10.4 Polyketides

Polyketides are a diverse group of natural compounds with powerful medicinal properties. They're made by enzymes that build complex structures from simple building blocks. Understanding how polyketides are made is key to creating new drugs with desired effects.

Polyketide synthase enzymes are the workhorses behind polyketide production. These large proteins have multiple parts that work together to assemble and modify polyketide chains. By tweaking these enzymes, scientists can engineer new polyketides with improved medicinal properties.

Polyketide biosynthesis

• Polyketides are a diverse class of natural products with a wide range of medicinal properties, making them important targets for drug discovery and development in medicinal chemistry
• Polyketide biosynthesis involves the assembly of simple carboxylic acid building blocks into complex structures through a series of enzymatic reactions
• Understanding the biosynthetic pathways and enzymes involved in polyketide production is crucial for engineering novel polyketide compounds with desired medicinal properties

Polyketide synthase (PKS) enzymes

• PKS enzymes are large, multi-domain proteins responsible for catalyzing the assembly of polyketide chains
• They consist of several catalytic domains, including acyltransferase (AT), ketosynthase (KS), and acyl carrier protein (ACP) domains
• PKS enzymes can be classified into type I, II, and III based on their structural organization and mode of action
  • Type I PKS enzymes are large, multi-modular proteins that function iteratively or modularly
  • Type II PKS enzymes are mono-functional proteins that work iteratively in a complex
  • Type III PKS enzymes are homodimeric proteins that function iteratively and independently of ACP

Acyl carrier proteins in PKS

• Acyl carrier proteins (ACPs) are essential components of PKS enzymes that shuttle the growing polyketide chain between catalytic domains
• ACPs are small, highly conserved proteins that are post-translationally modified with a phosphopantetheine arm, which serves as a flexible tether for the attachment of the growing polyketide chain
• The interaction between ACPs and other catalytic domains in PKS enzymes is crucial for the efficient and precise assembly of polyketide structures

Modular vs iterative PKS systems

• Modular PKS systems consist of multiple modules, each containing a set of catalytic domains responsible for one round of polyketide chain elongation and modification
  • Each module in a modular PKS system is used only once during the biosynthesis of a polyketide chain
  • Examples of modular PKS systems include the erythromycin and rapamycin biosynthetic pathways
• Iterative PKS systems consist of a single module that is used repeatedly to catalyze multiple rounds of polyketide chain elongation and modification
  • The catalytic domains in an iterative PKS system are used multiple times during the biosynthesis of a polyketide chain
  • Examples of iterative PKS systems include the lovastatin and aflatoxin biosynthetic pathways

Polyketide natural products

• Polyketides are a structurally and functionally diverse class of natural products with a wide range of medicinal properties, including antibacterial, antifungal, anticancer, and immunosuppressant activities
• The structural diversity of polyketides arises from the various ways in which the polyketide chains can be assembled, modified, and cyclized by PKS enzymes
• Understanding the structure-activity relationships of polyketide natural products is essential for the rational design and development of new polyketide-based drugs

Structural diversity of polyketides

• Polyketides can have diverse chemical structures, ranging from simple, linear chains to complex, polycyclic frameworks
• The structural diversity of polyketides is generated through a combination of factors, including:
  • The choice of starter and extender units incorporated into the polyketide chain
  • The number and type of catalytic domains present in the PKS enzymes
  • The order and arrangement of catalytic domains within the PKS modules
  • Post-PKS modifications, such as glycosylation, methylation, and oxidation

Aromatic vs non-aromatic polyketides

• Polyketides can be classified as aromatic or non-aromatic based on the presence or absence of aromatic rings in their structures
  • Aromatic polyketides, such as tetracyclines and doxorubicin, contain one or more aromatic rings that are formed through the cyclization and aromatization of the polyketide chain
  • Non-aromatic polyketides, such as erythromycin and avermectin, lack aromatic rings and often contain macrocyclic lactone or lactam rings
• The aromatic or non-aromatic nature of polyketides can influence their biological activities and physicochemical properties, such as solubility and stability

Linear vs cyclic polyketides

• Polyketides can also be classified as linear or cyclic based on the presence or absence of cyclic structures in their final form
  • Linear polyketides, such as the polyether ionophore monensin, consist of an unbranched chain of carbon atoms with various functional groups attached
  • Cyclic polyketides, such as the macrolide erythromycin, contain one or more rings formed through the cyclization of the polyketide chain
• The linear or cyclic nature of polyketides can impact their conformational flexibility, target binding, and pharmacokinetic properties

Medicinal properties of polyketides

• Polyketides exhibit a wide range of medicinal properties, making them valuable lead compounds for drug discovery and development
• The diverse biological activities of polyketides are attributed to their ability to interact with various cellular targets, such as enzymes, receptors, and nucleic acids
• Polyketide natural products have been used as antibacterial, antifungal, anticancer, and immunosuppressant agents, among others

Antibacterial polyketides

• Many polyketides possess potent antibacterial activities and have been used clinically to treat bacterial infections
  • Erythromycin and other macrolide antibiotics inhibit bacterial protein synthesis by binding to the 50S ribosomal subunit
  • Tetracycline antibiotics, such as doxycycline and minocycline, inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit
• The emergence of antibiotic resistance has led to the search for novel polyketide-based antibacterial agents with improved efficacy and reduced susceptibility to resistance mechanisms

Antifungal polyketides

• Several polyketides have been identified as potent antifungal agents, targeting various aspects of fungal cell biology
  • Amphotericin B, a polyene macrolide, binds to ergosterol in the fungal cell membrane, leading to the formation of pores and cell death
  • Griseofulvin, a spirocyclic polyketide, interferes with fungal cell division by disrupting microtubule assembly
• Antifungal polyketides are valuable tools for treating systemic and superficial fungal infections, particularly in immunocompromised patients

Anticancer polyketides

• Polyketides have shown promising anticancer activities by targeting various cellular processes involved in cancer cell growth and survival
  • Doxorubicin, an anthracycline polyketide, intercalates into DNA and inhibits topoisomerase II, leading to DNA damage and cell death
  • Epothilones, macrolide polyketides, stabilize microtubules and interfere with cell division, making them effective against taxane-resistant cancers
• The development of polyketide-based anticancer agents with improved selectivity, reduced toxicity, and the ability to overcome drug resistance is an active area of research

Immunosuppressant polyketides

• Some polyketides have immunosuppressant properties and are used to prevent organ rejection in transplant patients and to treat autoimmune disorders
  • Rapamycin (sirolimus), a macrocyclic polyketide, binds to the protein FKBP12 and inhibits the mTOR pathway, leading to suppression of T-cell activation and proliferation
  • Tacrolimus (FK506), another macrocyclic polyketide, binds to FKBP12 and inhibits calcineurin, a key enzyme in T-cell signaling
• The development of polyketide-based immunosuppressants with improved specificity and reduced side effects is an ongoing challenge in medicinal chemistry

Biosynthetic engineering of polyketides

• Biosynthetic engineering involves the manipulation of polyketide biosynthetic pathways to generate novel polyketide structures with improved or altered medicinal properties
• Advances in genetic engineering, metabolic engineering, and synthetic biology have enabled the rational design and optimization of polyketide biosynthetic pathways
• Biosynthetic engineering strategies for polyketides include modifying PKS enzymes, precursor-directed biosynthesis, mutasynthesis, and chemoenzymatic synthesis

Modifying PKS enzymes

• PKS enzymes can be engineered to alter the structure and properties of the polyketide products they generate
  • Domain swapping involves replacing catalytic domains in a PKS module with domains from other PKS systems to change the substrate specificity or stereochemistry of the resulting polyketide
  • Active site mutagenesis can be used to modify the catalytic activity or substrate specificity of individual PKS domains
• Modifying PKS enzymes enables the generation of polyketide analogs with altered chemical structures and potentially improved medicinal properties

Precursor-directed biosynthesis

• Precursor-directed biosynthesis involves feeding non-natural starter or extender units to the PKS enzymes to incorporate them into the polyketide chain
  • By using alternative starter units, such as benzoic acid or aminobenzoic acid, novel polyketide structures with altered substituents can be generated
  • Feeding non-natural extender units, such as fluoromalonyl-CoA or methylmalonyl-CoA, can lead to the incorporation of unique functional groups into the polyketide chain
• Precursor-directed biosynthesis enables the generation of polyketide analogs with modified chemical structures and potentially improved medicinal properties

Mutasynthesis for novel polyketides

• Mutasynthesis involves the use of genetically engineered bacterial strains that are deficient in the biosynthesis of natural starter or extender units
  • By feeding these mutant strains with non-natural starter or extender units, novel polyketide structures can be generated
  • Mutasynthesis has been successfully applied to generate analogs of erythromycin, rapamycin, and other polyketide natural products
• Mutasynthesis enables the generation of polyketide analogs with altered chemical structures and potentially improved medicinal properties

Chemoenzymatic synthesis of polyketides

• Chemoenzymatic synthesis involves the use of isolated PKS enzymes or domains in vitro to catalyze specific reactions in the polyketide biosynthetic pathway
  • By combining chemical synthesis with enzymatic transformations, complex polyketide structures can be generated with improved efficiency and selectivity
  • Chemoenzymatic synthesis has been used to generate analogs of erythromycin, pikromycin, and other polyketide natural products
• Chemoenzymatic synthesis enables the generation of polyketide analogs with modified chemical structures and potentially improved medicinal properties

Polyketide drugs

• Several polyketide natural products and their semisynthetic derivatives have been developed into clinically used drugs for the treatment of various diseases
• Polyketide drugs have diverse medicinal properties, including antibacterial, antifungal, anticancer, and immunosuppressant activities
• The success of polyketide drugs has driven the search for novel polyketide structures with improved efficacy, safety, and pharmacokinetic properties

Erythromycin and other macrolides

• Erythromycin is a 14-membered macrolide antibiotic that inhibits bacterial protein synthesis by binding to the 50S ribosomal subunit
  • Erythromycin and its semisynthetic derivatives, such as clarithromycin and azithromycin, are used to treat respiratory tract infections, skin infections, and sexually transmitted diseases
  • The development of new macrolide antibiotics, such as telithromycin and solithromycin, aims to overcome the increasing prevalence of erythromycin-resistant bacterial strains

Tetracycline antibiotics

• Tetracyclines are a class of broad-spectrum antibiotics that inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit
  • Tetracycline, doxycycline, and minocycline are commonly used tetracycline antibiotics for the treatment of respiratory tract infections, urinary tract infections, and acne
  • The development of novel tetracycline analogs, such as tigecycline and eravacycline, aims to overcome the growing problem of tetracycline resistance in bacteria

Lovastatin and other statins

• Lovastatin is a fungal polyketide that inhibits HMG-CoA reductase, a key enzyme in the cholesterol biosynthetic pathway
  • Lovastatin and other statins, such as simvastatin and atorvastatin, are used to lower blood cholesterol levels and reduce the risk of cardiovascular diseases
  • The development of novel statin analogs with improved efficacy, safety, and pharmacokinetic properties is an active area of research in medicinal chemistry

Epothilone anticancer agents

• Epothilones are macrolide polyketides that stabilize microtubules and interfere with cell division, making them effective anticancer agents
  • Ixabepilone, a semisynthetic analog of epothilone B, is approved for the treatment of metastatic breast cancer resistant to other chemotherapeutic agents
  • The development of novel epothilone analogs with improved selectivity, reduced toxicity, and the ability to overcome drug resistance is an ongoing challenge in cancer chemotherapy

Challenges in polyketide drug development

• Despite the success of polyketide drugs in the clinic, several challenges remain in the development of novel polyketide-based therapeutics
• These challenges include poor pharmacokinetic properties, toxicity and side effects, antibiotic resistance, and the need for improved drug properties
• Addressing these challenges requires a multidisciplinary approach involving medicinal chemistry, pharmacology, and biotechnology

Poor pharmacokinetic properties

• Many polyketide natural products have poor pharmacokinetic properties, such as low oral bioavailability, rapid metabolism, and limited tissue distribution
  • The large size and high polarity of many polyketides can limit their absorption and distribution in the body
  • The presence of reactive functional groups in polyketides can lead to rapid metabolism and excretion
• Strategies to improve the pharmacokinetic properties of polyketides include structural modifications, prodrug design, and formulation development

Toxicity and side effects

• Some polyketide drugs have been associated with significant toxicity and side effects, limiting their clinical use and patient compliance
  • The cardiac toxicity of doxorubicin and other anthracycline antibiotics is a major concern in cancer chemotherapy
  • The gastrointestinal side effects of erythromycin and other macrolide antibiotics can lead to patient discomfort and discontinuation of therapy
• The development of polyketide analogs with reduced toxicity and improved safety profiles is a key goal in medicinal chemistry

Antibiotic resistance to polyketides

• The widespread use of polyketide antibiotics has led to the emergence and spread of antibiotic resistance in bacterial pathogens
  • Resistance mechanisms against polyketide antibiotics include target modification, efflux pumps, and enzymatic inactivation
  • The development of novel polyketide antibiotics with activity against resistant bacterial strains is an urgent need in the face of the growing antibiotic resistance crisis
• Strategies to overcome antibiotic resistance include the discovery of new polyketide scaffolds, the development of combination therapies, and the use of adjuvants to potentiate the activity of existing antibiotics

Improving polyketide drug properties

• Improving the drug-like properties of polyketide natural products is a major challenge in medicinal chemistry
  • Polyketides often have poor solubility, stability, and permeability, which can limit their oral bioavailability and therapeutic efficacy
  • The presence of multiple chiral centers and reactive functional groups in polyketides can complicate their synthesis and scale-up
• Strategies to improve the drug-like properties of polyketides include structural simplification, bioisosteric replacement, and the use of prodrugs and formulations
• The application of modern drug discovery technologies, such as structure-based drug design, computational modeling, and high-throughput screening, can facilitate the optimization of polyketide drug properties