Antibiotics blocking protein synthesis Flashcards
PG Assembly
Vancomycin blocks transpeptidation step in addition to penicillins and cephalosporins by binding DalaDala on the end.
Mycobacterial Cell Wall
The mycobacterial cell envelope is extremely hydrophobic and forms a strong barrier: Mtb is highly resistant to AB.
The mycobacterial cell wall contains long fatty acids (C60-C90, lipophilic aliphatic carbons), the mycelia acids. Channel forming proteins functionally similar to the well known porins of GN bacteria have been demonstrated, revealing how hydrophilic molecules can pass through their hydrophobic cell wall.
In addition to PG, there is an arabinoglactan.
Encoated in grease; big layer that makes it hard to treat; in part reason it is highly resistant to drugs.
Isoniazid
AB exclusively used for mycobacterium TB.
Analog of nicotinamide
Clinical use:
-In combination with other drugs for the treatment of TB.
-As monotherpay for treatment of latent TB/
-In combination regimen for nonTB mycobacterial infections (less frequently).
Mode of action: complex
-Acts as a mimic of nicotinamide.
-Complex, Isoniazid-NAD adduct inhibits INHa
-The best defined mechanism is inhibition of mycelia acid (big greasy barrier on outside) biosynthesis; also different mechanisms; not precisely defined; unique to mTB because of mycolic acids.
Beta lactams that hit cell walls are more active against fast growing.
TB is slow growing
-Bactericidal but less active against fast growing cells.
Side effects:
-Low in general
-Peripheral neuropathy and CNS toxicity.
Other antiTB drugs: Rifampin, Streptomycin, Pyrazinamide, Ethambutol, Ethionamide.
Typical treatment: Rifampin, Isoniazid, Ethambutol, Pyraziamide 6-9 months for non-resistant TB).
Drug sensitive; typically 4 drugs for 3-6 months, then drop to 2 drugs for another 9 months.
Resistant: 2 years of therapy.
Inhibitors of protein synthesis
Efflux not as important are not as important then for things that need to be inside the cell to act.
Mechanisms of resistance.
AB need to be inside the cell to act.
Inhibitors of Protein Synthesis
Structure of the ribosome; 2 parts, one of the 50S and one is the 30S. Antibiotics block protein biosynthesis by acting on one or more steps that occur on the 30S and 50S subunits of the bacterial ribosome. Drugs that act at the 50S: -Macrolides -Lincosamides -Streptogramins -Everninomycins -Oxazolidinones -Lincosamides. Drugs that act at the 30S subunit: -Aminoglycosides -Tetracyclines Polypeptide exit tunnel tRNAs Ribosome has 3 sites: A site: Aminoacyl P site: peptidyl E site: Exit Crystallized structure finally gave us a view of how these AB work. RNA in ribosome; drugs bind and interact with RNA, not structural only.
Ribosome Diversity
Bacteria Ribosome Size: 70S Small subunit: Size- 30S Mass (MDa)-0.8 rRNAs-16S Number of r-proteins-20 Large subunit: Size-50S Mass (MDa)-1.6 rRNAs-23S, 5S Number of r-proteins-34 Higher the number the bigger the size. Eukaryotes: much larger ribosome: individual subunits are different sizes, rRNAs are different Comprised of proteins and RNA. Why we can target protein synthesis in bacteria and not have toxicity in humans; because of huge differences. 54 totally proteins to put together.
Basic ribosome structure: mRNA and tRNA
Threading of the mRNA into 30S subunit decoding region.
Placement of the ammoniacal (A), peptide (P), and peptide exit (E) codons of the mRNA in the decoding site.
Architecture of a tRNA highlighting the anti-codon loop that recognizes the codons on mRNA and the CCA talk where the main acid is covalently tethered and activated.
The mRNAs provide the instructional template.
The tRNAs transfer amino acids to the growing peptide chain and provide the anticodons for Watson Crick pairing at the A and P site at the 30S-mRNA interaction site.
tRNA responsible for tethering the right AA.
mRNA provides code for tRNA to bind; which AA will be put into growing protein.
A is where the tRNA comes in and the anticodon loop bp with that region and dictates which AA is next in line for potion synthesis.
P: action happens here; where incoming AA attached to CCA end of tRNA is pushed into, catalyzed to grow the peptide chain.
Signed up by shine dalgarno sequence; interact with 30S and lines up whole initiation complex here.
30S is the decoding subunit.
50S helps us catalyze things.
1. 30S- responsible for reading mRNA codons
2. Initiator tRNA for methionine in green-decoded in the A site.
3. If there is a match, the interfaces come together and translation begins.
See AA end of tRNA harbored in the 50S, where the chemistry happens.
30S decodes mRNA and tRNA; protein synthesis happens in the 50S.
Bacterial ribosome: the peptidyltransferase cycle
Step 1: Select the proper amino-acyl tRNA at A site; match with mRNA.
Step 2: Elongate the growing peptide-tRNA (at P site) as it is translocated onto the attacking ammoniacal group (at A site); P site have growing or nearly made peptide chain attached to previous tRNA; AA attached via carboxyl group to OH on the sugar at the CCA end of tRNA; amino group on AA is positioned in ribosome and ribosome catalyzes the nucleophilic attack of N on that mine group onto the attached polypeptide chain in the P site; when this happens, AA from A site to then form the new amide bond with peptide chain at P site and move on…
Step 3: Move the deacylated tRNA to E site (exited) and relocated the peptidyl-tRNA to P site.
Step 4: Select the next ammoniacal-tRNA to A site to start a new cycle of peptide elongation.
Antibiotics could interrupt the timing and specificity of any of these steps, and such disruptions are likely to slow down growth and/or be lethal to the bacteria.
No clear cut rules of whether tidal or just slow down growth.
Interact with the 30S Ribosomal Subunit
Tetracycline Spectinomycin (not approved) Kanamycin (aminoglycosides) Streptomycin; the first early protein synthesis inhibitor.
Interact with the 50S Ribosomal Subunit
Erythromycin; early members of this class Ketolide Troleandomycin Azithromycin (zythromax); modified form of erythromycin. Telithromycin Cethromycin Streptogramin A Streptogramin B Pristinamycin IIA Virginiamycin M Dalfopristin Pristinamycin IA Quinipristin Linezolid
30S Subunit of the Ribosome (decoding)
- Aminoglycosides: Interfere with initiation
2. Tetracyclines and Glycylcyclines: Block the incoming ammoniacyl tRNA.
Business end in terms of the peptide transfer center: 50S
- Macrolides and Ketolides: Bind at the polypeptide exit tunnel; block exit and stars biosynthesis of proteins.
- Lincosamides: Inhibt transpeptidation/translocation
- Amphenicols: Peptidyl transfer; chloramphenicols as example.
- Streptogramins: Inhibit transpeptidation/translocation
- Oxazolidinones: Initiation Inhibitor
- Mutilins: Peptidyl transfer
Aminoglycoside Antibiotics: Structures
Gentamicin C
Tobramycin
Netilmicin
All have same core in center
PRIMARILY USED FOR GN BACTERIAL INFECTIONS.
Streptomycin discovered in 1944
Aminoglycosides have been widely used in clinical setting due to bactericidal action, and synergy with other antibiotics such as beta lactams.
The hydrophilic sugars with multiple amino groups are protonated at physiological pH to function as polycations to target 16S rRNA; a lot of RNA where things are decoded and where peptide transfer occurs; pka of amino group is around 9, 99% protonated; physiology pH all these N are protonated; highly charged molecule in the gut does not transfer very well across mucosal membranes; not orally available, available via IV.
Not first line of AB therapy-pretty toxic.
Act on hairs in ears and effect hearing
Major side effects: nephrotoxciity and ototoxicity (ear).
Aminoglycoside AB: Mode of Action
Aminoglycosides bind the 16S rRNA on the 30S subunit notably at the A site for ammoniacal-tRNA binding.
RNA: big phosphate backbone; molecule with charged amino groups; nice attraction, negative and positive charges drives binding of aminocglycosides to ribosome.
Effects: see the inhibition of initiation of porin synthesis; blocks further translation and elicits premature termination.
Also results in incorporation in incorrect AA.
Cidal AB; complicated mechanism of doing more the stalling synthesis; hangs out, not diving and rapidly growing because cannot make proteins but won’t kill; doing this however, sending chunks of protein that aren’t fully formed=kill.
A site; where maniacal tRNA is coming in and binding.
Interaction of Gentamicin with minimized A site.
Resistance of AC; interaction of 3 rings of Gentamicin with the bases involved in fundamental A site.
See these positively charged groups interacting with P, idea that these positive charges interacting with specific P on RNA A site drives the inhibition of protein synthesis.
Ionic interactions are strongest; breaking interactions have to do with resistance mechanisms of AC.
Potent inhibitors of protein synthesis.
Tetracyclines and Glycylcyclines
Tetracycline
Chlortetracycline
Oxytetracycline
These last 3: 1940s-50s
Doxycycline (1950s)
DMG-MINO (1970s)
Tigecyline (2000s); glycylcycline; glycine on the side.
Structures are the major members of the tetracycline family of ABs
The recent approval of tigecycline, which is resistant to efflux, indicate continued interest in this class of ABs.
Primary mode of resistance to tetracycline is efflux (outside of cell less sensitive to efflux resistance mechanisms).
Major side effects: GI irritation, photosensitivity, discoloration of teeth.