Andrew G. Leach

MULTI-STEP ORGANIC SYNTHESIS USING SOLID-SUPPORTED REAGENTS AND SCAVENGERS: A NEW PARADIGM IN CHEMICAL LIBRARY GENERATION

1 Review 1.1 Overview 1.2 Solid-phase organic synthesis (SPOS) 1.3 Beyond conventional solid-phase organic synthesis 1.4 The review 1.5 Some definitions 1.6 Solid-supported reagents and scavengers 1.7 Multi-step use of solid-supported reagents and scavenging reagents 1.8 Conclusions and future perspective 2 Introduction to the tables 2.1 Organisation of tables (reagent and catalyst section) 2.2 Representative data entry (reagent and catalyst section) 2.3 Organisation of tables (scavenging agents section) 2.4 Representative data entry (scavenging agents section) 3 Tables of reagents and catalysts 4 Tables of scavengers 5 Other relevant reviews 5.1 Insoluble polymers 5.1.1 Structure and physical properties (insoluble polymers) 5.1.2 General (insoluble polymers) 5.1.3 Reactions (insoluble polymers) 5.1.4 Miscellaneous (insoluble polymers) 5.2 Soluble polymers 5.2.1 General (soluble polymers) 5.2.2 Reactions (soluble polymers) 5.3 Inorganic solids 5.3.1 Structure and physical properties (inorganic solids) 5.3.2 General (inorganic solids) 5.3.3 Reactions (inorganic solids) 5.3.4 Miscellaneous (inorganic solids) 5.4 Miscellaneous supports 5.4.1 Structure and physical properties (miscellaneous supports) 5.4.2 General (miscellaneous supports) 5.4.3 Reactions (miscellaneous supports) 5.4.4 Miscellaneous (miscellaneous supports) 5.5 Purification strategies 5.5.1 Various supports (purification strategies) 5.5.2 Insoluble polymers (purification strategies) 6 Acknowledgements 7 Abbreviations 8 References 1 Review

Beyond Picomolar Affinities: Quantitative Aspects of Noncovalent and Covalent Binding of Drugs to Proteins

More than half a century ago, Linus Pauling wrote: “enzymes are molecules that are complementary in structure to the activated complexes of the reactions that they catalyze, ···, [rather than] entering into reactions.”1 This model has had a profound impact on drug design. Structure-based drug design usually involves the conceptualization and synthesis of molecules that have shapes and binding surfaces that are highly complementary to a protein receptor or enzyme binding site.2, 3 The goal is to achieve high binding affinity and selectivity. A drug must also have appropriate ADMET properties, but affinity is the first step. Affinity and selectivity are generally improved by ensuring more perfect geometric and noncovalent interactions with a binding site. Crystal structures of a protein-ligand complex suggest structural modifications to better occupy a hydrophobic pocket. Such modifications can improve potency from the millimolar to the nanomolar range,4 and have helped lead to clinically approved compounds such as the HIV protease inhibitor nelfinavir.5, 6 Kuntz et al. have shown that small molecule affinity for protein binding sites resulting from noncovalent interactions generally peaks at 10 picomolar (10−11 M), corresponding to ΔGbinding of 15 kcal/mol.7 In contrast, binding constants for enzymes with transition states correspond to average Δ Gbinding of 22 kcal/mol, and up to 38 kcal/mol—many orders of magnitude stronger than can be attributed to noncovalent factors alone.8, 9 Earlier studies in our group have shown how these and other data point to the generality of covalent and partial covalent bonding in transition states of enzyme-catalyzed reactions.8, 9 This strength of binding may be achieved by fully covalent bonding such as Schiff base or acylenzyme intermediate formation, but partial covalent bonds that take place in general acid/base catalysis and interactions with metal cofactors can partially share electrons with the substrate or other reactants such as water molecules in the transition state.9 The harnessing of such strong covalent interactions could help provide the high potency that is needed at early stages of drug development. There has been a tendency to avoid covalent drugs, going back to studies in the early 1970s demonstrating hepatotoxicity as a result of covalent binding of compounds such as [14C]bromobenzene and acetaminophen.10, 11 At the same time, however, there are many examples of highly successful covalently acting drugs on the market, from proton pump inhibitors omeprazole and related compounds,12, 13 to the entire class of β-lactam antibiotics.14 The toxicity attributed to covalent binding is not an inherent feature of these interactions, per se, but rather a result of the specific spectrum of off-target modifications that may be made by the drug or even by metabolites of drugs whose primary mechanism of action is noncovalent.15, 16 Advances in chemical biology, along with bioinformatics data analysis methods, are increasingly able to unravel which covalent modifications are tolerable and which are toxic, suggesting a reevaluation of the role of covalent binding in drugs and drug leads.16–19 In this Perspective, the limits achievable by noncovalent binding in enzyme–inhibitor complexes, and the greater affinity achieved by covalent bonding of the drug to the receptor, are discussed. Selected examples of covalently acting drugs will be presented (for more comprehensive reviews see references 20, 21), as well as opportunities for their future structure-based design with advances in molecular modeling or screening with target-specific libraries.

Matched molecular pair analysis in drug discovery.

Multiple parameter optimisation in drug discovery is difficult, but Matched Molecular Pair Analysis (MMPA) can help. Computer algorithms can process data in an unbiased way to yield design rules and suggest better molecules, cutting the number of design cycles. The approach often makes more suggestions than can be processed manually and methods to deal with this are proposed. However, there is a paucity of contextually specific design rules, which would truly make the technique powerful. By combining extracted information from multiple sources there is an opportunity to solve this problem and advance medicinal chemistry in a matter of months rather than years.

Discovery of 4-Amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide (AZD5363), an Orally Bioavailable, Potent Inhibitor of Akt Kinases.

Wide-ranging exploration of analogues of an ATP-competitive pyrrolopyrimidine inhibitor of Akt led to the discovery of clinical candidate AZD5363, which showed increased potency, reduced hERG affinity, and higher selectivity against the closely related AGC kinase ROCK. This compound demonstrated good preclinical drug metabolism and pharmacokinetics (DMPK) properties and, after oral dosing, showed pharmacodynamic knockdown of phosphorylation of Akt and downstream biomarkers in vivo, and inhibition of tumor growth in a breast cancer xenograft model.

Use of small-molecule crystal structures to address solubility in a novel series of G protein coupled receptor 119 agonists: optimization of a lead and in vivo evaluation.

G protein coupled receptor 119 (GPR119) is viewed as an attractive target for the treatment of type 2 diabetes and other elements of the metabolic syndrome. During a program toward discovering agonists of GPR119, we herein describe optimization of an initial lead compound, 2, into a development candidate, 42. A key challenge in this program of work was the insolubility of the lead compound. Small-molecule crystallography was utilized to understand the intermolecular interactions in the solid state and resulted in a switch from an aryl sulphone to a 3-cyanopyridyl motif. The compound was shown to be effective in wild-type but not knockout animals, confirming that the biological effects were due to GPR119 agonism.

Side Chain Flexibilities in the Human Ether-a-go-go Related Gene Potassium Channel (hERG) Together with Matched-Pair Binding Studies Suggest a New Binding Mode for Channel Blockers

The cardiac hERG K(+) channel constitutes a long-standing and expensive antitarget for the drug industry. From a study of the flexibility of hERG around its internal binding cavity, we have developed a new structural model of drug binding to hERG, which involves binding orthogonal to the pore channel and therefore can exploit the up to 4-fold symmetry of the tetrameric channel. This binding site has a base formed by four tyrosine side chains that complement reported ligand-based pharmacophores. The model is able to rationalize reduced hERG potency in matched molecular pair studies and suggests design guidelines to optimize against hERG not relying simply on lipophilicity reduction. The binding model also suggests a molecular mechanism for the link between high-affinity hERG binding and C-type inactivation.

Inhibitors of the Tyrosine Kinase Ephb4. Part 1: Structure-Based Design and Optimization of a Series of 2,4-Bis-Anilinopyrimidines

A series of bis-anilinopyrimidines have been identified as potent inhibitors of the tyrosine kinase EphB4. Structural information from two alternative series identified from screening efforts was combined to identify the initial leads.

Protodeboronation of Heteroaromatic, Vinyl, and Cyclopropyl Boronic Acids: pH–Rate Profiles, Autocatalysis, and Disproportionation

pH-rate profiles for aqueous-organic protodeboronation of 18 boronic acids, many widely viewed as unstable, have been studied by NMR and DFT. Rates were pH-dependent, and varied substantially between the boronic acids, with rate maxima that varied over 6 orders of magnitude. A mechanistic model containing five general pathways (k1-k5) has been developed, and together with input of [B]tot, KW, Ka, and KaH, the protodeboronation kinetics can be correlated as a function of pH (1-13) for all 18 species. Cyclopropyl and vinyl boronic acids undergo very slow protodeboronation, as do 3- and 4-pyridyl boronic acids (t0.5 > 1 week, pH 12, 70 °C). In contrast, 2-pyridyl and 5-thiazolyl boronic acids undergo rapid protodeboronation (t0.5 ≈ 25-50 s, pH 7, 70 °C), via fragmentation of zwitterionic intermediates. Lewis acid additives (e.g., Cu, Zn salts) can attenuate (2-pyridyl) or accelerate (5-thiazolyl and 5-pyrazolyl) fragmentation. Two additional processes compete when the boronic acid and the boronate are present in sufficient proportions (pH = pKa ± 1.6): (i) self-/autocatalysis and (ii) sequential disproportionations of boronic acid to borinic acid and borane.

Inhibitors of the Tyrosine Kinase Ephb4. Part 2: Structure-Based Discovery and Optimisation of 3,5-Bis Substituted Anilinopyrimidines.

Crystallographic studies of a range of 3-substituted anilinopyrimidine inhibitors of EphB4 have highlighted two alternative C-2 aniline conformations and this discovery has been exploited in the design of a highly potent series of 3,5-disubstituted anilinopyrimidines. The observed range of cellular activities has been rationalised on the basis of physicochemical and structural characteristics.

Protein-Ligand Crystal Structures Can Guide the Design of Selective Inhibitors of the FGFR Tyrosine Kinase.

The design of compounds that selectively inhibit a single kinase is a significant challenge, particularly for compounds that bind to the ATP site. We describe here how protein-ligand crystal structure information was able both to rationalize observed selectivity and to guide the design of more selective compounds. Inhibition data from enzyme and cellular screens and the crystal structures of a range of ligands tested during the process of identifying selective inhibitors of FGFR provide a step-by-step illustration of the process. Steric effects were exploited by increasing the size of ligands in specific regions in such a way as to be tolerated in the primary target and not in other related kinases. Kinases are an excellent target class to exploit such approaches because of the conserved fold and small side chain mobility of the active form.