Genetically Encoded Fragment-Based Discovery (GE-FBD) from Phage-Displayed Macrocyclic Libraries with Genetically-Encoded Unnatural Pharmacophores

Abstract

<p>Genetically encoded fragment-based discovery (GE-FBD) from phage-displayed macrocyclic libraries with genetically-encoded unnatural pharmacophores<b></b></p><p>Late stage functionalization of genetically encoded 1,3-diketone macrocyclic phage libraries by pharmacophores containing hydrazine handles. </p>

Chemo-ribosomal synthesis of atropisomeric and macrocyclic peptides with embedded quinolines

“…Introducing these modifications earlier in the discovery process would be advantageous. Some important progress has been made, including the introduction of N-Me groups 83 , D-amino acids 84 , β 2 -and β 3 -amino acids, as well as linkers that introduce rings 7 or even appended pharmacophores 25,28 . Even with these developments, the chemistry available to ribosomally translated-peptides remains limited when compared to the vast array of transformations, functional groups, and architectures that are emblematic of small molecule pharmaceuticals and bioactive natural products.…”

“…Alternative macrocyclization strategies that generate stable and drug-like linkers are widely recognized as an unmet need 9,[22][23][24][25][26][27] . Chemistry that exploits the macrocyclization event to establish a known pharmacophore within the peptide backbone prior to biological display is a promising strategy towards this end 28 .…”

Strategies to expand peptide functionality through hybridisation with a small molecule component

“…41,42 In a recent extension of this approach, the post-translational incorporation of a 1,3-diketone greatly expanded the functionality that could be incorporated in the library. 43 Having installed the diketone on their ''silent barcode'' phage-displayed libraries, Derda and co-workers then diversified by using a Knorr pyrazole synthesis with a wide range of hydrazine containing reagents. Using this methodology, they were able to incorporate fluorophores, lipids, PEG chains, metal chelators and groups known to bind certain proteins.…”

Expanding the Chemical Diversity of Genetically Encoded Libraries

“…Libraries with fixed cysteines flanking the randomized portions can be reacted with bifunctional alkyl halide linkers to form side chain to side chain macrocycles (Figure .2). A wide array of linkers have been used for this kind of chemistry, ,,,, including some more exotic examples, such as dichloroacetone, which can be reacted with hydroxylamines in situ to yield the corresponding oximes, or 1,5-dichloropentane-2,4-dione, which can be reacted with hydrazines to further increase diversity of the resulting modified libraries via Knorr pyrazole synthesis . An additional cyclization involves the reaction of the N-terminal free amine and side chain amine of a fixed C-terminal lysine with the cross-linking agent disuccinimidyl glutarate (DSG) to form head to side chain cycles (Figure A.2). ,,, DSG has been used primarily with mRNA display libraries, , where library translation with rabbit reticulocyte lysate provides immediate access to the free N-terminal amine, which would otherwise be formylated in prokaryotic translation systems, but modification of yeast display libraries with DSG has been recently reported .…”