8. Medicinal Chemistry of Antimicrobials Flashcards
Antibiotics - History
- Rich history of bacterial treatments dating back thousands of years
+ Chinese used mouldy soyabean curd to treat boils
+ Honey used to prevent infection of arrow wounds in the Middle Ages - Paul Ehrlich developed the 1st purely synthetic antimicrobial in 1910 as part of a SAR study
- In 1928 Alexander Fleming discovered penicillin – marking the beginning of the “Golden Age of Antibiotics”
+ Awarded the Nobel Prize in Physiology or Medicine, 1945, along with Sir Howard Florey & Sir Ernst Chain “for the discovery of penicillin & its curative effect in various infectious diseases” - Dorothy Hodgkin later confirmed the structure of penicillin using X-ray crystallography
+Awarded Nobel Prize in Chemistry, 1964, for this & other work
Bacterial cell targets
Ribosomes:
- Chloramphenicol
- Streptomycin
- Tetracyclines
Nuclear material (DNA/RNA):
- Rifampicins
- Quinolones
Outer membrane (gram negative)
Cell wall (peptidoglycan)
- Penicillins
- Cephalosporins
Plasma membrane:
- Polymyxins
Enzymes:
- Sulfonamides
Mechanism of action: Bacterial cellular targets
- Inhibition of cell metabolism – antimetabolites inhibit an enzyme-catalysed reaction which is unique to bacterial cells (e.g. folate biosynthesis)
- Inhibition of cell wall biosynthesis – causes bacterial cell lysis & death
- Plasma membrane interactions – affects membrane permeability - Disruption of protein synthesis – essential proteins & enzymes cannot be made
- Inhibition of nucleic acid transcription/replication – prevents cell division
Mechanism of Action: Bacterial cell wall
- Bacterial cell wall has a peptidoglycan structure
+ Made up of parallel series of sugar backbones [N-acetylmuramic acid (NAM or MurNAc) & N-acetylglucosamine (NAG or GlcNAc)]
+ NAM is bound to short peptide chains
+ Cross-linking between peptide chains confers strength & rigidity to the 3D structure - Transpeptidase enzyme recognises the terminal D-Ala-D-Ala motif of one peptide chain, & cleaves the terminal D-Ala residue
- Terminal glycine of another peptide chain then enters active site & forms a peptide bond to the alanine -> cross link to reinforce cell wall
Penicillins - key structural features
- Acyl side chain
- Thiazolidine ring
- Beta lactam ring
Penicillins - Mechanism of action
- Penicillin has similar conformation to the D-Ala-D-Ala substrate
- Penicillin binds in active site & beta-lactam reacts with serine in active site
+ Cyclic so this reaction doesn’t release from the active site
+ Blocks the pentaglycine chain (or water) from entering & cleaving penicillin from the active site - By inhibiting the transpeptidase enzyme, bacterial cell walls can no longer form cross links -> weakened cell wall swells & bursts (cell lysis)
Properties of penicillin G
- Inactive against beta-lactamase producing organisms e.g. 95% of S. aureus strains now produce beta-lactamase enzymes
+ Beta-lactamases are mutated forms of transpeptidase enzyme – bind & cleave beta-lactam of penicillin using serine residue in active site
+ Able to hydrolyse the ester link between penicillin & the active site, so ring-opened penicillin is released very rapidly from the enzyme - Acid sensitive so cannot be taken orally
- Only active against a narrow range of Gram-positive & negative bacteria
- Can improve properties through modification of amino acyl side chain only!
+ Rest of structure is important
Beta-lactamase resistant penicillins
Use of steric bulk on acyl side chain to block penicillins from binding the beta-lactamase active sites
- Steric shield cannot be too bulky, or it cannot bind the target transpeptidase enzyme active site
- Difficult to find balance in size of amino acyl group
Reduction of acid sensitivities
- Under acidic conditions (e.g. in stomach) the acyl sidechain of penicillin G can open up the beta-lactam ring, rendering it ineffective – “inbuilt self-destruct mechanism”
- Remedy this by using an electron withdrawing group on acyl side chain
- Reduces nucleophilic character of carbonyl oxygen – better acid stability
Broad spectrum penicillins
- Hydrophobic groups on side chain favour activity against Gram-positive bacteria, but have poor activity against Gram-negative bacteria e.g. penicillin G
- Hydrophilic groups have little effect on Gram-positive bacteria, but have increased activity against Gram-negative bacteria e.g. penicillin T
- Hydrophilic groups in alpha-position to acyl carbonyl group have greatest enhancement of Gram-negative activity -> allows passage through porins in outer membrane e.g. amoxicillin
Ampicillin prodrugs
- Ampicillin has a electrophilic EWG so is acid stable
- However, it is zwitterionic at physiological pH so poorly absorbed through gut wall
- Masking charged carboxylic acid as an ester gives improved absorption in the GI tract
- Ester is cleaved by esterase enzymes to give the active broad-spectrum antibiotic
Penicillins - SAR studies
Cis stereochemistry:
- Relative stereochemistry between bicyclic ring & amino acyl side chain important
Sulfur atom:
- Common but not essential
Bicyclic system essential:
- Confers greater ring strain on Beta-lactam
Carboxylate essential:
- Carboxylate binds charged lysine in active site
- Esters useful as prodrugs
Beta-lactam:
- Strained beta-lactam ring is essential
Aminoacyl side chain is essential:
- EWGs reduce acid sensitivity
- Bulky groups con fer resistance to beta-lactamases
- Hydrophilic groups improve activity against Gram-negative bacteria
Glycopeptides
Inhibitors of cell wall synthesis
Properties of vancomycin
- Vancomycin is a narrow-spectrum antibiotic produced by streptomyces orientalis - Major last line of defence against MRSA & other drug resistant infections
- No activity against Gram-negative bacteria - Large molecule so unable to cross outer cell membrane of Gram-negative bacteria
- Large & lipophilic so cannot cross GI mucosa
+ IV administration required for most infections
+ Can be administered orally for treatment of gut infections e.g. C. difficile
Adverse effects include:
- Fever, rashes & local phlebitis at the site of injection
- Nephrotoxicity & ototoxicity
Features of vancomycin
- Heptapeptide backbone is responsible for binding target
- Cyclisation between aromatic rings makes the heptapeptide backbone extremely rigid
Vancomycin - mechanism of action
Vancomycin has a pocket where the D-Ala-D-Ala tail of the cell wall building block fits
- 5 H-bonds hold building block in vancomycin pocket
- Dimerisation then occurs where 2 peptide-bound vancomycin units H-bond to each other
- Vancomycin forms steric shield, preventing D-Ala-D-Ala interacting with transpeptidase -> No cross linking
Vancomycin analogues (Teicoplanin)
- Teicoplanin is similar to vancomycin but longer lasting & less toxic
- Possesses a long alkyl chain which anchors it to the surface of the cell membrane -> perfectly positioned to interact with cell wall building blocks
- Unable to form dimers
Viral replication
- Binding
- Fusion
- Location to nucleus
- Replication
- Transcription
- Translation
- Assembly
- Budding
- Release
DNA replication
- Helicase unwinds the DNA double helix
- DNA polymerase “reads” the DNA strand
- Adds nucleoside triphosphate building blocks to the 3’ end of the DNA chains
- Creates 2 identical DNA duplexes from the original double stranded DNA
Nucleoside analogue
- Most of the drugs with activity against DNA viruses have been developed against herpesviruses – nucleoside analogues particularly effective
+ Used for treatment of cold sores, shingles, genital herpes, glandular fever etc
+ Also useful treatments for Burkitt’s lymphoma & Kaposi’s sarcoma
Aciclovir (Zovirax) discovered by compound screening - An analogue of the nucleoside deoxyguanosine
- Normally incorporated into DNA during DNA replication (as triphosphate)
- Catalysed by DNA polymerase
Nucleoside analogues - mechanism of action
Aciclovir is a prodrug -> first needs to be converted to triphosphate
- This only occurs in infected cells (using viral thymidine kinase for first P)
- Host cell thymidine kinase is 100x less effective at producing monophosphate
Aciclovir is then converted to the triphosphate, which binds to DNA polymerase
- Competitive inhibition – prevents normal nucleotide binding
- No sugar unit so growing DNA chain cannot be extended
Improvement of oral bioavailability
Aciclovir is very polar, so has low oral bioavailability (15-30%)
- (pre)prodrugs have improved bioavailability
Valaciclovir 3-5 fold improved bioavailability
- Transported across cell membranes of gut wall by hPEPT-1 & HPT-1 transporter proteins
- Hydrolysed to aciclovir in liver/gut wall
Improvement of activity spectrum
Some viruses lack thymidine kinase (or the enzyme acts very slowly)
- Normal nucleoside analogues inactive against these viruses as they cannot be activated in infected cells
Ganciclovir is an analogue of acyclovir, similar structure
- BUT can also be converted to the monophosphorylated nucleotide by kinases other than thymidine kinase
- Can be used for treatment of viruses that do not encode thymidine kinase, e.g. cytomegalovirus (CMV)
- Low oral bioavailability can again be improved by use of (pre)prodrug strategy, i.e. valganciclovir
ProTide (Prodrug nucleotide) approach -> first phosphate already attached
- Charged phosphate is masked with an amino ester & an aryl group
- Following absorption, enzymatic cleavage reveals the nucleotide
SARS-CoV-2
Remdesivir is a ProTide nucleotide with a very broad spectrum of activity
- Targets viral RNA-dependent RNA polymerase (RdRp); has some activity against RNA viruses, e.g. West Nile virus, Lassa fever virus, MERS-COV, SARS-CoV, Ebola virus etc
- Addition of 1’ cyano group improved selectivity for viral rather than mitochondrial RNA polymerase
- FDA issued emergency use authorisation for hospitalised COVID-19 patients on May 1st 2020
- Clinical studies have since shown little benefit
