An overview of the drug discovery process “ Hit to Lead” Nature Review Drug Discovery,8, 892 2009.
From Hit to Lead
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
From Hit to Lead
For a hit to become a lead it must:
Show structure-activity relationships (SAR)
Activity should be sensitive to structure
Losing activity is NOT a negative result!
The compound should have handles for reactivity
Able to modify
Most scaffolds are retained during optimization
Compounds should be simple
Stereocenters = cost
Should show activity in a cellular assay (or in vivo)
Can your hits get into a cell or a target tissue?
Should show lead-like molecular properties
Expedite and simplify further optimization
Lead Optimization Nat Rev Drug Disc 2, 369-78, 2003 Medicinal chemist In vivo efficacy is key
An overview of the drug discovery process
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?
Approaches to synthesis - discovery
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
An overview of the drug discovery process
S ynthesis of an active pharmaceutical ingredient (API)
Syntheses that are scalable from gms to kgs
Syntheses that avoids metals, such as Pd
Metal impurities must be minimal in the final compound
Removal of metals can be very expensive
Syntheses that can be purified easily
Salt forms are often used as APIs due to their greater stability and solubility
As the f ocus of chemistry efforts shift from making a library of many compounds to making large amounts of one compound , strategies change
Discovery synthesis vs API synthesis: A case study The chosen compound 5 has a m ethyl group added in the last step via a Pd catalyzed reaction as part of a parallel chemistry scheme
Synthetic scheme for compound 5 as an API W. Hu et al. / Bioorg. Med. Chem. Lett. 17 (2007) 414–418 Methyl group is set early in the synthesis via a cyclization reaction “ Green chemistry”
The path to drug discovery begins with the selection of the library picked for screening
Libraries should be chosen for the same reasons that compounds are chosen later in development
There are a variety of complimentary ways to get hits
Optimization of hits toward clinical candidates
Increase of potency and selectivity
Increase of in vivo efficacy
Maintenance of potency and selectivity; optimization of other factors
Incorporation of drug-like molecular property filters in the front end of discovery facilitates this process
Chemists use standard tools in drug discovery regardless of the therapeutic area
Many factors influence all steps of drug discovery, from choosing how to find a hit to choosing a clinical candidate
Drug discovery chemistry works to find compounds that are potent and selective with ADME properties that forecast in vivo efficacy in the clinic
Discovery synthesis and design should be efficient and make the best compounds possible to guarantee success
Chemistry efforts are led by biological results
Constant communication and feedback between team members of different disciplines gives the best chance to overcome the many obstacles and to succeed in the discovery of an efficacious drug
Thank you for your attention!
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
Just What in Fact, is a Natural Product?
~ 300,000 distinct compounds from microbes, plants, and other organisms
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
Characteristics of Protein folds
Distinct sequences often adopt very similar folds
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
Natural Products Bind Proteins
As substrates for via PKS, NRPS, tailoring enzymes, etc.
Outcome of selective pressure to binding protein and cellular targets
Domains of these fold targets are conserved in the “protein foldome”
Natural product ligands leverage these properties in their mechanism and properties
Natural products, by virtue their origin, are within or at least proximal to, biologically relevant chemical space.
Polyketide Immunophilin Ligand Family Salituro, G. et. al., Tet. Lett., 1995 , 36(7), 997-1000 Summers, M.Y.; Leighton, M.; Liu, D.; Pong, K.; Graziani, E.I., J. Antibiot., 2006 , 59(3), 184-189.
Natural Products lead to Unanticipated Drug Targets and Mechanisms FKBP binding domain mTOR effector domain Sehgal, S.N.; Baker, H.; Vézina, C., J. Antibiot., 1975, 28(10), 721-726. Choi, J.; Chen, J.; Schrieber, S.L.; Clardy, J., Science, 1996, 273, 239-241.
Rapamycin binds tightly to FKPB12 via FKBP binding domain