 Structure of CMX‐157.

Figure 1.12 Structure of fozivudine tidoxil.

Figure 1.13 Activation of HepDirect prodrugs.

Figure 1.14 Structure of pradefovir (MB06866).

Figure 1.15 Design rationale of HepDirect prodrugs of adefovir.

Figure 1.16 Lead optimization for the discovery of pradefovir (MB06866).

Figure 1.17 Structure of MB07133.

Figure 1.18 Structure of non‐nucleoside prodrug MB07811.

Figure 1.19 Activation of phosphoramidate/phosphonamidate prodrugs.

Figure 1.20 Structure of sofosbuvir (PSI‐7977).

Figure 1.21 The design rationale of sofosbuvir (PSI‐7977).

Figure 1.22 Structure of tenofovir alafenamide fumarate (TAF).

Figure 1.23 Structure of remdesivir (GS‐5734).

Figure 1.24 Structure of AT‐527.

Figure 1.25 Structure of GS‐6620.

Figure 1.26 Structure of NUC‐1031.

Figure 1.27 Structure of NUC‐3373.

Figure 1.28 Structure of stampidine.

Figure 1.29 Structure of thymectacin.

Figure 1.30 Structure of BMS‐986094 (INX‐08189).

Figure 1.31 Structure of PSI‐353661.

Figure 1.32 Structure of GS‐9131.

Figure 1.33 Structure of uprifosbuvir (MK‐3682).

Figure 1.34 Structure of CL‐096.

Figure 1.35 Structure of IDX‐184.

Figure 1.36 Discovery of CL‐206, a new phosphoramidate prodrug with an...

Scheme 1.1 Synthesis of carbonyloxymethyl phosphate diester prodrugs.

Scheme 1.2 Synthesis of carbonyloxymethyl phosphonate diester prodrugs.

Scheme 1.3 Synthesis of alkoxyalkyl phosphate monoester prodrugs.

Scheme 1.4 Synthesis of alkoxyalkyl phosphonate monoester prodrugs.

Scheme 1.5 Synthesis of HPMP‐adenine prodrug (16).

Scheme 1.6 Synthesis of prodrug brincidofovir (CMX‐001).

Scheme 1.7 Synthesis of HepDirect phosph(on)ate prodrugs.

Scheme 1.8 Enantioselective synthesis of pradefovir and the other

cis

‐isomer...

Scheme 1.9 Synthesis of phosphoramidate prodrugs.

Scheme 1.10 Synthesis of phosphonamidate prodrugs.

Scheme 1.11 Asymmetric synthesis of sofosbuvir (PSI‐7977).

Scheme 1.12 Preparation of tenofovir alafenamide fumarate (GS‐7340).

Scheme 1.13 Asymmetric synthesis of remdesivir (GS‐5734).

Scheme 1.14 Catalytic asymmetric synthesis of uprifosbuvir (MK‐3682)....

Chapter 2

Figure 2.1 General structure of CDNs.

Figure 2.2 Ribose conformation of CDNs.

Figure 2.3 dsDNA‐induced cGAS‐STING pathway.

Figure 2.4 Molecular basis of dsDNA sensing by cGAS.

Figure 2.5 Activation mode of STING stimulated by CDN.

Figure 2.6 Molecular basis of hSTING activation by CDNs. (a) The structure o...

Figure 2.7 SNP distribution of hSTING protein.

Figure 2.8 Proposed degradation mechanism of 2′,3′‐cGAMP by (a) ...

Figure 2.9 CDN‐based therapy for anti‐tumor treatment.

Figure 2.10 Structure of ADU‐S100.

Figure 2.11 cGAS‐STING pathway and autoimmune diseases.

Figure 2.12 Inhibitors of cGAS‐hSTING pathway.

Figure 2.13 Drug delivery systems of CDNs.

Figure 2.14 SATE‐ and DTE‐based prodrug of CDN.

Figure 2.15 Non‐nucleotide‐based STING agonist.

Scheme 2.1 Solid phase synthesis of CDNs ‐ 1.

Scheme 2.2 Solid phase synthesis of CDNs ‐ 2.

Scheme 2.3 Solid phase synthesis of CDNs – 3.

Scheme 2.4 Solution‐phase chemistry for the synthesis of CDNs. (a) Phosphotr...

Scheme 2.5 Stereo‐controlled synthesis of thiophosphate substituted CDNs.

Chapter 3

Figure 3.1 The crystal structures of cADPR and NAADP. The dotted green circl...

Figure 3.2 The crystal structure of the ADP‐ribosyl cyclase. The cyclase is ...

Figure 3.3 Crystallographic visualization of the cyclization of a substrate ...

Figure 3.4 Compartmentation of the two topological types of CD38. Type III C...

Figure 3.5 The structure of SARM1. (a) Illustration of the domains of human ...

Figure 3.6 The reactions catalyzed by SARM1. All the substrates and products...

Figure 3.7 Working model of axonal degeneration. After injury or chemotherap...

Figure 3.8 The metabolism and functions of ADPR in mammalian cells. (a)–(c) ...

Chapter 4

Figure 4.1 Chemical structure of selenium‐modified nucleic acids (SeNA).

Figure 4.2 The 2′‐SeCH

3

modifications of the ribose are implanted in A...

Scheme 4.1 Synthesis of NTPαSe analogs.

Scheme 4.2 Synthesis of 2‐Se‐U/T modified DNA and RNA.

Figure 4.3 X‐ray crystal structures of the Se‐DNA and Se‐RNA. (a) Se‐DNA: (...

Figure 4.4 Crystal and structure of the 4‐Se‐U RNA hexamer, (5′‐U‐

Se

U‐...

Figure 4.5 The neutron‐diffraction‐determined structures of the Se‐DNA: d[G...

Scheme 4.3 Simple and mild synthesis of dNTPαSe analogs via the one‐pot stra...

Figure 4.6 (a) Amplification curves; single‐digit copies of DNA molecules we...

Chapter 5

Figure 5.1 Diagram of TFO structure and Hoogsteen pairing. (a) Parallel/pyri...

Figure 5.2 Structure and DNA binding mode of PNA. (a) Chemical structure of ...

Figure 5.3 PIPs structure and DNA binding modes. (a) Schematic hydrogen inte...

Chapter 6

Figure 6.1 Genome synthesis. (a) The synthetic genome is designed from nativ...

Figure 6.2 Design a synthetic genome. The native sequence of prokaryotic gen...

Figure 6.3 Assembly of an entire synthetic genome from scratch. (a) Oligonuc...

Figure 6.4 Genome transplantation.

Figure 6.5 Genome transplantation between yeast and

M. mycoides

.

Figure 6.6 Consolidation synthetic yeast chromosome into one strain.

Figure 6.7 The strategies used for long DNA segments transfer. (a) Cationic ...

Figure 6.8 Genome bug mapping and debugging. (a) Mapping and debugging desig...

Chapter 7

Figure 7.1 Mechanism of sodium bisulfite deamination of cytosine to uracil a...

Figure 7.2 The principle of 5mC‐retained whole‐genome amplification (5mC‐WGA...

Figure 7.3 Scheme of TET‐assisted pyridine borane sequencing of 5mC (TAPS)....

Figure 7.4 Scheme demonstrating of oxidation‐assisted bisulfite sequencing....

Figure 7.5 Scheme of β‐glucosyltransferase based methods for 5hmC Profiling....

Figure 7.6 Scheme of hmC‐CATCH or CAM‐seq.

Figure 7.7 Outline of reduced bisulfite sequencing to map 5fC in DNA (redBS‐...

Figure 7.8 Chemical molecule “AI”‐mediated cyclization labeling of 5fC and s...

Figure 7.9 Detection method of EDC‐catalyzed chemical labeling of 5caC with ...

Figure 7.10 Scheme of “fU‐Seq” based on chemical labeling.

Figure 7.11 Scheme of dU‐seq based on selective labeling and pull‐down techn...

Figure 7.12 RNA epigenetic modifications in mRNA.

Figure 7.13 Scheme of m

6

A‐seq, PA‐m

6

A‐seq and miCLIP based on anti‐m

6

A antib...

Figure 7.14 Scheme of m

6

A‐SEAL assisted by FTO oxidation.

Figure 7.15 Scheme of TAWO‐seq based on peroxotungstate oxidation.

Figure 7.16 Scheme of mapping methods for pseudouridine in transcriptome‐wid...

Figure 7.17 Scheme of ICE‐seq based on chemical labeling.

Chapter 8

Figure 8.1 Clinical drug candidates discovered from DNA‐encoded chemical lib...

Figure 8.2 (a) The general scheme for DNA‐encoded chemical library (DEL). (b...

Figure 8.3 (a) The ESAC approach for encoding DEL. (b) The second‐generation...

Figure 8.4 (a) IDUP. (b) Binder Trap Enrichment. (c) and (d) Two approaches ...

Figure 8.5 An example of DEL selection result analysis and plotted in “finge...

Chapter 9

Figure 9.1 Advantages of nucleic acid–based carriers in drug delivery system...

Figure 9.2 (a) Chemical structures of each nucleotide. (b) Watson–Crick base...

Figure 9.3 (a) DNA Holliday junction structure. (i) Mobile Holliday junction...

Figure 9.4 (a) Double‐crossover (DX) DNA structure. (b) Two‐dimensional latt...

Figure 9.5 (a) Various RNA‐based nanostructures by RNA–DNA hybrids.(b) R...

Figure 9.6 X‐, Y‐, and T‐DNA blocks can be extended into macroscopic materia...

Figure 9.7 (a) Design of eight‐stranded DNA octahedron cage (left) and 3D is...

Figure 9.8 Rationally designed various DNA origami.

Figure 9.9 (a) Micrometer‐scale DNA origami arrays with arbitrary shapes....

Figure 9.10 DNA origami with curvature. (a) Dolphin‐shaped DNA origami struc...

Figure 9.11 (a) Reconfiguration of DNA origami tripods and its confirmation ...

Figure 9.12 (a) Schematic illustration of RCT process and its microscopic st...

Figure 9.13 (a) Process of complexation between DNA and inorganic materials ...

Figure 9.14 (a) Multimeric production of DNA nanostructures by RCA.(b) O...

Figure 9.15 (a) Aptamer‐conjugated DNA dendrimer and DOX delivery into targe...

Figure 9.16 Enzymatic replication‐based AS1411 apatamer‐expressed RNA nanove...

Figure 9.17 Folic acid expressed on DNA tetrahedron and its tumor‐specific d...

Figure 9.18 (a) Bio‐orthogonal conjugation‐induced functionalization of DNA ...

Figure 9.19 RGD‐conjugated DNA nanostructure for the cellular uptake. (b) Qu...

Figure 9.20 (a) Synthesis of anti‐EGFR Ab‐conjugated RNA nanoball. (b) Cytom...

Figure 9.21 (a) Synthesis of cetuximab‐expressed DNA tetrahedron nanostructu...

Figure 9.22 (a) Synthesis of CPP‐labeled DNA tetrahedron through click chemi...

Figure 9.23 Virus capsid‐encapsulated DNA origami‐based delivery system. (a)...

Figure 9.24 (a) pH‐responsive transformation system between i‐motif quadrupl...

Figure 9.25 (a) UV and visible light‐responsive cis‐trans conformation‐based...

Figure 9.26 (a) Conceptual illustration of DNA nanorobot which is controllab...

Figure 9.27 (a) ATP‐responsive DOX release system. (b) Time‐dependent releas...

Figure 9.28 (a) Catalytic reaction and DOX release system, triggered by miRN...

Figure 9.29 miRNA‐responsive CRISPR‐Cas9 switch system for selective genome ...

Figure 9.30 (a) Tri‐stimuli‐responsive DOX and PND delivery system with DNA ...

Figure 9.31 (a) Self‐assembly of aptamer‐tethered DNA nanotrain with DOX loa...

Figure 9.32 (a) DOX encapsulation in DNA origami and their cellular uptake. ...

Figure 9.33 (a) Main components of the DNA nanoclew and DOX release with its...

Figure 9.34 (a) Design of Endo28‐3WJ. (b) Fluorescence spectra depending on ...

Figure 9.35 (a) Synthesis of PTX‐4WJ RNA nanoparticle through click chemistr...

Figure 9.36 (a) Schematic illustration of antigen–adjuvant–DNA complex and i...

Figure 9.37 (a) Fabrication of TRAIL‐DNA nanoclews complex by Ni

2+

‐His tag a...

Figure 9.38 (a) Synthesis of β‐gal functionalized SNA by click chemistr...

Figure 9.39 (a) Synthesis of enzyme‐loaded DNA tetrahedron with L‐DNA strand...

Figure 9.40 (a) Design of the CpG‐expressed DNA dendrimer. (b, c) The level ...

Figure 9.41 (a) Synthesis of CpG‐expressed DNA tetrahedron and its cellular ...

Figure 9.42 (a) Assembly of CpG‐decorated DNA origami. (b) The level of TNF‐

Figure 9.43 (a) Synthesis of triangle, square, and pentagon‐shaped RNA struc...

Figure 9.44 (a) Design and synthesis of the CpG ODN‐embedded DNA micropartic...

Figure 9.45 (a) Synthesis of DNA nanogel and the mechanism of siRNA release ...

Figure 9.46 (a) Fabrication of siRNA‐embedded RNA microsponge by RCT. (b) SE...

Figure 9.47 (a) Synthesis of BRC by cRCT. (b) Time‐dependent siRNA generatio...

Figure 9.48 (a) Synthesis of DNA shuriken. (b) The effect of DNA shuriken on...

Figure 9.49 (a) Fabrication of Poly‐sgRNA/siRNA nanoparticle. (b) GFP gene k...

Figure 9.50 (a) aPD1‐encapsulated and restriction enzyme‐induced cleavable C...

Chapter 10

Figure 10.1 ChemDraw representation of human DAMGO‐

MAOA

PNA‐AF488, WT4879. T...

Figure 10.2 ChemDraw representation of human Cal560‐AEEA‐

HTT

PNA‐AEEA‐IGF1 t...

Scheme 10.1 Synthesis of peptide‐PNA conjugates. Monomers were coupled in

N

‐...

Figure 10.3 HPLC profiles of (a) Tyr‐

D

‐Ala‐Gly‐

N

‐MePhe‐Ser‐AEEA‐CAT GGT GCT ...

Figure 10.4 Specificity of uptake in SH‐SY5Y (▪) and CHO‐K1 (▲) cells of WT4...

Figure 10.5 Confocal fluorescent images of WT4879 uptake in SH‐SH5Y cells. (...

Figure 10.6 Confocal fluorescent images of (a) WT4879 uptake in CHO‐K1 cells...

Figure 10.7 Confocal fluorescent images of live SH‐SY5Y cells showing the (a...

Figure 10.8 Quantization of RFP for labeled Rab5 and AlexaFluor 488 for WT48...

Figure 10.9 Cell viability analysis of SH‐SY5Y cells using MTT assay for dif...

Figure 10.10 Representative analytical HPLC of

H. sapiens

Cal560‐

HTT

PNA‐

D

(C...

Figure 10.11 Representative MALDI‐ToF mass spectrum of

H. sapiens

Cal560‐

HTT

Figure 10.12 Fluorescent

HTT

imaging agent cellular uptake. HEK293T cells we...

Figure 10.13 siRNA knockdown of

HTT

mRNA in HEK293T cells. Each bar represen...

Figure 10.14 Fluorescence images of HEK293T cells transfected with siRNA, th...

Figure 10.15 Average cell fluorescence intensities in HEK293T cells transfec...

Chapter 11

Figure 11.1 The lipid‐based delivery system of siRNA in the clinical stage....

Figure 11.2 The mechanisms of ON

in vivo

(a) Active inhibition, (b) Physical...

Figure 11.3 Therapeutic areas covered by liposome‐based products.

Figure 11.4 Common cationic lipid structure.

Figure 11.5 The formulation of Patisiran.

Figure 11.6 Structure of several ionic nucleoside and nucleotide lipids.

Figure 11.7 The structure of LU, DOTA, DOCA, DNTA, DNCA, and CLD.

Figure 11.8 Oligonucleotide drug general conjugation strategy.

Figure 11.9 (a) The general structure of GalNAc

3

conjugate from Alnylam and ...

Figure 11.10 (a) Lipid molecules used for long‐acting polypeptide modificati...

Figure 11.11 Self‐assembly properties of lipid‐conjugated nucleic acids.

Figure 11.12 An environmentally sensitive and biodegradable PEG linker.

Figure 11.13 The uptake and endocytosis mechanism of 3′,3″‐bis‐p...

Figure 11.14 The strategy of antibody/ antibody fragment‐ON conjugation.

Figure 11.15 The chemical structure of CD, CSN, PEI, PLL, PLGA, and dendrime...

Figure 11.16 The composition of cyclodextrin polymer nanoparticles.

Figure 11.17 Examples of common chemical structure used in phosphate linkage...

Figure 11.18 Nucleoside analogues could be applied on the modification of ol...

Figure 11.19 Modifications can be applied on nucleic acid base.

Chapter 12

Figure 12.1 Schematic structure of Cas9 and sgRNA. Chemically modified nucle...

Figure 12.2 Delivery of gene‐editing components. For

in vivo

gene editing, g...

Figure 12.3 Targeting

CCR5

gene to cure HIV. The co‐receptor help HIV‐1 ente...

Figure 12.4 Pre‐clinical CCR5 ablation with CRISPR in HSPCsCCR5 was abla...

Chapter 13

Figure 13.1 Schematic representation of SELEX technology.

Figure 13.2 (a) The typical structure types of aptamers. It represents aptam...

Figure 13.3 (a–f) Illustration of aptamers against different targets and the...

Figure 13.4 (a) Illustration of the molecular interaction mechanism.(b) ...

Figure 13.5 (a) Illustration of chemical modifications on aptamer.(b) Ch...

Figure 13.6 The mechanism of aptamer blocking SARS‐CoV‐2 infection.

Figure 13.7 Schematic illustration of aptamer‐anchored AIE‐dots (Apt‐AIE dot...

Figure 13.8 Aptamer‐induced protein‐specific bioorthogonal modification tech...

Figure 13.9 The strategy of aptamer‐based biomarker discovery in cells.

Figure 13.10 Noncovalent conjugation of aptamer‐DOX. (a) Physical‐conjugate ...

Figure 13.11 Covalent conjugation of aptamer‐drug conjugation. (a) Sgc8c‐DOX...

Figure 13.12 Aptamer–synergistic drug conjugates. (a) Conjugation of an apta...

Figure 13.13 Regulatory mechanisms of synthetic aptamer/aptazyme riboswitche...

Chapter 14

Figure 14.1 Starting libraries of indole (a) and stiff‐stilbene (b) derivati...

Figure 14.2 Model of the intercalation of 360A into the tetrahelical folded

Figure 14.3 Copper metallacrown (a) and trisubstituted fan‐shaped trinuclear...

Figure 14.4 Molecular structure of APC.

Figure 14.5 Chemical structures of the most efficient anthraquinone‐(pyrrol)...

Figure 14.6 Examples of studied Neomycin conjugates.

Figure 14.7 Examples of tri‐substituted (CM03, (a) and cyclic (b) naphthalen...

Figure 14.8 Chemical structures of perylene derivatives tested for their G4 ...

Figure 14.9 AN‐1 and structurally related derivatives.

Figure 14.10 Scheme of the substitution pattern considered for indolo‐naphth...

Figure 14.11 Different scaffolds and substitution patterns used for the sele...

Figure 14.12 Examples of small molecules designed to simultaneously recogniz...

Figure 14.13 Example of cyclic (a) and staple (b) peptides.

Figure 14.14 BMVC, a G4 ligand studied by G4 microarray.

Figure 14.15 Example of fluorescent G4 ligands (a and b) and of ligand (c) a...

Figure 14.16 Noncytotoxic Au(I) complex.

Guide

Cover Page

Series Page

Title Page

Copyright Page

PREFACE

CONTRIBUTORS

FOREWORD

INTRODUCTION

Table of Contents

Begin Reading

Index

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Wiley Series in Drug Discovery and Development

Binghe Wang, Series Editor

A complete list of the titles in this series appears at the end of this volume.

NUCLEIC ACIDS IN MEDICINAL CHEMISTRY AND CHEMICAL BIOLOGY

DRUG DEVELOPMENT AND CLINICAL APPLICATIONS

Edited by

LIHE ZHANG

Peking University

Beijing, China

XINJING TANG

Peking University

Beijing, China

ZHEN XI

Nankai University

Tianjin, China

JYOTI CHATTOPADHYAYA

University of Uppsala

Uppsala, Sweden

This edition first published 2023© 2023 John Wiley & Sons, Inc.

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Library of Congress Cataloging‐in‐Publication DataNames: Zhang, Lihe, editor. | Tang, Xinjing, editor. | Xi, Zhen, editor. | Chattopadhyaya, Jyoti, editor.Title: Nucleic acids in medicinal chemistry and chemical biology: drug development and clinical applications / Lihe Zhang (Peking University, Beijing, China), Xinjing Tang (Peking University, Beijing, China), Zhen Xi (Nankai University, Tianjin, China), Jyoti Chattopadhyaya (University of Uppsala, Uppsala, Sweden).Description: Hoboken, NJ : Wiley, 2023. | Series: Wiley series in drug discovery and development | Includes bibliographical references and index.Identifiers: LCCN 2022033410 (print) | LCCN 2022033411 (ebook) | ISBN 9781119692744 (hardcover) | ISBN 9781119692751 (adobe pdf) | ISBN 9781119692782 (epub)Subjects: LCSH: Nucleic acids–Therapeutic use. | Pharmaceutical chemistry.Classification: LCC RM666.N87 N835 2023 (print) | LCC RM666.N87 (ebook) | DDC 615.1/9–dc23/eng/20221005LC record available at https://lccn.loc.gov/2022033410LC ebook record available at https://lccn.loc.gov/2022033411

Cover Design: WileyCover Image: Courtesy of Xiaoxuan Su and Yu Zhang

PREFACE

As is often the case, research progress involving a given class of compounds can be limited by its availability. As a consequence of extensive investigations carried out by many laboratories, it is now possible to acquire (modified) DNAs and RNAs of diverse structure commercially, or by following detailed preparative descriptions in the literature. This certainly now includes the nucleic acids that encode many proteins, facilitating the enhanced study of both classes of molecules. The increased accessibility of such molecules is clear from the range of topics addressed in the current volume.

One would expect advances of understanding in many areas of inquiry to be enabled by ready access to nucleic acids and molecules with which they interact. The chapters in this volume certainly provide this increased level of insight into biological systems and their modes of function. Perhaps somewhat more surprising is the large increase in the number of applications reflected in the individual chapters of this volume. These now extend well beyond the development of new therapeutic strategies to a great variety of new tools to interrogate detailed elements of biological and biochemical processes. A number of these applications are introduced briefly below as part of this preface to illustrate the expanded reach of current studies in nucleic acids.

The current volume addresses several aspects of ongoing research activities pertinent to the medicinal chemistry of nucleic acids. Three chapters deal with nucleoside and nucleotide analogues as physiological mediators. Among these is Chapter 1, which deals with nucleoside analogues that function in biological systems as phosphorylated species. Such nucleoside analogues are generally not internalized by cells when phosphorylated due to the accompanying negative charge and often cannot be phosphorylated efficiently intracellularly. An alternative is the administration of neutral phosphate and phosphonate prodrugs. These can be unmasked within cells using any of several strategies. Chapter 2 discusses the structures of the cyclic dinucleotides and the mechanisms that they use to produce an immune response. This includes the STING (stimulator of interferon) pathway and the identification of hSTING protein, which has 379 amino acids and for which 3 structural domains have been defined. There are potential applications in anticancer therapy (via IFN, cytotoxic T‐lymphocytes, and natural killer cells). The cyclic dinucleotides are good candidates for adjuvant chemotherapy with numerous therapeutic agents. Cyclic dinucleotides are also potentially useful for the treatment of autoimmune diseases resulting from STING gain‐of‐function mutations. Chapter 3 discusses cyclic ADP‐ribose and NAADP, two Ca‐mobilizing messengers. They have numerous biological functions, including Ca trafficking processes and the transfer of mitochondria from human astrocytes to glioma cells. The chapter also discusses their enzymatic synthesis (involving ADP‐ribosyl cyclase and CD38). Type III CD38 may also be involved in the endogenous production of cyclic ADP‐ribose, while type II CD38 is implicated in the endogenous production of NAADP. Recently, it was shown that protein SARM1, not at all similar to CD38, is expressed in neuronal tissue that biosynthesizes both mediators.

Two additional chapters are also concerned with medicinal chemistry. These include Chapter 14, which details the use of structurally distinct forms of G‐quadruplexes as targets for selective binding by small molecules. The small molecules include derivatives of indoles and bis‐indoles, which have been functionalized with side chains that can be protonated to enable specific types of G‐tetrad interactions. Recently discovered ligands include copper metallocrowns and trisubstituted fan‐shaped trinuclear Pt(II) complexes. Additionally, carbohydrates have been used to functionalize G‐tetrad binders, imparting increased affinity and selectivity, as well as improved solubility. Finally, Chapter 8 describes the use of DNA‐encoded chemical libraries as a strategy for drug discovery. There is a surprisingly large number of strategies that can be employed to utilize DNA encoding for the discovery of small molecules potentially useful as drugs, and this chapter cites several small‐molecule clinical candidates discovered from DNA‐encoded libraries.

Of continuing interest to the nucleic acids community are the numerous studies that employ molecules capable of interacting selectively with nucleic acids. These studies have provided very important insights in the past and promise to continue to do so. Chapter 5 discusses work that has been done to define and utilize compounds that can bind to chromosomal DNA in a sequence‐specific fashion. As noted, intervening at the level of cellular DNA is very attractive conceptually because the number of target molecules is minimal. The authors compare several natural, mostly protein‐based systems (including CRISPR/Cas9, TALENs, ZNF, and TFOs) to synthetic peptide nucleic acids (PNA) and pyrrole‐imidazole polyamides, noting key differences and issues. The chapter notes recent initiatives, including targeted mutagenesis, homologous recombination, and the use of PNA for dsDNA invasion, as well as potential applications (e.g. gene editing, gene modulation via epigenetics, and PNA regulation of gene structure). Chapter 12 provides a highly informative summary of the basics of gene editing with CRISPR/Cas9 for therapeutic applications. It also includes the details of a clinical trial to counter the effects of HIV infection by ablating the CCR5 gene. Yet another example of molecules that interact selectively with nucleic acids is provided in Chapter 10, which deals with the fluorescence hybridization imaging of neurological disease mRNAs in live neuronal cells. MAOs occur in the mitochondrial outer membrane. The imaging probes included MAOA‐specific PNA dodecamers, separated by an N‐terminal spacer to a μ‐opioid receptor targeting peptide, with a spacer and fluorophore at the C‐terminus. These were delivered into SH‐SY5Y neuroblastoma cells through μ‐opioid receptor‐mediated endocytosis.

Two strategies that have been pursued for a number of years continue to receive substantial attention. One of these, oligonucleotide therapeutics, has arguably become even more active in the past several years. The comprehensive review of this topic in Chapter 11, comparing ASOs and siRNAs, includes a discussion of adjuvant delivery by GalNAc and lipids. Antibodies have also been used as conjugates. Oligonucleotide drugs can work by active mechanisms involving degradation of endogenous mRNA target sequences (by RNase H or argonaute‐2). An additional mechanism involves physical blocking, e.g. by translation arrest or modulation of RNA processing. Finally, Chapter 13 describes the properties functions and applications of aptamers, single‐stranded DNA or RNA that can bind selectively to a specific target. Aptamers occur in nature as riboswitches and can be selected to mediate enzyme inhibition, growth factor neutralization, immune function, and antiviral activity.

The remaining four chapters deal with modified nucleic acids. There are numerous modified nucleosides that appear both in RNA and DNA, and these have a variety of functions. High density CpG methylation of DNA promoter regions can block transcription factor binding and diminish gene expression. Likewise, post‐transcriptional modification of mRNA can affect its stability and expression efficiency. There is a strong link of epigenetic modifications and disease, as well established for cancers. Chapter 7 outlines techniques used to detect and characterize such modifications. Also of interest is Chapter 6, which describes the preparation of modified genomes and organisms. Such modified genomes contain new structural features, such as the elimination of repetitive sequences to improve stability, the minimization of genome size, and recoding (simplification) of genomes. The crystallization of nucleic acid structures and their characterization by X‐ray crystallography is greatly facilitated by the introduction of Se atoms at specific positions. As described in Chapter 4, there are now methods for effecting substitutions throughout the entire DNA oligonucleotide structure. Finally, the study of DNA origami has become very popular and has led to a variety of techniques for preparing highly specialized structures. Chapter 9 focuses on the preparation of nucleic acid‐based nanocarriers that can be used for drug delivery, including three‐dimensional cages. These include bio‐orthogonal conjugation‐induced functionalization of DNA nanocages. RGD‐conjugated DNA structures showed high binding affinity to HeLa cells, and a cell‐penetrating peptide (CPP)‐modified DNA nanostructure developed to facilitate endocytosis‐mediated uptake into target cells.

Sidney M. Hecht

Arizona State University

CONTRIBUTORS

Junbiao Chang College of Chemistry, Zhengzhou University, Zhengzhou, China; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China

Cen Chen SeNA Research Institute, Chengdu, Sichuan, China

Hongkui Deng School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life Sciences, Peking University, Beijing, China

Sangwoo Han Department of Chemical Engineering, University of Seoul, Seoul, Republic of Korea

Zhen Huang SeNA Research Institute, Chengdu, Sichuan, China; College of Life Sciences, Sichuan University, Chengdu, Sichuan, China; Department of Biochemistry, Szostak‐CDHT Large Nucleic Acids Institute, Chengdu, Sichuan, China

Yoonbin Ji Department of Chemical Engineering, University of Seoul, Seoul, Republic of Korea

Dajeong Kim Department of Chemical Engineering, University of Seoul, Seoul, Republic of Korea

Hon Cheung Lee State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China

Jong Bum Lee Department of Chemical Engineering, University of Seoul, Seoul, Republic of Korea

Xiaoyu Li Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, China; Laboratory for Synthetic Chemistry and Chemical Biology, Health@InnoHK Program by Innovation and Technology Commission, Hong Kong, China

Yizhou Li Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China

Yue Liu Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China

Yulin Liu School of Basic Medical Sciences, State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center and the MOE Key Laboratory of Cell Proliferation and Differentiation, College of Life Sciences, Peking‐Tsinghua Center for Life Sciences, Peking University, Beijing, China

Dejun Ma Department of Chemical Biology and State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China

Sunghyun Moon Department of Chemical Engineering, University of Seoul, Seoul, Republic of Korea

Manlio Palumbo Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy

Yufei Pan State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China

Ganesh N. Pandian Institute for Integrated Cell‐Material Sciences (iCeMS), Kyoto University, Kyoto, Japan

Shuang Peng College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China

Claudia Sissi Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy

Hiroshi Sugiyama Institute for Integrated Cell‐Material Sciences (iCeMS), Kyoto University, Kyoto, Japan; Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan

Shicheng Sun The Murdoch Children's Research Institute, Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia

Weihong Tan The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China; Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, China

Zhenghua Wang Department of Chemical Biology and State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China

Xiaocheng Weng College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China

Eric Wickstrom Laboratory of Molecular Design, Thomas Jefferson University, Philadelphia, PA, USA

Zhen Xi Department of Chemical Biology and State Key Laboratory of Elemento‐Organic Chemistry, College of Chemistry, Nankai University, Tianjin, China

Ze‐Xiong Xie Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China

Fukang Yang SeNA Research Institute, Chengdu, Sichuan, China

Shilian Yang Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China

Zhenjun Yang State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China

Wenquan Yu College of Chemistry, Zhengzhou University, Zhengzhou, China

Zutao Yu Institute for Integrated Cell‐Material Sciences (iCeMS), Kyoto University, Kyoto, Japan

Kexin Yuan College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China

Ying Jin Yuan Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China

Liqin Zhang State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China

Guixian Zhao Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China

Yong Juan Zhao Ciechanover Institute of Precision and Regenerative Medicine, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, China

Zilong Zhao Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, China

Xiang Zhou College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China

Xinyang Zhou State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China; School of Criminal Investigation & Forensic Science, People's Public Security University of China, Beijing, China

Rui Ying Zhu Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China

Guangrong Zou College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, Hubei, China

FOREWORD

NUCLEIC ACID‐BASED THERAPEUTICS: A TOUR DE FORCE

As the serial editor, it gives me special pleasure to write a foreword for this volume focused on nucleic acids in the Wiley Series in Drug Discovery and Develop to showcase past accomplishments and envision future opportunities. This is the second edition of a monograph published in 2011. This new edition includes both updates of some earlier chapters and new chapters that discuss various aspects of nucleic acid‐based therapeutics. The foreword by Professor Sidney Hecht provides comprehensive highlights of this new edition. Thus, this foreword aims to complement by providing some context and background for this monograph. First, the Wiley Series in Drug Discovery and Develop published its inaugural book in 2004. Since then, about 30 volumes have been published covering a broad range of subjects that impact drug discovery and development. The monograph on nucleic acid is especially important because of the central roles that this field has played in advancing biomedical science. Since the historical work by many on DNA structures culminating with the proposal of the double helix structure for DNA by Watson and Crick in the 1950s, discoveries of milestone nature have continued in the nucleic acid field. The human genome project was a monumental undertaking that has fundamentally transformed the biomedical field. Further, the nucleic acid field has been recognized with the Nobel Prize no less than seven times in the past 20 years in areas including telomeres and chromosomal protection, RNA interference, split genes, genome editing, DNA repairs, DNA chemistry (PCR and site‐directed mutagenesis), and ribosomal structures and functions. With all the advancements in the nucleic acid field as the background, the first edition of this book was a tremendous success, which led to the commissioning of the second edition nine years later. Furthermore, the nucleic acid field has seen much progress including CRISPR gene editing, antisense therapy, DNA‐encoded library, and nanoparticle‐based delivery, which need to be reflected in a new edition, especially in relation to their application in developing new therapeutics.

In terms of medicinal chemistry work in the field of nucleosides, nucleotides, and nucleic acids, there has been an impressive number of success stories from nucleoside‐based small‐molecule drugs. However, oligonucleotides and nucleic acids are somewhat different. On one hand, they present exciting opportunities in precision and specificity in addressing the various underlying molecular mechanisms of diseases. On the other hand, the development of oligonucleotide‐/nucleic acid‐based therapeutics also faces unique challenges in delivery. Nevertheless, it is exciting to see the tremendous progress that has been made along this line. One transformative example is the recent success of mRNA‐based vaccines for the SARS‐CoV‐2 virus, which are poised to rescue the world from the possibly catastrophic consequence of a pandemic that at times seemed to be out of control. The success of these mRNA‐based vaccines also helps to break the myth of “drug‐likeness” that has hovered over the field of nucleic acid‐based therapeutics for a long time. At a time when nucleic acid‐based approaches are positioned to bring a large number of unique solutions to issues of human health and suffering, this volume timely focuses on the medicinal chemistry and therapeutic application aspects of oligonucleotides and nucleic acids including important drug delivery approaches. It is quite a tour de force covering past accomplishments and, yet more importantly, it envisions future opportunities for much more to come. It is hoped that this volume will help to stimulate increasing interests in this field in order to accelerate the development of nucleic acid‐based therapeutics.

On a personal note, the lead editor, Professor Zhang, and his wife, Professor Peiying Zhang, were my professors when I was an undergraduate student at Peking University Health Sciences Center (then Beijing Medical College). Thus, it is with special personal gratitude that I write this foreword to express my appreciation of Professor Zhang’s efforts in leading a group of four editors in organizing this book and very importantly of his contributions to the development of the nucleic acid chemistry field in China and worldwide.

With much progress made in the past few decades, the time has come for nucleic acids to be a major force in the development of therapeutic options with precision and specificity!

Binghe Wang

April 11, 2021, On Lake Allatoona

INTRODUCTION

In 2011, we invited some scientists to contribute their research progress in areas of nucleic acid medicinal chemistry and published a collection of these articles, named by Medicinal Chemistry in Nucleic Acids by Wiley. As nine years passed since the publishing of above book, and many new developments have been achieved in nucleic acid medicinal chemistry and chemical biology, we think that it’s right time to publish a new edition in this field.

Nucleoside, nucleotide, and nucleobase analogues have been widely utilized for the treatment of viral pathogens, neoplasms, and in anticancer chemotherapy for decades. Nucleoside analogues are known to be incorporated into DNA and RNA, producing the replication and transcription inhibition, respectively. It is believed that nucleoside transporter proteins are responsible for cellular uptake of these nucleoside derivatives. Once they enter cells, some kinases phosphorylate nucleoside analogues to the corresponding mono‐, di‐, and triphosphates. Nucleoside triphosphate analogues are regarded as the active cytotoxic form that leads to cell apoptosis as these are substrates for DNA polymerases and can be incorporated into DNA. When they integrated into an elongate viral DNA chain, the nucleotide inhibitor works as a chain terminator to terminate viral DNA synthesis [1–4]. Moreover, certain nucleoside 5‐O‐triphosphate analogues also can be incorporated into RNA to inhibit RNA synthesis. Currently, thousands of nucleoside and nucleotide derivatives are synthesized and their synthetic strategy is highlighted [5].

The attractive progress in this field would be new anti‐HBV and anti‐HCV drugs approved for market. The first‐generation anti‐HBV drug is Entecavir, which was approved by FDA in 2005 [6]. Tenofovir (TFV) was originally described as anti‐HIV agent in 1993 under the name of (R)‐PMPA. Then many TFV derivatives were synthesized through modification of phosphate moiety such as tenofovir disoproxil fumarate (TDF). Tenofovir alafenamide (TAF) can be considered a new prodrug of TFV with enhanced delivery to lymphoid and hepatocytes. Its active diphosphate metabolite can target RNA‐dependent DNA polymerase (reverse transcriptase) of both HIV and HBV. TAF is equally potent as an antiretrovirus agent at a 30‐fold lower dose than TDF. TAF (Vamlidy), approved by FDA in 2016, is not only described for the treatment and prevention of HIV infections but also shows promise for the treatment of HBV infections [7] (Figure 1).

Figure 1 Structures of entecavir, tenofovir (TFV), and its derivatives TDV and TAF.

HCV is a potentially life‐threatening disease and may lead to progressive liver damage and liver failure consequently. The first generation of anti‐HCV drug is sofosbuvir. It undergoes the intracellular metabolism to its pharmacologically active form, uridine analogue triphosphate (GS‐461203). This active metabolite is then incorporated into HCV RNA by NS5B RNA‐dependent RNA polymerase and leads to the chain termination of HCV RNA. In vitro, the polymerase activity of the recombinant NS5B from several different HCV genotypes can be inhibited by GS‐461203. This magic anti‐HCV drug is a fixed‐dose combination tablet containing sofosbuvir and NS5A/B protease inhibitors velpatasvir and voxilapavir for oral administration [8]. Another fixed dosage combination tablet named Harnovi in market, where NS5A/B protease inhibitor ledipasvir is used instead of velpatasvir and voxilapavir (Figure 2).

Figure 2 Structure of Sofosbuvir.

Oligonucleotides targeting RNA have attracted substantial interest from both academic institutions and pharmaceutical companies. Antisense, Aptamer, and siRNA oligonucleotides are designed based on different mechanisms and developed to be new agents for the sequence‐specific gene silencing of target cellular mRNAs or selective interaction with target proteins. And the potential of mRNA technology for rapid vaccine development is valuable in light of COVID‐19 pandemic [9].

The first antisense oligonucleotide drug is Vitravene, which was developed by Isis Pharmaceutics and approved by FDA in 1998 for the specific treatment of CMV Retinitis. Followed by Vitravene, an aptamer drug (Pegaptanib) was approved by FDA in 2003 targeting of VEGF (vascular endothelial growth factor) for the treatment of diabetic macular edema (DME). However, the in vivo therapeutic potency of the aptamer drug is crucially limited by their inherent physicochemical characteristics which may affect pharmacokinetic properties. These effects result in metabolic instability, rapid renal filtration, rapid distribution from the plasma compartment into the tissues (for example the liver or spleen), nonspecific immune activation, and polyanionic effects [10]. Pegaptanib has been superseded by VEGF‐specific monoclonal antibodies that show improved therapeutic effects. Another antisense oligonucleotide Kynamro that targets messenger RNA for apolipoprotein B was developed and approved by FDA (2013) to treat homozygous familial hypercholesterolemia, FoFH. The wide adoption of RNA‐based therapeutics across the biopharmaceutical industry takes a few more years. Recent research achievements have begun to open a new area for RNA‐based therapeutics, especially new delivery systems are developed for oligonucleotide drugs, such as N‐acetylgalactosamine (GalNAc) conjugation [11] and lipid nanoparticle for the delivery drugs into hepatocytes. And several candidates were further developed for the treatment of hepatic viruses, liver‐centric genetic diseases, and cardiometabolic disorders. Drug formulations of RNA‐based therapeutics have made significant progress including pharmacodynamics‐related challenges in targeting specificity, off‐target RNAi activity and immune‐mediated cytotoxicity, and pharmacokinetics‐related challenges in systemic circulation, cellular uptake, and endosomal escape [12, 13]. In 2016, two antisense oligonucleotides, Eteplirsen (Exondys 510) and Spinraza (Nusinersen) were also approved by FDA for the treatment of Duchenne muscular dystrophy (DMD) and spinal muscular atrophy (SMA), respectively.

RNA interference (RNAi) is a hot field in nucleic acid drug development by the use of small inhibitory double‐stranded RNA(siRNA) to target degradation of the sequence‐specific cellular mRNAs, and as a result to silencing gene expression. With the more recent development of RNAi in mammalian systems, investigators have opened a new therapeutic approaches in human genetics and/or infectious diseases. Patisiran is the first RNAi therapeutics, approved by FDA in 2018, targeting transthyretin (TTR) for the treatment of polyneuropathy in adult patients with hereditary transthyretin‐mediated (hATTR) amyloidosis, a progressive, debilitating, chronic, and often fatal disease. Another antisense oligonucleotide Givosiran for the treatment of hATTR has also been approved in 2019. Very recently, Novartis receives positive opinion for Leqvio (Inclisiran) from Committee for Medicinal Products for Humen Use (CHMP) of European Medicines Agency (EMA), a potential first‐in‐class siRNA for the treatment of high cholesterol. Inclisiran has already been approved by FDA now. In 23 November 2020, FDA approved another siRNA drug, Oxlumo (Lumasiran), for the treatment of primary hyperoxaluria type 1 (PH1) to lower oxalate in urine. Oxlumo works by degrading hydroxyacid oxidase 1(HAO1) messenger RNA and reducing the synthesis of glycolate oxidase, which inhibits hepatic production of oxalate, the toxic metabolite responsible for the clinical manifestations of PH1. Up to now, 431 RNA‐based therapeutics are in different stage for clinic trials [9]. A blowout growth of RNA‐based therapeutics will be expected in the future drug market.

Nucleic acid detection has shown a wide range of applications, including diagnostics, biosensing and bioimaging, affinity isolation, biomarker discovery. Recent advances in the sequence‐specific detection of nucleic acids now provide a number of options for rapid and cost‐effective diagnostics, such as nanomaterial‐based nucleic acid detection approaches [14] and point‐of‐care CRISPR/Cas nucleic acid detection [15]. With the more recent development of sgRNA in CRISPR/Cas systems, investigators attempt the development of new therapeutic approaches in human genetics and/or infectious diseases. On another hand, precision medicine and gene therapy became a very hot field. Recent technological and analytical advances in genomics have made it possible to rapidly identify and interpret the genetic variation underlying a single patient’s disease. The current COVID‐19 pandemic presents a serious public health crisis, and a better understanding of the spread scope and pathway of the virus would be aided by more widespread testing. Nucleic‐acid‐based tests currently offer the most sensitive and early detection of COVID‐19 [16].

RNA epigenetics is another hot research area in RNA chemical biology [17]. Many research contributions are still trying to figure out how and why around 170 different chemical modifications impact RNA biology. Now, increasing evidences suggest that RNA methylation plays the key role in diseases from cancers to infectious diseases. RNA methylation to form N6‐methyladenosine (m6A) in mRNA accounts for the most abundant mRNA internal modification and has emerged as a widespread regulatory mechanism that controls gene expression in diverse physiological processes. For DNA, RNA, and histones alike, three factors, writers, readers and erasers, are most important for these regulation process: “writers” add post‐synthesis modifications that alter the molecular structure to either recruit or repel “readers.” Readers interpret those marks to alter transcription in the case of DNA and histones, or to modulate translation and degradation in the case of RNA. And “erasers” remove the modifications, restoring the unaltered functions of the source materials. For histone biology, drug developers have already made inroads against all three components of the writer–reader–eraser paradigm. The same things are going to do in RNAs, small‐molecule inhibitors of the METTL3–METTL14 complex, which regulates epigenetic marks on RNA, have been developed for clinic trials [18]. On the another hand, many RNAs fold into structures that can be selectively targeted with small molecules, which makes it possible to develop sequence‐based design of ligands targeting RNAs [19].