Anthony G. Coyne

Water: Nature’s Reaction Enforcer—Comparative Effects for Organic Synthesis “In-Water” and “On-Water”

3.1.2. Huisgen [3 + 2] Cycloaddition Reaction 6313 3.1.3. Claisen Rearrangement 6315 3.2. Multicomponent Reactions 6316 3.3. Nucleophilic Ring-Opening Reactions 6316 3.4. Wittig Reaction 6318 3.5. Bioorthogonal Reactions 6318 4. Catalyzed Reactions 6319 4.1. Metal-Catalyzed Reactions 6319 4.1.1. Pericyclic Reactions 6320 4.1.2. Arylation Reactions 6321 4.1.3. Olefin Metathesis 6323 4.1.4. Mizoroki-Heck Reaction 6324 4.1.5. Suzuki Reaction 6325 4.1.6. Sonogashira Reaction 6327 4.1.7. Transfer Hydrogenation 6327 4.1.8. Lewis Acid Catalysis 6328 4.2. Organocatalyzed Reactions 6330 4.2.1. Pericyclic Reactions 6330 4.2.2. Michael Reaction 6331 4.2.3. Mannich Reaction 6332 4.2.4. Aldol Reaction 6333 5. Conclusion 6334 6. Supporting Information Available 6335 7. References 6335

Fragment-Based Approaches in Drug Discovery and Chemical Biology

Fragment-based approaches to finding novel small molecules that bind to proteins are now firmly established in drug discovery and chemical biology. Initially developed primarily in a few centers in the biotech and pharma industry, this methodology has now been adopted widely in both the pharmaceutical industry and academia. After the initial success with kinase targets, the versatility of this approach has now expanded to a broad range of different protein classes. Herein we describe recent fragment-based approaches to a wide range of target types, including Hsp90, β-secretase, and allosteric sites in human immunodeficiency virus protease and fanesyl pyrophosphate synthase. The role of fragment-based approaches in an academic research environment is also examined with an emphasis on neglected diseases such as tuberculosis. The development of a fragment library, the fragment screening process, and the subsequent fragment hit elaboration will be discussed using examples from the literature.

Drugging challenging targets using fragment-based approaches

Fragment-based approaches have now become firmly established in the drug discovery armoury. After notable early successes against protein kinases, the versatility and power of fragment-based approaches are increasingly being demonstrated on more diverse and difficult protein targets. This review highlights seven examples including targeting protein-protein interactions, a RNA polymerase and a DNA-binding protein. It shows how fragment-based approaches using small libraries have been successful when large HTS screens have failed. It also highlights the range of biophysical approaches being used and the interplay between experimental and in silico screens. The examples all show the iterative way in which potency is built up by synthetic elaboration of the initial fragment hits.

Water and Organic Synthesis: A Focus on the In-Water and On-Water Border. Reversal of the In-Water Breslow Hydrophobic Enhancement of the Normal endo-Effect on Crossing to On-Water Conditions for Huisgen Cycloadditions with Increasingly Insoluble Organic Liquid and Solid 2π-Dipolarophiles

Measurements of the endo/exo product ratios for Huisgen cycloadditions with a series of vinyl ketones, alkyl acrylates, and substituted styrenes as dipolarophiles with phthalazinium and pyridazinium dicyanomethanide 1,3-dipoles in acetonitrile and water show that as the reactions change from in-water (large hydrophobic enhancement of endo-products) to on-water, the hydrophobic enhancement of the endo-products is reduced and partially reversed (relative to acetonitrile). An expected increase of the endo-effect with increasing hydrophobic character of the dipolarophile is overcome by decreasing water solubility causing changeover to on-water conditions. On-water reactions do not show increased cycloaddition endo-effects (relative to organic solvents) as do in-water reactions.

Organic synthesis reactions on-water at the organic–liquid water interface

Organic reactions that occur at the water interface for water-insoluble compounds, and reactions in water solution for water soluble compounds, has added a powerful dimension to prospects for organic synthesis under more beneficial economic and environmental conditions. Many organic molecules are partially soluble in water and reactions that appear as heterogeneous mixtures and suspensions may involve on-water and in-water reaction modes occurring simultaneously. The behavior of water molecules and organic molecules at this interface is discussed in the light of reported theoretical and experimental studies. The on-water catalytic effect, relative to neat reactions or organic solvents, ranges from factors of several hundred times to 1-2 times and it depends on the properties of reactant compounds. In some cases when on-water reactions produce quantitative yields of water-insoluble products they can reach ideal synthetic aspirations.

Small‐Molecule Inhibitors That Target Protein–Protein Interactions in the RAD51 Family of Recombinases

The development of small molecules that inhibit protein–protein interactions continues to be a challenge in chemical biology and drug discovery. Herein we report the development of indole‐based fragments that bind in a shallow surface pocket of a humanised surrogate of RAD51. RAD51 is an ATP‐dependent recombinase that plays a key role in the repair of double‐strand DNA breaks. It both self‐associates, forming filament structures with DNA, and interacts with the BRCA2 protein through a common “FxxA” tetrapeptide motif. We elaborated previously identified fragment hits that target the FxxA motif site and developed small‐molecule inhibitors that are approximately 500‐fold more potent than the initial fragments. The lead compounds were shown to compete with the BRCA2‐derived Ac‐FHTA‐NH2 peptide and the self‐association peptide of RAD51, but they had no effect on ATP binding. This study is the first reported elaboration of small‐molecular‐weight fragments against this challenging target.

Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors

The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (KD = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (KD = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV–vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.

Understanding “On-Water” Catalysis of Organic Reactions. Effects of H+ and Li+ Ions in the Aqueous Phase and Nonreacting Competitor H-Bond Acceptors in the Organic Phase: On H2O versus on D2O for Huisgen Cycloadditions

For a typical Huisgen cycloaddition, carried out on water, the behavior of water molecules at the oil-water interface depended on the properties of the reactants. With weakly basic reactants, a small quantity of added H(+) (HClO4, 0.0001-0.01 M) present in the aqueous phase had negligible effects, but larger quantities of H(+) (HClO4, 0.1-3.0 M) increased the catalytic effect and caused protons to cross the water-organic interface and affect the products. Added Li(+) ions (LiClO4, 0.1-3.0 M) had no effect for on-water reactions but enhanced the rates and endo products for in-water reactions. For these cycloaddition reactions, the product endo:exo ratios, when compared to those in organic solvents, can be used to distinguish between the on-water and in-water modes. Comparisons of organic reactions on H2O and on D2O indicate that on-water catalysis ranges from weak to strong trans-phase H-bonding for reactants with basic pK(a) < ca. -6 and to interfacial proton transfer for reactants with higher basic pK(a) > ca. 2 (pKa of conjugate acid). Water shows a chameleon-type response to organic molecules at hydrophobic surfaces.

Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121.

Freedom to merge: A combination of crystal structure examination and in silico predictions made it possible to overcome the conformational limitations of fragment merging and escape the internal strain in a series of weakly binding merged fragments that target M. tuberculosis CYP121. The insights attained provide a new perspective and guide for prioritizing synthetic efforts toward fragment merging in future and ongoing fragment‐based ligand discovery campaigns.imageWILEY-VCH

Substrate Fragmentation for the Design of M. tuberculosis CYP121 Inhibitors

The cyclo‐dipeptide substrates of the essential M. tuberculosis (Mtb) enzyme CYP121 were deconstructed into their component fragments and screened against the enzyme. A number of hits were identified, one of which exhibited an unexpected inhibitor‐like binding mode. The inhibitory pharmacophore was elucidated, and fragment binding affinity was rapidly improved by synthetic elaboration guided by the structures of CYP121 substrates. The resulting inhibitors have low micromolar affinity, good predicted physicochemical properties and selectivity for CYP121 over other Mtb P450s. Spectroscopic characterisation of the inhibitors′ binding mode provides insight into the effect of weak nitrogen‐donor ligands on the P450 heme, an improved understanding of factors governing CYP121–ligand recognition and speculation into the biological role of the enzyme for Mtb.