Novel Tetrapeptide Inhibitors of Bacterial Protein Synthesis Produced by a. Streptomyces sp. FLAVIA MARINELLI

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1 ovel Tetrapeptide Inhibitors of Bacterial Protein Synthesis Produced by a Streptomyces sp. FLAVIA MARIELLI DBSM, University of Insubria, Varese Italy Vicuron Pharmaceuticals, Gerenzano Research Center, Varese, Italy

2 The emergence of multidrug-resistant microbial pathogens is driving the search for novel and more effective antibiotics igh throughput screening using assays based on validated and established specific vital targets Chemical diversity produced by novel species of actinomycetes and fungi Streptomyces 15% ther actinomycetes 48% ther bacteria 1% Fungi 35% Myxobacteria 0.4%

3 A validated established specific antibiotic target is the bacterial translation machinery Aminoglycosides, Tetracyclines Macrolides, Liconsamides, Streptogramins Everninomycins, xazolidinones Cloramphenicol

4 Structural complexity of ribosomes, recently pointed out by cristallography... J.M. arms, F. Schlünzen

5 ...and functional complexity of the translation apparatus including, in addition to ribosomes, IFs, EFs, RFs, tras and aminoacyl tra synthetases as potential antibiotic targets...

6 Translational apparatus still offers remarkable opportunities for identifying unique inhibitors capable of bypassing existing resistance mechanisms Design of a TS procedure to identify inhibitors targetting transational steps other than elongation and likely escaped from screens using traditional assays

7 Bacterial protein synthesis cell-free assay 027 mra Translation Poly (U) Translation 027 mra Poly(U) UUUUUUUUUUU Ions, ATP & GTP Aminoacids E. coli S30 Radioactive Phe Incubation 60, 37 C Ions, ATP & GTP Aminoacids E. coli S30 Radioactive Phe Incubation 60, 37 C 027 peptide Poly (Phe) Met Thr Ile Phe

8 027mRA containing natural initiation signals AGGU 9 nu AUG UAA SD spacer IT T. I. R. Translation Initiation Region containing the Shine and Dalgarno (SD) sequence separated by a spacer of 9 nucleotides from the Initiation triplet (IT) Coding sequence (Met,Thr, Ile, Phe) for 35 aminoacids Termination codon

9 ur TS procedure : Primary screening of extracts from actinomycetes by a bacterial protein synthesis cell free system programmed with a novel mra (027mRA) containing natural initiation signals Secondary screening to discard those hits also active in yeast protein cell free system Tertiary screening to discard those hits also active in bacterial protein synthesis cell free system programmed with the conventional synthetic poly(u) mra mainly fishing inhibitors of the elongation step Elimination of known compounds (LC-MS) and of false positives (hit refermentation and retesting)

10 GE81112, complex of factor A, B, B1: a novel tetrapeptide constituited by uncommon aminoacids... R1 5 6 AA ' 2 1 5' AA2 R AA ' 1 5' 2' 3 2 AA4 1 4' 5' 2' Cl R= R1= R= R1= 2 R= R1= 2 AA1: 3-hydroxy-pipecolinic acid Factor A MW 643 Factor B MW 658 Factor B1 MW 657 AA2: 2-amino-5-[(aminocarbonyl)oxy]-4- hydroxypentanoic acid in factor A and B AA3: histidine in factor A, 2-2 substituted in factor B and B1 AA4: β-hydroxy-(2 -chloro)-histidine

11 3 J MBC correlation...whose structures have been elucidated by MR spectroscopy (DQF-CSY, TCSY, RESY, MQC, MBC)... Cl RESY correlation 2 2 L.Brandi et al Biochemistry 45: Cl

12 ...and by igh-resolution Electrospray Ionization Mass Spectroscopy, fragmentation studies and confirmed by GC-MS of the hydrolized and derivatized aminoacids... [M+] + m/z A =644 (m/z B =659) AA4 2 2 b3 m/z=457(472) (AA1+AA2) R + 2 Cl -shift R (170) -AA3 2 R Cl + R 2 -Cl m/z=608(623) m/z=626(641) (AA1+AA2) R Cl y 2 : AA3+AA4 m/z=343(358) -C AA4-137(152) -AA3 m/z=582(597) R Cl -shift 2 2 AA3 m/z=156(171) Cl Y1: AA4 m/z=206 R AA3 m/z=156(171) b1: AA1 m/z=128 2 b 2 : AA1+AA2 m/z= AA AA2 m/z=175

13 GE81112 is produced by a novel species of Streptomyces deposited as DSM Time course of Streptomyces sp. DSM fermentation at 300 l 10 scale: antibiotic is produced extracellularly with a maximum productivity of 10 mg/l 0 biomass [pmv%] and potency [mg/l] biomass GE , fermentation time (hours) p 9,00 7,00 p E. Selva et al 2003 W Patent 03/ L.Brandi et al Biochemistry 45:

14 GE81112 inhibits in vitro bacterial protein synthesis with IC 50 values of ca. 0.07µg/ml and 10 µg/ml in the cell free systems directed by the 027 mra or by the polyu mra, respectively. It does not inhibits protein synthesis in Saccharomyces cerevisiae cell free system E.coli 027mRA Inhibition (%) E.coli poly(u) mra S.cerevisiae 027 mra 0 0,01 0, GE (µg/ml)

15 GE81112 inhibits in vivo bacterial protein synthesis as confirmed by inhibiton test of macromolecular syntheses in whole cells of B.subtilis and E.coli DA RA Precursor incorporation (CPM) Precursor incorporation (CPM) Control curve chloramphenicol addition Time (min) Time (min) Protein synthesis Cell Wall GE81112 addition Precursor incorporation (CPM) Time (min) Precursor incorporation(cpm) Time (min) Time of antibiotic addition

16 GE81112 stably binds to the 30S ribosomal subunit and inhibits the formation of fmet-puromycin. fmet-puro formation * Translational activity of 30S ribosomal subunits pre-incubated with GE81112, centrifuged through a sucrose cushion and supplemented with a stochioemtric amount of control 50S GE (µg/ml) Translational activity of 50S ribosomal subunits pre-incubated with GE81112, centrifuged through a sucrose cushion and supplemented with a stochioemtric amount of control 30S *formation of fmet-puromycin requires the correct binding and positioning of the initiator tra in the ribosomal P site as well the proper functioning of the peptidyl transferase center in the 50S subunit. Since GE81112 binds to 30 S and not to 50S, it likely inhibits the initiation phase

17 GE81112 interfers with the fmet-tra binding to the P-site blocking the entry to the small ribosome unit. It is more efficient and more specific than the other P-site inhibitors.i.e edeine, pactamycin and kasugamycin

18 Antimicrobial spectrum of GE81112: it is active to Gram-negatives and Gram-positives when grown in minimal media MIC (µg/ml) Strain (Medium) Factor A Factor B Factor B1 Staphylococcus aureus ATCC19636 (CAMB) >512 >512 >512 Streptococcus pyogenes L49 (TB) > Streptococcus pneumoniae L44 (TB) Enterococcus faecalis Van A L560 (CAMB) Moraxella catarrhalis L3292 (CAMB) Bacillus subtilis ATCC6633 (AM3) > Bacillus subtilis ATCC6633 (MM asp) Escherichia coli L47 (CAMB) > Escherichia coli L47 (MM) Candida albicans L145 (MM 40) >512 >512 >512 Candida albicans L145 (RPMI) >512 >512 >512

19 Cells grown in minimal medium were more susceptible to GE81112 than those growth on rich medium: competition by medium components (oligopeptides) during GE81112 uptake MIC (µg/ml) Casam inoacids (%) B.subtilis E.coli

20 Conclusions ovel chemical structure : low molecular weight hydrophylic tetrapeptide different from other known classes of protein synthesis inhibitors Specific and efficient mechanism of action on the initiation phase of bacterial protein synthesis Poor antimicrobial activity due to permeability problems GE81112 is a unique scaffold for designing new drugs

21 Letizia Brandi Attilio Fabbretti Alessandro Maio Claudio.Gualerzi Ameriga Lazzarini, Linda Cavaletti, Luciano Gastaldo Monica Abbondi, Emiliana Corti, Daniele Losi, Stefano Donadio Alessandra Marazzi, Marina Feroggio, Luigi Colombo, Enrico Selva