Medicinal chemistry in drug discovery in big pharma: past, present and future.

The changes in synthetic and medicinal chemistry and related drug discovery science as practiced in big pharma over the past few decades are described. These have been predominantly driven by wider changes in society namely the computer, internet and globalisation. Thoughts about the future of medicinal chemistry are also discussed including sharing the risks and costs of drug discovery and the future of outsourcing. The continuing impact of access to substantial computing power and big data, the use of algorithms in data analysis and drug design are also presented. The next generation of medicinal chemists will communicate in ways that reflect social media and the results of constantly being connected to each other and data.

Base-Controlled Diastereoselective Synthesis of Either anti- or syn-ß-Aminonitriles.

Deprotonation of secondary alkane nitriles with nBuLi and addition to aryl imines gives kinetic anti-ß-aminonitriles. Use of LHMDS allows reversible protonation of the reaction intermediate to give syn-ß-aminonitriles. The pure diastereosiomers can be isolated in good yields, and the mechanism was elucidated.

Reductive conjugate addition nitro-Mannich route for the stereoselective synthesis of 1,2,3,4-tetrahydroquinoxalines.

A concise, high yielding and structurally divergent synthesis of complex 1,2,3,4-tetrahydroquinoxalines with excellent diastereoselectivity is described. A wide array of nitroalkenes and imines derived from commercially available aromatic aldehydes and 2-chloroanalines were subjected to a key reductive conjugate addition nitro-Mannich reaction to give diastereomerically pure ß-nitro amines. Sequential reduction of the nitro function followed by Pd-catalyzed intramolecular N-arylation of the resultant primary amine onto the 2-chloroanailine gives highly substituted 1,2,3,4-tetrahydroquinoxalines. Non basic imines were found to participate better in the nitro-Mannich reaction if the stronger acid methanesulfonic acid was used to promote the reaction. The 3 step reaction sequence should be useful for the array synthesis of drug like scaffolds.

Synthesis and determination of absolute configuration of a non-peptidic αvß6 integrin antagonist for the treatment of idiopathic pulmonary fibrosis.

A diastereoselective synthesis of (S)-3-(3-(3,5-dimethyl-1H-pyrazol-1-yl)phenyl)-4-((R)-3-(2-(5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl)ethyl)pyrrolidin-1-yl)butanoic acid (1), a potential therapeutic agent for the treatment of Idiopathic Pulmonary Fibrosis, which is currently undergoing Phase I clinical trials is reported. The key steps in the synthesis involved alkylation of 2-methylnaphthyridine with (R)-N-Boc-3-(iodomethyl)-pyrrolidine, and an asymmetric Rh-catalysed addition of an arylboronic acid to a 4-(N-pyrrolidinyl)crotonate ester. The overall yield of the seven linear step synthesis was 8% and the product was obtained in >99.5% ee proceeding with 80% de. The absolute configuration of 1 was established by an alternative asymmetric synthesis involving alkylation of an arylacetic acid using Evans oxazolidinone chemistry, acylation using the resulting 2-arylsuccinic acid, and reduction. The absolute configuration of the benzylic asymmetric centre was established as (S).

Stereoselective synthesis of 1,2-diamine containing indolines by a conjugate addition nitro-Mannich reaction.

A conjugate addition nitro-Mannich reaction followed by nitro reduction and intramolecular N-arylation gives diastereomerically pure substituted 1,2-diamine containing indolines. Placing the N-arylation cyclisation handle on the imine precursor derived from an ortho-bromine substituted aromatic aldehyde gave the corresponding ß-nitroamines in 55-72% yields as single diastereoisomers. Nitro reduction was effected with modified quantities of Zn/HCl and a subsequent Pd(0) catalysed Buchwald Hartwig cyclisation gave indoline products in 40-70% yields as single diastereoisomers.

A practical drug discovery project at the undergraduate level.

In this article, we describe a practical drug discovery project for third-year undergraduates. No previous knowledge of medicinal chemistry is assumed. Initial lecture workshops cover the basic principles; then students, in teams, seek to improve the profile of a weakly potent, insoluble phosphatidylinositide 3-kinase delta (PI3Kδ) inhibitor (1) through compound array design, molecular modelling, screening data analysis and the synthesis of target compounds in the laboratory. The project benefits from significant industrial support, including lectures, student mentoring and consumables. The aim is to make the learning experience as close as possible to real-life industrial situations. In total, 48 target compounds were prepared, the best of which (5b, 5j, 6b and 6ap) improved the potency and aqueous solubility of the lead compound (1) by 100-1000 fold and ≥tenfold, respectively.

Factors determining the selection of organic reactions by medicinal chemists and the use of these reactions in arrays (small focused libraries).

Synthetic organic reactions are a fundamental enabler of small-molecule drug discovery, and the vast majority of medicinal chemists are initially trained--either at universities or within industry--as synthetic organic chemists. The sheer breadth of synthetic methodology available to the medicinal chemist represents an almost endless source of innovation. But what reactions do medicinal chemists use in drug discovery? And what criteria do they use in selecting synthetic methodology? Why are arrays (small focused libraries) so powerful in the lead-optimization process? In this Minireview, we suggest some answers to these questions and also describe how we have tried to expand the number of robust reactions available to the medicinal chemist.

Rhodium carbene routes to oxazoles and thiazoles. Catalyst effects in the synthesis of oxazole and thiazole carboxylates, phosphonates, and sulfones.

Dirhodium tetraacetate catalyzed reaction of alpha-diazo-beta-keto-carboxylates and -phosphonates with arenecarboxamides gives 2-aryloxazole-4-carboxylates and 4-phosphonates by carbene N-H insertion and cyclodehydration. In stark contrast, dirhodium tetrakis(heptafluorobutyramide) catalysis results in a dramatic change of regioselectivity to give oxazole-5-carboxylates and 5-phosphonates. Alpha-diazo-beta-ketosulfones behave similarly and give 5-sulfonyloxazoles upon dirhodium tetrakis(heptafluorobutyramide) catalyzed reaction with carboxamides. The analogous reactions of thiocarboxamides give the corresponding thiazole-5-carboxylates, -phosphonates, and -sulfones.

A concise route to pyridines from hydrazides by metal carbene N-H insertion, 1,2,4-triazine formation, and Diels-Alder reaction.

A simple, new three-step sequence for the conversion of hydrazides into pyridines is reported in which the key steps are N-H insertion by a copper carbene intermediate derived from alpha-diazo-beta-ketoesters into the hydrazide, reaction with ammonium acetate to give 1,2,4-triazines, followed by Diels-Alder reaction with norbornadiene.

The rhodium carbene route to oxazoles: a remarkable catalyst effect.

Dirhodium tetraacetate catalysed reaction of alpha-diazo-beta-keto-carboxylates and -phosphonates with arenecarboxamides gives 2-aryloxazole-4-carboxylates and 4-phosphonates by carbene N-H insertion and cyclodehydration; in stark contrast, dirhodium tetrakis(heptafluorobutyramide) catalysis results in a dramatic change of regioselectivity to give oxazole-5-carboxylates and 5-phosphonates.

Identification and optimisation of a novel series of pyrimidine based cyclooxygenase-2 (COX-2) inhibitors. Utilisation of a biotransformation approach.

Many years of work have been invested in the identification of potent and selective COX-2 inhibitors for the treatment of chronic inflammatory pain. One issue faced by workers is the balance between the lipophilicity required for potent enzyme inhibition and the physical properties necessary for drug absorption and distribution in vivo. Frequently approaches to reduce lipophilicity through introduction of polar functionality is hampered by highly challenging chemistry to prepare key molecules. We have complemented traditional synthetic chemistry with a biotransformations approach which efficiently provided access to an array of key target molecules.

The cyclooxygenase-2 inhibitor GW406381X [2-(4-ethoxyphenyl)-3-[4-(methylsulfonyl)phenyl]-pyrazolo[1,5-b]pyridazine] is effective in animal models of neuropathic pain and central sensitization.

The pathogenic form of the cyclooxygenase (COX) enzyme, COX-2, is also constitutively present in the spinal cord and has been implicated in chronic pain states in rat and man. A number of COX-2 inhibitors, including celecoxib and rofecoxib, are already used in man for the treatment of inflammatory pain. Preclinically, the dual-acting COX-2 inhibitor, GW406381X [2-(4-ethoxyphenyl)-3-[4-(methylsulfonyl)phenyl]-pyrazolo[1,5-b]pyridazine, where X denotes the free base], is as effective as rofecoxib and celecoxib in the rat established Freund's Complete Adjuvant model with an ED(50) of 1.5 mg/kg p.o. compared with 1.0 mg/kg p.o. for rofecoxib and 6.6 mg/kg p.o. for celecoxib. However, in contrast to celecoxib (5 mg/kg p.o. b.i.d.) and rofecoxib (5 mg/kg p.o. b.i.d.), which were without significant effect, GW406381X (5 mg/kg p.o. b.i.d.) fully reversed mechanical allodynia in the chronic constriction injury model and reversed thermal hyperalgesia in the mouse partial ligation model, both models of neuropathic pain. GW406381X, was also effective in a rat model of capsaicin-induced central sensitization, when given intrathecally (ED(50) = 0.07 mug) and after chronic but not acute oral dosing. Celecoxib and rofecoxib had no effect in this model. Several hypotheses have been proposed to try to explain these differences in efficacy, including central nervous system penetration, enzyme kinetics, and potency. The novel finding of effectiveness of GW406381X in these models of neuropathic pain/central sensitization, in addition to activity in inflammatory pain models and together with its central efficacy, suggests dual activity of GW406381X compared with celecoxib and rofecoxib, which may translate into greater efficacy in a broader spectrum of pain states in the clinic.

A simple solid phase diversity linker strategy using enol phosphonates.

Polymer bound lactam enol phosphonates can be easily generated using simple phenol on polystyrene resin. These stable, storable compounds can be released in a diversity cleavage strategy, using Suzuki cross coupling conditions, to provide 2-arylenamides in moderate to good overall yields.

Acetylene-based analogues of thiolactomycin, active against Mycobacterium tuberculosis mtFabH fatty acid condensing enzyme.

Analogues of the natural antibiotic thiolactomycin, with acetylene-based side chains, have the highest recorded in vitro inhibitory activity against the recombinant Mycobacterium tuberculosis beta-ketoacyl-ACP synthase mtFabH condensing enzyme. In particular, 5-[3-(4-acetyl-phenyl)-prop-2-ynyl]-4-hydroxy-3,5-dimethyl-5H-thiophen-2-one exhibited more than an 18-fold increased potency, compared to thiolactomycin, against this key condensing enzyme, involved in M. tuberculosis mycolic acid biosynthesis. Analogues of the antibiotic thiolactomycin, with acetylene-based side chains, have the highest recorded activity against cloned mtFabH condensing enzyme.

Biphenyl-based analogues of thiolactomycin, active against Mycobacterium tuberculosis mtFabH fatty acid condensing enzyme.

Analogues of the antibiotic thiolactomycin, with biphenyl-based 5-substituents, were found to have excellent in vitro inhibitory activity against the recombinant Mycobacterium tuberculosis beta-ketoacyl-ACP synthase mtFabH condensing enzyme. In particular, 5-(4'-benzyloxy-biphen-4-ylmethyl)-4-hydroxy-3,5-dimethyl-5H-thiophen-2-one exhibited approximately a 4-fold increased potency against this key condensing enzyme involved in M. tuberculosis mycolic acid biosynthesis, compared to thiolactomycin.

The design of novel N-4'-pyridinyl-alpha-methyl proline derivatives as potent catalysts for the kinetic resolution of alcohols.

A novel family of chiral acylation catalysts based on a N-4'-pyridinyl-alpha-methyl proline structure has been studied. A set of 31 compounds has been easily prepared and screened in the kinetic resolution of racemic alcohol 33 resulting in high enantioselectivities in most cases. From results obtained, H-bonding interactions between the catalyst and the substrate would appear essential to afford high enantioselectivity during the catalytic acylation. Additional solvent dependence and anhydride studies have been made to better identify the mechanism. This work has been further extended to the study of a number of structurally different alcohols. Ethanolamine derivatives in particular were found to be highly effective substrates (up to S = 18.8) in the kinetic resolution.

Analogues of thiolactomycin: potential drugs with enhanced anti-mycobacterial activity.

Analogues of the antibiotic thiolactomycin (TLM) have been synthesized and have been shown to have enhanced activity against whole cells of Mycobacterium tuberculosis H37Rv and against mycolic acid biosynthesis in cell extracts of Mycobacterium smegmatis. TLM has a methyl-branched butadienyl side chain attached at position 5 on a 'thiolactone' ring, namely 4-hydroxy-3,5-dimethyl-5H-thiophen-2-one. Various combinations of strong bases were explored to create a reactive anion at position 5 on the thiolactone ring which could react with halides to produce 5-substituted derivatives; the best reagent was two equivalents of lithium-bis-(trimethylsilyl)amide in tetrahydrofuran. The analogue with a 5-tetrahydrogeranyl substituent showed the best biological activity with an MIC(90) for M. tuberculosis of 29 micro M and 92% mycolate inhibition in extracts of M. smegmatis, as compared to 125 micro M and 54%, respectively, for TLM; other related C(10) and C(15) isoprenoid derivatives had similar biological activity. These isoprenoid-based derivatives did not inhibit type II fatty acid synthase from M. smegmatis, but compounds with iso-butyl and iso-butenyl side chains did show some inhibitory activity against this enzyme. These short-chain derivatives did not inhibit mycolate synthesis or have significant antibiotic activity. Treatment of the thiolactone with a weaker base, sodium hydride in tetrahydrofuran, gave 3-alkyl-3,5-dimethyl-thiophene-2,4-dione analogues, which had no effect on fatty acid or mycolate synthesis. However, the geranyl derivative had an MIC(99) of 60 micro M for M. tuberculosis, one quarter that (240 micro M) of TLM, demonstrating its excellent antibiotic potential against an unknown cellular target.