Table of Contents
Related Titles
Title Page
Copyright
Preface
List of Contributors
Chapter 1: A Chemist's Survey of Different Antibiotic Classes
1.1 Introduction
1.2 Aminoglycosides
1.3 β-Lactams
1.4 Linear Peptides
1.5 Cyclic Peptides
1.6 Thiazolylpeptides
1.7 Macrolactones
1.8 Ansamycins–Rifamycins
1.9 Tetracyclines
1.10 Oxazolidinones
1.11 Lincosamides
1.12 Pleuromutilins
1.13 Quinolones
1.14 Aminocoumarins
References
Chapter 2: Antibacterial Discovery: Problems and Possibilities
2.1 Introduction
2.2 Why Is Antibacterial Discovery Difficult? The Problems
2.3 Target Choice: Essentiality
2.4 Target Choice: Resistance
2.5 Cell Entry
2.6 Screening Strategies
2.7 Natural Products
2.8 Computational Chemistry, Virtual Screening, Structure- and Fragment-Based Drug Design (SBDD and FBDD)
2.9 Conclusions
References
Chapter 3: Impact of Microbial Natural Products on Antibacterial Drug Discovery
3.1 Introduction
3.2 Natural Products for Drug Discovery
3.3 Microbial Natural Products
3.4 The Challenge of Finding Novel Antibiotics from New Natural Sources
3.5 Workflow for Drug Discovery from Microbial Natural Products
3.6 Antimicrobial Activities: Targets for Screens
3.7 Natural Products: A Continuing Source for Inspiration
3.8 Genome Mining in Natural Product Discovery
3.9 Conclusions
References
Chapter 4: Antibiotics and Resistance: A Fatal Attraction
4.1 To Be or Not to Be Resistant: Why and How Antibiotic Resistance Mechanisms Develop and Spread among Bacteria
4.2 Bacterial Resistance to Antibiotics by Enzymatic Degradation or Modification
4.3 Antibiotic Target Alteration: The Trick Exists and It Is in the Genetics
4.4 Efflux Systems
4.5 The Case Stories of Intrinsic and Acquired Resistances
4.6 Strategies to Overcome Resistance
References
Chapter 5: Fitness Costs of Antibiotic Resistance
5.1 Introduction
5.2 Methods to Estimate Fitness
5.3 Factors Affecting Fitness
5.4 Mechanisms and Dynamics Causing Persistence of Chromosomal and Plasmid-Borne Resistance Determinants
References
Chapter 6: Inhibitors of Cell-Wall Synthesis
6.1 Introduction
6.2 MraY Inhibitors
6.3 Lipid II Targeting Compounds
6.4 Bactoprenol Phosphate
6.5 Conclusions
Acknowledgments
References
Chapter 7: Inhibitors of Bacterial Cell Partitioning
7.1 Introduction
7.2 Bacterial Cell Division
7.3 Cell Division Proteins as Therapeutic Targets
7.4 Status of FtsZ-Targeting Compounds: From Laboratory to Clinic
7.5 Conclusion
Acknowledgment
Abbreviations
References
Chapter 8: The Membrane as a Novel Target Site for Antibiotics to Kill Persisting Bacterial Pathogens
8.1 Introduction
8.2 The Challenge of Treating Dormant Infections
8.3 Discovery Strategies to Prevent or Kill Dormant Bacteria
8.4 Why Targeting the Membrane Could Be a Suitable Strategy
8.5 Target Essentiality and Selectivity
8.6 Multiple Modes of Actions
8.7 Therapeutic Use of Membrane-Damaging Agents against Biofilms
8.8 New Approaches to Identifying Compounds That Kill Dormant Bacteria
8.9 Challenges for Biofilm Control with Membrane-Active Agents
8.10 Potential for Membrane-Damaging Agents in TB Disease
8.11 Application to Treatment of Clostridium difficile Infection
8.12 Is Inhibition of Fatty Acid/Phospholipid Biosynthesis Also an Approach?
8.13 Concluding Remarks
References
Chapter 9: Bacterial Membrane, a Key for Controlling Drug Influx and Efflux
9.1 Introduction
9.2 The Mechanical Barrier
9.3 Circumventing the Bacterial Membrane Barrier
9.4 Conclusion
Acknowledgments
References
Chapter 10: Interference with Bacterial Cell-to-Cell Chemical Signaling in Development of New Anti-Infectives
10.1 Introduction
10.2 Two-Component Systems (TCSs) as Potential Anti-Infective Targets
10.3 WalK/WalR and MtrB/MtrA: Case Studies of Essential TCSs as Drug Targets
10.4 Targeting Nonessential TCS
10.5 Non-TCSs Targeting Biofilm Formation and Quorum Sensing in Pseudomonas spp.
10.6 Conclusions
References
Chapter 11: Recent Developments in Inhibitors of Bacterial Type IIA Topoisomerases
11.1 Introduction
11.2 DNA-Gate Inhibitors
11.3 ATPase-Domain Inhibitors
11.4 Simocyclinones, Gyramides, and Other Miscellaneous Inhibitors
11.5 Conclusions and Perspectives
References
Chapter 12: Antibiotics Targeting Bacterial RNA Polymerase
12.1 Introduction
12.2 Antibiotics Blocking Nascent RNA Extension
12.3 Antibiotics Targeting RNAP Active Center
12.4 Antibiotics Blocking Promoter Complex Formation
12.5 Inhibitors Hindering σ–Core Interactions
12.6 Inhibitors with Unknown Mechanisms and Binding Sites
12.7 Conclusions and Perspectives
References
Chapter 13: Inhibitors Targeting Riboswitches and Ribozymes
13.1 Introduction
13.2 Riboswitches as Antibacterial Drug Targets
13.3 Ribozymes as Antibacterial Drug Targets
13.4 Concluding Remarks and Future Perspectives
References
Chapter 14: Targeting Ribonuclease P
14.1 Introduction
14.2 Targeting RNase P with Antisense Strategies
14.3 Aminoglycosides
14.4 Peptidyltransferase Inhibitors
14.5 Substrate Masking by Synthetic Inhibitors
14.6 Peculiar Behavior of Macrolides on Bacterial RNase P
14.7 Antipsoriatic Compounds
14.8 Conclusions and Future Perspectives
References
Chapter 15: Involvement of Ribosome Biogenesis in Antibiotic Function, Acquired Resistance, and Future Opportunities in Drug Discovery
15.1 Introduction
15.2 Ribosome Biogenesis
15.3 Antibiotics and Ribosome Biogenesis
15.4 Methyltransferases
15.5 Methyltransferase Integration into the Ribosome Biogenesis Pathway
15.6 Ribosome Biogenesis Factors, Virulence, and Vaccine Development
References
Chapter 16: Aminoacyl-tRNA Synthetase Inhibitors
16.1 Introduction
16.2 Enzymatic Mechanism of Action of aaRS
16.3 aaRS Inhibitors
16.4 Considerations for the Development of aaRS Inhibitors
16.5 Conclusions
References
Chapter 17: Antibiotics Targeting Translation Initiation in Prokaryotes
17.1 Introduction
17.2 Mechanism of Translation Initiation
17.3 Inhibitors of Folate Metabolism
17.4 Methionyl-tRNA Formyltransferase
17.5 Inhibitors of Peptide Deformylase
17.6 Inhibitors of Translation Initiation Factor IF2
17.7 ppGpp Analogs as Potential Translation Initiation Inhibitors
17.8 Translation Initiation Inhibitors Targeting the P-Site
References
Chapter 18: Inhibitors of Bacterial Elongation Factor EF-Tu
18.1 Introduction
18.2 Enacyloxins
18.3 Kirromycin
18.4 Pulvomycin
18.5 GE2270A
References
Chapter 19: Aminoglycoside Antibiotics: Structural Decoding of Inhibitors Targeting the Ribosomal Decoding A Site
19.1 Introduction
19.2 Chemical Structures of Aminoglycosides
19.3 Secondary Structures of the Target A Sites
19.4 Overview of the Molecular Recognition of Aminoglycosides by the Bacterial A Site
19.5 Role of Ring I: Specific Recognition of the Binding Pocket
19.6 Role of Ring II (2-DOS Ring): Locking the A-Site Switch in the “On” State
19.7 Dual Roles of Extra Rings: Improving the Binding Affinity and Eluding Defense Mechanisms
19.8 Binding of Semisynthetic Aminoglycosides to the Bacterial A Sites
19.9 Binding of Aminoglycosides to the Antibiotic-Resistant Bacterial Mutant and Protozoal Cytoplasmic A Sites
19.10 Binding of Aminoglycosides to the Human A Sites
19.11 Other Aminoglycosides Targeting the A Site but with Different Modes of Action
19.12 Aminoglycosides that Do Not Target the A Site
19.13 Nonaminoglycoside Antibiotic Targeting the A Site
19.14 Conclusions
References
Chapter 20: Peptidyltransferase Inhibitors of the Bacterial Ribosome
20.1 Peptide Bond Formation and Its Inhibition by Antibiotics
20.2 Puromycin Mimics the CCA-End of tRNAs
20.3 Chloramphenicols Inhibit A-tRNA Binding in an Amino-Acid-Specific Manner
20.4 The Oxazolidinones Bind at the A-Site of the PTC
20.5 Lincosamide Action at the A-Site of the PTC
20.6 Blasticidin S Mimics the CCA-End of the P-tRNA at the PTC
20.7 Sparsomycin Prevents A-Site and Stimulates P-Site tRNA Binding
20.8 Pleuromutilins Overlap A- and P-Sites at the PTC
20.9 The Synergistic Action of Streptogramins at the PTC
20.10 Future Perspectives
References
Chapter 21: Antibiotics Inhibiting the Translocation Step of Protein Elongation on the Ribosome
21.1 Introduction
21.2 Translocation: Overview
21.3 Antibiotics Inhibiting Translocation
21.4 Antibiotics Inhibiting Translocation in Eukaryotes
21.5 Antibiotics Inhibiting Ribosome Recycling in Bacteria
21.6 Perspective
References
Chapter 22: Antibiotics at the Ribosomal Exit Tunnel – Selected Structural Aspects
22.1 Introduction
22.2 The Multifunctional Tunnel
22.3 A Binding Pocket within the Multifunctional Tunnel
22.4 Remotely Acquired Resistance
22.5 Resistance Warfare
22.6 Synergism
22.7 Pathogen and “Patients” Models
22.8 Conclusion and Future Considerations
Acknowledgments
References
Chapter 23: Targeting HSP70 to Fight Cancer and Bad Bugs: One and the Same Battle?
23.1 A Novel Target: The Bacterial Chaperone HSP70
23.2 An In vivo Screening for Compounds Targeting DnaK
23.3 Drugging HSP70
23.4 Cooperation between the Bacterial Molecular Chaperones DnaK and HtpG
23.5 Drugging HSP90
References
Index
Related Titles
Phoenix, D.A., Dennison, S., and Harris, F.
Antimicrobial Peptides
2013
Print ISBN: 978-3-527-33263-2, also available in electronic formats
Sköld, O.
Antibiotics and Antibiotic Resistance
2011
Print ISBN: 978-0-470-43850-3, also available in electronic formats
Selzer, P.M. (ed.)
Antiparasitic and Antibacterial Drug Discovery
From Molecular Targets to Drug Candidates
2009
Print ISBN: 978-3-527-32327-2, also available in electronic formats
Arya, D.P. (ed.)
Aminoglycoside Antibiotics
From Chemical Biologyto Drug Discovery
2007
Print ISBN: 978-0-471-74302-6, also available in electronic formats
Tolmasky, M. and Bonomo, R. (eds.)
Enzyme-Mediated Resistance to Antibiotics
2007
Print ISBN: 978-1-555-81303-1
The Editors
Claudio O. Gualerzi
Laboratory of Genetics
Department of Biosciences and
Biotechnology
University of Camerino
62032 Camerino
Italy
Letizia Brandi
Laboratory of Genetics
Department of Biosciences and
Biotechnology
University of Camerino
62032 Camerino
Italy
Attilio Fabbretti
Laboratory of Genetics
Department of Biosciences and
Biotechnology
University of Camerino
62032 Camerino
Italy
Cynthia L. Pon
Laboratory of Genetics
Department of Biosciences and
Biotechnology
University of Camerino
62032 Camerino
Italy
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Resistance to antibiotics has increased and is still growing so that almost every human pathogen has acquired resistance to at least one class of antimicrobials that are in clinical use. The fairly large number of fatalities caused by untreatable bacterial infections in recent years underlies the existence of an antibiotic-emergency, which renders formidable the health threat caused by infectious diseases by both conventional pathogens and emerging killer “superbugs”.
It seems clear that the drive of big pharmaceutical companies toward research and development of anti-infectives is long gone and has rapidly brought to an end the golden era of antibiotics. Nevertheless, the world is currently experiencing an increasing demand for therapeutic means to fight and overcome infectious diseases responsible for the majority of nosocomial infections and deaths.
Aside from economic reasons, a number of frustrating and expensive strategic mistakes have undoubtedly contributed to determine the disengagement of the big pharma and the consequent present shortage of antibiotics. Several recent publications have dealt with the analysis of “what went wrong” in antibiotic research; despite some understandable differences in evaluating the specific significance that different factors have played in generating the present situation, there is almost unanimous consensus in identifying at least some of the causes of the past failures. In turn, the lessons learned from these mistakes now form the basis for designing new strategies for the discovery and development of new antibiotics. More specifically, great hopes have been placed on the design of miniaturized, intelligent in vitro or in vivo screening tests, some of which are directed towards identifying inhibitors of novel or underexploited targets, on the use of new generation repertoires of select natural compounds instead of large chemical libraries, and on bioinformatics, NMR- and crystallography-based technologies such as fragment-based drug discovery and structure-based rational design. Also, the rediscovery of molecules detected and subsequently neglected during the golden years of antibiotic research may prove to be an excellent starting material for the successful development of anti-infective agents.
Beyond the enormous impact that antibiotics had in safeguarding human health over the last half century, the paramount importance of these compounds in contributing to the progress of science, genetics, and molecular biology in particular, should not be neglected. Indeed, the number of fundamental biological functions whose molecular mechanisms have been elucidated with the help of antibiotics is countless, as is the number of essential genes, such as those encoding the two subunits of gyrase, the elongation factor EF-G, and an entire cluster of ribosomal protein genes, to name a few which have been identified and initially characterized through the study of antibiotic resistance.
In light of these considerations, in addition to a few chapters that are devoted to general aspects such as a survey of the chemical classes of antibiotics and antibiotic resistance and fitness cost of resistance, most of the chapters of this book cover individual biological functions and biomolecules representing specific antibiotic targets. In this way, the reader should be able to appreciate the strict inter-relationship between biological mechanisms, on the one hand, and the nature and mechanism of inhibition of antibiotics, on the other.
Claudio O. Gualerzi
Letizia Brandi
Attilio Fabbretti
Cynthia L. Pon
List of Contributors
More than 20 novel classes of antibiotics were produced between 1930 and 1962. Since then, only four new classes of antibiotics were marketed. Interestingly, none of these new classes is really novel: daptomycin, approved in 2000, was discovered in the early 1980s; linezolid, approved in 2000, derives from a synthetic lead discovered in the 1970s; pleuromutilins, approved in 2007, have been widely used for about 30 years in veterinary medicine; fidaxomicin, approved in 2011, was first reported in the 1970s. This chapter reviews the main classes of antibiotics in clinical use organized by their chemical structure. For each class, the natural or synthetic origin and a description of the chemical structure are presented. The mechanism of action and spectrum of activity are only briefly indicated as they are discussed more deeply in the subsequent chapters. A short summary of the early structure–activity relationships (SARs) leading to the most known derivatives is described followed by a short overview of the most recent analogous currently under clinical development [1–3].
Aminoglycosides (Figure 1.1) were first established as antibiotics in the 1940s and are still widely used worldwide. They are obtained by fermentation of Streptomyces, Micromonospora, and Bacillus; irreversibly inhibit protein synthesis by acting on the ribosome; and are especially active against gram-negative bacteria. They chemically consist of an aminocyclitol substituted with amino sugars. A classification proposed by Umezawa was based on the central structure, which can be streptamine 1, 2-deoxystreptamine 2, or streptidine 3. A relevant number of natural and semisynthetic derivatives have been obtained since their discovery with the aim of bettering the toxicity issues linked to these structures, mainly oto- and nephrotoxicity, and to fight the increased resistance that mostly arises from structural modification of the aminoglycosides by specific enzymes expressed by resistant strains. These studies highlighted the importance of the number and position of the amino groups for the antibacterial activity. For example, the derivatization of the amino and alcoholic groups in kanamycin 4 resulted in an increased potency together with a reduced susceptibility to the inactivating enzymes that act by acetylation of 2′- and 6′-position and by phosphorylation on position 3′. Recently, interest in this class increased again owing to their spectrum of activity and the observed synergistic activity with other antibiotic classes [1]. Among the recent derivatives, plazomicin (ACHN-490) 5, a semisynthetic derivative of sisomycin, shows significant improved activity against amikacin- and/or gentamicin-resistant strains and is currently under phase II clinical study [2, 3].
Figure 1.1 Aminoglycosides and β-lactam antibiotics.
β-Lactam antibiotics, discovered in the 1930s and produced by the fungus Penicillium, are a wide class of antibiotics, characterized by the presence of an azetidinone nucleus containing the carbonyl β-lactam, essential for the activity. Different subclasses of β-lactams can be defined depending on the chemical substitutions of the central β-lactamic core (Figure 1.1). The azetidinone can be fused with a saturated or unsaturated pentacycle or hexacycle and position 1 of this ring can be occupied by a sulfur, oxygen, or carbon atom. Thus, penicillins, including penams, carbapenams, and oxopenams, contain a saturated pentacle (see penicillin B 6 and ampicillin 7), penems, and carbapenems contain an unsaturated pentacycle (imipenem 8) and cephalosporins, including cephems, carbacephems, and oxacephems, contain an unsaturated hexacyle (cefotaxime 9). Finally, the azetidinone can be alone and not fused with another ring originating monolactams or monobactams (aztreonam 10). All β-lactams act on cell-wall biosynthesis, targeting the penicillin-binding protein (PBP) enzymes involved in the biosynthesis of the peptidoglycan. In the many decades after penicillin discovery in the 1930s, a huge number of natural, synthetic, and semisynthetic β-lactams were discovered and produced [4]. Initially, position 6 of penicillin was extensively modified to increase the stability of the β-lactam and to overcome the resistance mostly mediated by the production of a PBP with reduced affinity for β-lactams. In cephalosporins, a similar approach by modification of the side chain in position 7 gave rise to new generations of semisynthetic cephalosporins. Initially active mainly on gram-positive bacteria, newer generations have significantly greater gram-negative antimicrobial properties. In the next generations, the N-acyl side chain was then coupled with structurally complex heterocycles at position C-3 containing a positive charge at their terminus (Figure 1.1) [5]. The resulting chephalosporins CXA-101 11, ceftaroline 12, and ceftobiprole 13 have exceptional gram-positive activity that also crosses over to some gram negatives [6]. The same type of positively charged heterocycle was also incorporated in position C-2 of the carbapenems (ME-1036 14). The injectable carbapenem PZ-601 15 has shown potent activity against drug-resistant gram-positive pathogens, including methicillin-resistant Staphylococcus aureus (MRSA), and is currently undergoing phase II studies. Among monobactams, in which aztreonam is the only representative widely used in clinics, the newest generation incorporates a siderophore substructure to facilitate bacterial uptake (BAL-30072 16). Finally, combinations of a β-lactam with a β-lactamase inhibitor have been successfully used to achieve antibacterial efficacy without accelerating resistance development. Clavulanic acid was the first β-lactamase inhibitor used in combination drugs followed by sulbactam and tazobactam, and more recently BAL29880 17, all possessing a β-lactam chemical structure [5]. Recently, a novel bicyclic, non-β-lactam β-lactamase inhibitor (NXL104 18) is under clinical evaluation [7].
In this family, gramicidins, dalbaheptides, and lantibiotics are grouped. In all these molecules, the main peptidic chains remain linear and no cyclization occurs at the N- or C-terminal amino acid, yet rings can be present because of cyclization between side chains belonging to different residues. Gramicidin D is a heterogeneous mixture of six strictly related compounds, gramicidins A, B, and C obtained from Bacillus brevis and collectively called gramicidin D [8]. In contrast to gramicidin S, which is a cyclic peptide, gramicidin D contains linear pentadecapeptides with alternating l- and d-amino acids, sharing the general formula: formyl-l-X-Gly-l-Ala-d-Leu-l-Ala-d-Val-l-Val-d-Val-l-Trp-d-Leu-l-Y-d-Leu-l-Trp-d-Leu-l-Trp-ethanolamine, where amino acids X and Y depend on the gramicidin molecule. X can be Val and iLeu, while Y represents an aromatic amino acid among which are Trp, Phe, and Tyr. The alternating stereochemical configuration (in the form of d and l) of the amino acids is crucial for antibiotic activity. In membranes, gramicidin adopts a β-helix three-dimensional conformation forming channels that are specific to monovalent cations, thus increasing the permeability of the bacterial cell membrane and thereby destroying the ion gradient between the cytoplasm and the extracellular environment.
Dalbaheptides (Figure 1.2) are composed of seven amino acids cross-linked to generate a rigid concave shape. This configuration forms the basis of their particular mechanism of action that involves the complexation with the d-alanyl-d-alanine terminus of bacterial cell-wall components. As this mechanism of action is the distinguishing feature of these glycopeptides, the term dalbaheptide, from d-al(anyl-d-alanine)b(inding)a(ntibiotics) having hept(apept)ide structure, has been proposed to distinguish them within the larger and diverse groups of glycopeptide antibiotics [9]. Five of the seven amino acids forming the peptidic skeleton are common to all dalbaheptides. Vancomycin 19, the first dalbaheptide introduced into clinical practice in 1959, was isolated from Streptomyces orientalis (now Amycolatopsis orientalis) [4]. In 1988, teicoplanin 20 was also introduced. Glycopeptide antibiotics are restricted to treating gram-positive infections as they cannot penetrate the outer membrane of gram-negative bacteria. As vancomycin has been increasingly used for the treatment of a wide range of infections, second-generation glycopeptides with improved profile over vancomycin were developed. Even though recently innovative synthetic methods allowed successful total syntheses of these complex structures, fermentation followed by semisynthetic modification remains the prevalent way to explore SARs and the only practicable route to bulk production of clinical candidates. In general, the presence of specific sugars is of vital importance for dalbaheptide activity as aglycones are uniformly less active. At the same time, most efforts to change the natural heptapeptide backbones have resulted in reduced activity. Nevertheless, modification of the natural structure has led to novel, resistance-breaking dalbaheptides that contain structural elements promoting dimerization, to tight binding with the biological target, and lipophilic side chains that enhance membrane anchoring. An additional amino sugar at residue 6 and aromatic chlorine substituents promote favorable dimerization, and substitution of the free carboxylate function by basic carboxamides increases the activity against staphylococci. From these studies, three semisynthetic second-generation drugs have been advanced to clinical development. Oritavancin 21, derived from the vancomycin-related glycopeptide chloroeremomycin, dalbavancin 22, a derivative of the teicoplanin-related glycopeptide A40926, and telavancin 23 were approved by the Food and Drug Administration (FDA) in the United States in 2009 [10, 11].
Figure 1.2 Dalbaheptide antibiotics.
Lantibiotics are small peptides (19–38 amino acids) produced mostly from strains belonging to the Firmicutes and, to a lesser extent, to the Actinobacteria, that undergo extensive posttranslational modifications to yield the active structures. The modifications common to all lantibiotics involve the dehydration of serine and threonine residues to yield 2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb), respectively (Figure 1.3). This is followed by the stereospecific intramolecular addition of a cysteine residue onto Dha or Dhb to form a lanthionine (Lan) or methyllanthionine (MeLan) bridge, respectively. The term lantibiotic is, in fact, derived from Lan-containing antibiotics. Other modifications can be present on these molecules: for instance, C-terminal Cys residues may form S-aminovinyl-cysteine (AviCys) while N-terminal residues can contain 2-oxopropionyl (OPr) and 2-oxobutyryl groups (OBu). Their antimicrobial activity is limited to gram-positive bacteria; the prototype molecule is nisin 24, discovered in the 1920s and used as a food preservative for 40 years [12]. Lantibiotics are divided into two classes according to their biogenesis: Lan formation in class I compounds requires two separate enzymes, a dehydratase and a cyclase, whereas a single enzyme carries both activities for class II lantibiotics. Although compounds from both classes exert their antimicrobial activity by binding to Lipid II, thus inhibiting cell-wall biosynthesis, they do so by binding to different portions of this key peptidoglycan intermediate. Moreover, lantibiotics bind Lipid II at a site different from that affected by vancomycin and related glycopeptides, and they are active against multidrug-resistant (MDR) gram-positive pathogens and have attracted attention as potential drug candidates. The compound NVB302 25, a semisynthetic derivative of deoxyactagardine B 26, is currently a developmental candidate [13]. Independently, a screening program designed to detect cell-wall-inhibiting compounds turned out to be very effective in identifying lantibiotics [14]. Among the new lantibiotics identified, the most active compound was NAI-107 27, containing two previously unknown modifications: a chlorinated tryptophan and a mono- or dihydroxylated proline. It is currently a developmental candidate for the treatment of nosocomial infections by gram-positive pathogens [15]. The same screening program led to the identification of additional class I lantibiotics from actinomycetes. Among them, the compound 97518 28 is structurally related to NAI-107 but contains two carboxylic acids [16] (the unmodified carboxy-terminal amino acid and an aspartic residue) and afforded improved derivatives by chemical modification of the acidic residues [17].
Figure 1.3 Lantibiotics.
For simplicity, all cyclic peptides are grouped in this family (Figure 1.4 and Figure 1.5). Nevertheless, while the first described gramicidin S is a simple cyclopeptide, the later described antibiotics are more complex structures containing additional chemical groups that identify the molecules as glycosylated peptides when they contain sugar moieties (mannopeptimycin 31), lipopeptides when they contain a lipophilic side chain (polymixin 33, friulimicin 35), lipodepsipeptides when apart from the lipophilic chain a lactone is present in the cycle (daptomycin 36, lotilibcin 37), and glycolipodepsipeptide when all these characteristics are present (Ramoplanin 38). Gramicidin S is an antibiotic effective against some gram-positive and gram-negative bacteria as well as some fungi, which was discovered in 1942 and produced by the gram-positive bacterium B. brevis. Gramicidin S is a cyclodecapeptide, constructed as two identical pentapeptides joined head to tail, formally written as cyclo(-Val-Orn-Leu-D-Phe-Pro)2. Streptogramins are natural products produced by various members of the Streptomyces genus. This family of antibiotics consists of two subgroups, A and B, which are simultaneously produced in a ratio of roughly 70 : 30 [18]. Both subgroups inhibit protein synthesis by binding to the ribosome. Group A streptogramins are cyclic polyunsaturated macrolactones. Structural variations in type A streptogramins can arise from desaturation of the proline residue and by its substitution for alanine or cysteine residue. Examples of group A streptogramins are pristinamycin IIA (same as virginiamycin M1), madumycin II, and the semisynthetic derivative dalfopristin 29. Group B streptogramins are cyclic hepta- or hexadepsipeptides, for example, pristinamycin IA, virginiamycin S, the semisynthetic quinupristin 30. The invariant N-terminal threonine residue is N-acetylated with 3-hydroxypicolinic acid and forms a cyclizing ester linkage with the C-terminal carboxyl group of the peptide via its secondary hydroxyl group. Synercid (composed of a mixture of quinupristin and dalfopristin) is not orally available and is administered by intravenous routes. Efforts have therefore been made to generate new orally active streptogramins. In particular, a new oral streptogramin, designated NXL-103, has been shown to be very effective against a number of gram-positive and gram-negative organisms. Mannopeptimycins [19] are glycosylated cyclic hexapeptides that contain both stereoisomers of the unusual amino acid β-hydroxy-enduracididine. They also contain an unusual N-glycosidic bond, which links a mannose sugar to one of the β-hydroxy-enduracididine residues. They were originally isolated in the 1950s from Streptomyces hygroscopicus but the chemical complexity and the lack of broad-spectrum activity reduced prospects for further development. Mannopeptimycin 31 affects cell-wall biosynthesis and recently renewed interest in it has derived from its activity against MDR gram-positive pathogens. SAR data derived from the natural congeners, chemical derivatization, precursor-directed biosynthesis, and pathway engineering were employed for optimization [20]. These data demonstrated that antibacterial activity was enhanced by hydrophobic O-acylation of either of the two O-mannoses, particularly the terminal one, while it was reduced by esterification of the N-linked mannose or serine moieties. AC98-6446 32 represents an optimized lead obtained by adamantyl ketalization of a cyclohexyl analog prepared by directed biosynthesis. Polimixins 33 and colistins 34 have a general structure consisting of a cyclic peptide with a long hydrophobic tail [21, 22]. They are produced by the gram-positive Bacillus polymyxa and are selectively toxic for gram-negative bacteria owing to their specificity for the lipopolysaccharide (LPS) molecule that characterizes many gram-negative outer membranes. The hydrophobic tail is important in causing membrane damage, suggesting a detergent-like mode of action. Polymixin nonapeptide, devoid of the hydrophobic tail, still binds to LPS, and causes some degree of membrane disorganization but no longer kills the bacterial cell. Polymixin B (colistin) was approved for clinical use in 1958 but its systemic toxicity, particularly nephrotoxicity, has limited its use to topical applications for the most part. Nevertheless, currently, polymyxins have been revived to treat infections due to multiply resistant gram-negative bacteria. Friulimicin B 35 consists of a macrocyclic decapeptide core with an exocyclic asparagine acylated with a branched unsaturated lipophilic chain. Structurally, friulimicin belongs to the amphomycin family of cyclic lipopeptides, whose members differ in amino acids and fatty acid substituent. The correct structure of amphomycin (35b) was actually established almost 50 years after its discovery, along with friulimicin characterization. These studies revealed that the friulimicin producer Actinoplanes friuliensis makes macrocyclic decapeptides with an exocyclic acylated aspartic residue, identical to previously described amphomycin, tsushimycin, parvuline, and aspartocin, as well as compounds with an exocyclic asparagine, such as friulimicin [23]. Notwithstanding the structural similarity to daptomycin, amphomycin has a different mechanism of action; it has long been known to inhibit cell-wall biosynthesis and has completed phase I clinical trials. Daptomycin 36 is a cyclic lipodepsipeptide produced by Streptomyces roseosporus consisting of 13 amino acid cyclic peptides with a decanoyl side chain [24]. Discovered in the late 1980s, it is the first lipopeptide approved for clinical use (2003) in the treatment of gram-positive infections. Daptomycin acts on the membrane and causes rapid depolarization, resulting in a loss of membrane potential leading to inhibition of macromolecular syntheses and ultimately bacterial cell death. Its distinct mechanism of action means that it may be useful in treating infections caused by MDR bacteria. Lotilibcin (WAP-8294A2) 37 is a complex of 20 closely related components produced by a gram-negative bacterium Lysobacter sp. They are cyclic depsipeptides containing 12 amino acid residues and one 3-hydroxy-fatty acid residue. WAP-8294A2 was isolated as the major component, and showed a strong activity against gram-positive bacteria without posing any cross-resistance [6]. Ramoplanin 38 is a glycolipodepsipeptide antibiotic isolated from fermentation of Actinoplanes sp. containing 17 amino acids and a mixture of l and d amino acids as well as several nonproteinogenic side chains [25]. The first amino acid in the depsipeptide is acylated at the amino terminus with a lipid unsaturated substituent slightly different for three congeners. It is active against gram-positive aerobic and anaerobic bacteria, including vancomycin-resistant enterococci. Ramoplanin inhibits bacterial cell-wall biosynthesis by a mechanism different from those of other cell-wall synthesis and therefore does not show cross-resistance with them. Because of its potent antimicrobial activity, ramoplanin could be an effective antibiotic for treating serious gram-positive infections. However, it showed poor local tolerability upon intravenous injection and it is under development for prevention and treatment of Clostridium difficile-associated diarrhea, acting locally by decolonizing the gut. Semisynthetic derivatives of the natural molecules have been produced by selective removal and replacement of the original fatty acid chain with different chemical residues [26].
Figure 1.4 Cyclic peptide antibiotics (part I).
Figure 1.5 Cyclic peptide antibiotics (part II).
Thiazolylpeptides are highly modified, ribosomally synthesized peptides that inhibit bacterial protein synthesis. They are characterized by a sulfur-containing macrocyclic structure, which possess a tri- or tetra-substituted nitrogen-containing heterocycle core (Figure 1.6). Micrococcin was the first thiopeptide ever discovered (1948); it was produced by a Micrococcus sp. Other members of this class are produced by Streptomyces (thiostreptone 39) and Planobispora sp. (GE2270 40). Nearly all of the thiopeptides inhibit protein synthesis; however, their cellular targets are distinct. For example, the structurally complex polycycles of nocathiacin 41 [27] and thiostrepton 39 bind to the 23S ribosomal ribonucleic acid (rRNA) component of the bacterial 50S ribosomal subunit, while GE2270 40 and the thiomuracin 42 monocycles target the elongation factor Tu [28]. Most thiazolylpeptides show potent activity against gram-positive pathogens and this unique class of thiopeptides represents a significant and promising lead for antibiotic drug discovery, yet their poor solubility has limited clinical progress; only a derivative of GE2270 has entered clinical trials for the topical treatment of acne (NAI-Acne), in which the natural carboxy terminal is replaced by a semisynthetic amide residue [11]. Additional novel derivatives of GE2270 have recently been identified, where the natural carboxy-terminal amino acids are replaced by cycloalkylcarboxylic acid side chains by amide or urethane bond [29], and novel water-soluble derivatives of nocathiacin were also recently reported [27].
Figure 1.6 Thiazolylpeptide and macrolide antibiotics.
Macrolides (Figure 1.6) are composed of a macrolacton, usually of 14–16 atoms, and at least 2 neutral- or amino sugars linked to the macrocycle, usually cladinose and desosoamine. Erythromycin A 43, the prototype of this class, was first isolated from Streptomyces erythreus in 1952 [4]. Since their discovery, a significant number of new natural and semisynthetic derivatives have been produced. Despite the availability of total synthesis tools, semisynthesis still remains the only possibility for all marketed macrolides; nevertheless, molecular diversity was obtained in macrolides, not only by classical semisynthesis but also by combinatorial biosynthesis through modification of the polyketide biosynthetic machinery [4]. Among the most interesting semisynthetic derivatives, the azalides, obtained by Beckmann rearrangement from erythromycin A, have increased activity against gram-negative bacteria. Among them, azytromycin 44 was commercialized at the end of the 1980s. More recently, to overcome the several mechanisms involved in the resistance against this class, new macrolides named ketolides were rediscovered, in which 3-cladinose, erroneously considered for many years as a crucial structural element for antibiotic activity, is replaced with a 3-ketone substituent. Novel ketolides were demonstrated to have increased stability in acidic media and potent activity against erythromicin- and penicillin-resistant enterococci together with an enhanced pharmacokinetic profile. Among them, telithromycin 45 was the first ketolide approved for clinical use in the 2000s. Further improvement led to cethromycin 46 and solithromycin 47 as lead compounds, currently under clinical development [3]. Both are characterized by the presence of a cyclic carbamate group at the 11, 12-position that enhances the activity against susceptible and resistant strains by stabilizing the ketolide conformation.
Difimicin 48 (Figure 1.7) belongs to an 18-member family of actinomycete-produced macrocycles, independently discovered under the names of lipiarmycin, clostomycin, and tiacumicin [13]. Compounds in the family differ for variations in the macrolide ring and for the nature and position of the acyl residue esterified on the sugars, with the major component carrying an isopropyl ester at position 4″. Among the natural congeners, lipiarmycin B 49 is less active than lipiarmycin A against all bacterial species, thus indicating that the position of the isobutyl residue on methyl rhamnose affects in vitro activity. Difimicin is a potent inhibitor of bacterial RNA polymerase (RNAP) and is currently under registration for the treatment of C. difficile infections.
Figure 1.7 Macrociclic antibiotics, rifamycins, and tetracyclines.
The class of ansamycins is characterized by a cyclic structure in which an aliphatic chain forms a bridge between two nonadjacent positions of a cyclic π-system, similar to the handle of a basket or ansa (in Latin, hence the name). They are produced by strains of several genera of the order Actinomycetales. The most important ansamycins are rifamycins (Figure 1.7). They have an aliphatic ansa chain constituted of 17 atoms, are antibacterial, and selectively inhibit RNA polymerase. Following the first rifamycin isolation in 1957 (rifamycin SV 50), extensive programs of semisynthesis led to the preparation and evaluation of a large number of rifamycin analogs with the aim of obtaining a compound with better oral absorption, more prolonged antibacterial levels in blood, and greater antimicrobial activity [30]. These studies gave important information on the SAR in rifamycins. The minimal requirements for antibiotic activity appeared to be the presence of the two hydroxyls at C21 and C23 positions of the ansa chain and the two polar groups at C1 and C8 positions of the naphtoquinonic nucleus, together with a conformation of the ansa chain that resulted in certain specific geometric relations among these four functional groups. Position 3 of the aromatic nucleus has been extensively derivatized, mainly starting from the readily available intermediate 3-formyl rifamycin 51 resulting in the synthesis of interesting compounds, among them rifapentin 52, currently used for the treatment of tuberculosis in the United States, rifaximin 53, and rifalazil 54. Novel benzoxazinorifamycins have been recently synthesized and screened. Among them, novel derivatives (ABI-0043 55 is the main example) that possess both the ability to suppress the emergence of rifamycin-resistant mutants and show increased activity against mutants resistant to other rifamycins have been identified [30].
Tetracyclines are characterized by a polycyclic structure consisting of a highly functionalized and partially reduced naphthacene (Figure 1.7). They are usually produced by strains of Streptomyces aureofaciens and Streptomyces rimosus and, more recently, by Micromonospora and Actinomadura brunea. These molecules bind to the ribosome-inhibiting protein synthesis and are classified as broad-spectrum antibiotics. The first member of the group chlorotetracycline (aureomycin 5657585960