Hits from HTS screening- may have many potential scaffolds
Hit-to-lead involves synthesis of many compounds to determine what is important
Need to see if there is room to improve the compound
Synthesis HTS HIT/Natural Product Essential scaffold Synthesis Potential lead compound
Hit to lead – fragment evolution Nature Reviews Drug Discovery 3, 660-672 (August 2004) Fragment evolution – aided by structure of fragment in the protein Essential fragment Synthesis to increase potency Potential lead compound
Hits from Fragment based screening- may have many potential scaffolds
Hit-to-lead involves synthesis to expand the core to move from binding to activity
Most efficient when aided by structure-based methods
Medicinal Chemistry Refinement Synthesis of compounds Screen for activity AND/OR Screen against activity AND/OR Screen for ADME Data Analysis (SAR trends) Refinement of criteria Planning Many compounds must be made! What are the strategies used for efficient synthesis? What tools are in the chemists’ synthetic toolbox?
Compounds are made in bunches, not as single efforts
The more molecules made at once, the better to understand trends i n efficacy, physicochemical properties, etc.
If one compound fails to show the expected in vivo pharmacology , others are there to fall back on-
Is it the scaffold?
Is it the target?
Without a variety of lead compounds, you won’t know!
Compounds may show similar activity, but vary greatly in selectivity, or ADME properties
Making series of compounds helps to spot trends to guide future research
Parallel synthesis of groups of compounds made by facile reactions from a common intermediate
Allows response to biological data with the shortest turnaround time possible
A case study for library design R. J. Gillespie et al. / Bioorg. Med. Chem. 17 (2009) 6590 – 6605 A diversifiable scaffold with three synthetic handles Facile coupling reactions with commercially available amines create a library to explore space around this position The more reactive chloride can be replaced with various groups through carbon-carbon bond formation The chloride can be substituted with various heteroatoms and groups Straightforward chemistries and commercial reagents allow for rapid diversification Prioritization is necessary
A structure – toxicity study - A 2A antagonists A2A binding: 2.8 nm A1 binding: 601 nm 3mg/kg p . o . efficacious in vivo for anti-cataleptic activity Molecular Weight: 449.51 log P: 3.33 tPSA: 100.51 hERG inhibition of 81% Maintain potency and selectivity while decreasing hERG % inhibition J. J. Matasi et al. / Bioorg. Med. Chem. Lett. 15 (2005) 3670–3674 J. J. Matasi et al. / Bioorg. Med. Chem. Lett. 15 (2005) 3675–3678
Natural Products as Drug Starting Points Frank E. Koehn 6 th Drug Discovery for Neurodegeneration February 13 th , 2012 New York, NY
PKS Engineering of Rapamycin 1) Gregory, M.A. and Leadlay, P.F. et al., Angew. Chem. Int. Ed. 2005, 44, 4757-4760. 2) Gregory, M. A. and Leadlay, P.F. et al., Org. & Biomol. Chem. 2006, 4, 3565-3568. rapamycin X X methylation and oxidation Pipecolate Incorporating Enzyme
Rationale for NP Biological Bias is Based on Protein Fold Space Properties
Protein sequence space is essentially infinite- at 300 aa, possible sequences = 20 300 >>> than particles in known universe (10 80 )
Total complement of estimated world proteome 10 10
Most proteins resemble other proteins - built by amplification, recombination, divergence from a basic set of folding units- domains
Around 100 domain families have been recognized by sequence
Only ca. 1000 folds are populated in nature
Subdomain level - recurrent local arrangements of secondary structures
Biophysical constraints limit the number of folded conformations
Highly similar sequences can adopt very different folds
Identical peptide sequences can have different conformations in different proteins
A single protein chain may encode for more than one structural domain.
Similar domains are formed via different “methods”
Structure is conserved far more than sequence .
Distinct Sequences Often Adopt Very Similar Folds Superposition of 3 proteins of similar structure but distinct sequences. 1 -Isomerase from Rhodopseudomonas palustris 2 - B chain of limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis 3 - Putative polyketide cyclase from Acidithiobacillus ferrooxidans a) 1 and 2 b) 2 and 3 c) 1 and 3 <20% sequence identity in aligned regions Regions of overlap in protein 1 Regions of overlap in protein 2 A- Proteins with virtually identical structure and little or no sequence similarity Current Opinion in Structural Biology 2009, 19:312–320, J Biol Chem 2009, 284:992-999 B- Proteins with high sequence similarity and no structure similarity Arl2 (BART) from Homo sapiens and ADP-ribosylation factor-like protein 2-binding protein from Danio rerio – 72%
Domains in Related Enzymes can be Formed in Distinctly Different Ways
Dimerization domain of GDP-mannose dehydogenase from P. aeruginosa
(b) Central dimerization domain of UDP-glucose dehydrogenase from S. pyogenes
(c) Single chain domain of ovine 6-phosphogluconate dehydrogenase The blue and yellow fragments highlight the correspondence with the chains shown in (b).
Current Opinion in Structural Biology 2009, 19:312–320