COMPOUND LIBRARIES
Introduction
Background
The present invention relates to compounds capable of binding to G-protein coupled receptors. In particular, libraries of compounds are provided for use in screening programmes against GPCR targets as well as the individual compounds for use in hit to lead and lead optimisation projects and similar stages in the drug discovery process.
The method also provides methods for making compounds and libraries .
As part of the process of discovering drugs or agrochemicals it is customary to screen libraries of compounds against biological targets to discover "Hits' which are then further developed into 'Leads' and subsequently drugs or agrochemicals by using the techniques of medicinal chemistry. Accordingly the success or not of a drug or agrochemical discovery project is critically dependent on the quality of the hit and this in turn is dictated by the quality of the screening library.
Technological advances have enabled screening on a very large scale and the screening of hundreds of thousands of compounds at the start of a discovery program is routine. This, however, does entail a significant cost. The hits obtained from such screening efforts are not all of the best quality and often take a large amount of subsequent time and effort in order to get a good lead. It has been estimated that only about 25% of projects actually get to the lead optimisation
stage and part of the reason for this is the intractability of hits from high throughput screening.
Screening libraries are commonly collections of compounds from several sources. As a result, they typically contain compounds synthesised as a part of previous projects in the history of a company. With regard to drug discovery, these collections will be drug-like but are likely to be limited in scope and will be directed to certain areas of a particular project. It has been the common practice of many pharmaceutical companies in recent times to augment the collections by purchasing either single compounds from vendors or by contracting the synthesis of combinatorial libraries of compounds. The singly purchased compounds may have been selected to fill in areas of compound space poorly represented in the compound collections . Combinatorial libraries are typically synthesised around well-performing chemistries with some design based on producing 'diversity' in compound space.
A complementary approach, and one that is increasingly preferred, is to screen focused libraries against the target of choice. Focused libraries are becoming of increasing importance in their ability to generate hits capable of rapid expansion in many areas including GPCRs . Such libraries are slightly more expensive to prepare but have attributes of reliability, reproducibility and provide a considerably higher hit rate: typically 10-100 fold and above compared with random screening. They are, however, very difficult to design and their efficiency relates directly to the amount of effort that, has gone into the design. Using focused libraries, it is usually possible to get a number of hits in the low micromolar and below range. As there is a defined set of compounds there
is the potential to observe indications of SAR in a chemical series and progress the chemistry efficiently.
G-protein-coupled receptors (GPCRs) are very important in the regulation of numerous body processes and a significant proportion of all drugs work by interaction with these receptors. There are several hundred known, many of which are orphans - those receptors that have no established ligands . They fall into a class of 7-transmembrane receptors and there is only one X-ray structure known, that of the bovine rhodopsin receptor, and this is at a resolution of 2.8 Angstroms and is thus not suitable for accurate modeling work. In addition, the rhodopsin receptor is somewhat unusual in its interactions with its ligand and is not used as a drug target. Nevertheless, the overall three dimensional arrangement can be deduced from the X-ray and is in accordance with previous work based upon bacteriorhodopsin receptor which is not G-protein- coupled.
GPCRs are most often characterised by sequence homology as being comprised of several sub-families. Most attention currently is directed towards Family A receptors as being the most tractable class historically and also the one with the most potential targets .
Family A comprises about 300 receptors that are potential drug targets, approximately half of which have known ligands and the rest, the so-called orphan receptors. The group of druggable receptors is composed, essentially of two types: those whose natural ligand interacts wholly within the transmembrane domain, such as the aminergic, nucleotide-like, prostaglandih receptors, etc. and those peptide liganded receptors, which have a large part of their interactions in
the extracellular region and which may insert a peptide loop or tail into the transmembrane region to effect signal transduction. Examples of this class are angiotensin, cholecystokinin and opioid receptors . Irrespective of the mode of action of the natural ligand or the GPCR family, the vast majority of drug molecules interact in the all-helical domain of the transmembrane region with exceptions being those mimics of glutamate at the metabotropic glutamate receptor and some peptide therapeutics administered parenterally. In looking for lead molecules for an unexplored or orphan GPCR it therefore makes sense to concentrate on interactions in the transmembrane domain.
The focused library provided herein is designed to interact with a range of the family A receptors. Each library is a defined set of compounds which will enhance the probability of finding a small molecule which will interact with one or more type of GPCR receptor.
For example, focused libraries can be provided having compounds which will interact with aminergic GPCRs, and peptidic GPCRs requiring an obligatory positive charge in ligands, or other types or groups of GPCRs.
Focused libraries according to this invention can provide hit rates of 1-13% or more for the requisite predicted GPCRs from both a ine- and peptide-liganded classes and with agonists and antagonists .
Summary of Invention
We provide herein a "focused" library of compounds which will provide "leads" for ligands which bind to Family A G-Protein coupled receptors .
In the context of the present invention, "library" means a group of compounds which are structurally related by virtue of a core chemical structure (or "scaffold") but which differ from each other by virtue of permutation of specific substituent groups attached to the scaffold.
Generally speaking such a library will consist of or comprise a number of compounds, e.g. as many as about 100, 1000,2000, 3000 or indeed 10,000 compounds. The number of compounds should be sufficient to provide an adequate diversity of related compounds without being so large as to be unduly complex/expensive to produce.
In the context of the present invention the terms "permitted substituents" and analogous terms are used to refer to defined chemical groups which may be attached to a "scaffold" to provide permutations of the chemical structure of related compounds .
Where the chemical formulae of permitted substituents are shown in this description and claims, the substituent may appear in the compound exactly as shown- (i.e. simply covalently bonded to the scaffold) or may be a derivative of
the shown chemical formula of the substituent by virtue of use of a reactive group to couple the substituent to the scaffold.
It will be appreciated that the total number of permutations created by the permitted substituents may be a very large number, far greater in magnitude than the actual number of compounds in an actual library. In other words, the number of possible compounds for any "virtual" library may well greatly exceed the number of synthesised compounds making up an embodiment of the "real" library. The invention is intended to encompass libraries having all, and a number, which is less than all, of the permitted substitutions represented by compounds therein.
It will be appreciated that some specific combinations of permitted substituents may be more or less difficult to synthesise and/or use in a focused library of the invention. This does not detract from the generality of applicability of the invention as described herein. It is to be expected that real libraries will be synthesised from a selected group of permutations/combinations of permitted substituents, taking into consideration factors affecting the intended purpose of the library and its cost and complexity of synthesis.
Even if theoretically permitted, it is currently considered unlikely that any compound would be prepared for inclusion in a focused library if it had either or both of the following properties
(1) molecular weight >700
(2) log p <-3 or >9 (an index of lipophilicity as calculated using commercially available
"Chemenlighten 2.8" and "Biobyte" software for the log p calculation) .
The present invention provides novel focused libraries of compounds . Most of the compounds defined by the permitted substitutions on the scaffolds are also novel compounds per se and the invention is intended to encompass each individual novel compound. Any known compound having a structural formula identical to any one of the compounds covered by the formulae of scaffolds and permitted substitutions described herein is hereby explicitly disclaimed per se.
DESCRIPTION OF THE INVENTION
Library 4 has been designed to take advantage of a common recognition feature of G-protein coupled receptors, namely the 'benzhydryl' or 'rabbit ears' arrangement of aromatic rings. At the same time this library utilises several themes common in GPCRs selecting for subsets which recognise basic and 'acidic' ligands. Examples of drugs which interact with receptors of this type are sertindole, devazepide and brompheniramine, however there are many more.
There appear to be around three separate recognition sites for the 'rabbit ears' moiety in GPCRs and the molecular interactions are presumed to be a feature of aromatic-aromatic interactions in an all-helical receptor environment. In addition to utilizing this recognition function this library has a wide focus in its ability to pick up the recognition features provided by TM3 aspartates for basic groups and also by interactions, typically with histidines in TM6 in basic environments for acidic groups and in other environments for more neutral carboxylate bioisosteres . A final feature of the design extends this recognition site for a subset of compounds to recruit antagonist recognition sites around TM7.
The invention provides a library comprising or consisting of a set of structurally related compounds of general formula A:
A
wherein X is a carbon chain (CH2)n, and n = 2 or 3 , or alternatively X-N-R3 form part of a 5 or 6 member saturated ring;
Rl is a hydrogen, alkyl, alkoxy or halogen;
R2 is an optionally substituted aryl or heteroaryl group;
R4 is an optionally substituted alkyl, acyl or sulphonyl group; where R3 does not form part of a ring it may be hydrogen or an optionally substituted alkyl;
and Y can be nitrogen or carbon.
Structural Novelty of Compounds of Library 4
Compounds of the following general formulae are unknown
wherein Y = CH, or N, and n = 1 or 2 ;
wherein X as defined in formula A is (CH2)
n (n=2 or 3); and
Methods for Synthesising Scaffolds of Library 4
Compounds of formula 4 can be made according to Scheme 1
.COOH X
(5) Scheme 1 (6)
Nitriles ( 1) selected from List 1 are reacted with Grignard reagents (R2MgZ) , selected from List 2 wherein Z = chloro or
bromo to give the amines (2) . These are then reacted with a range of t-butyloxycarbonyl protected amino acids selected from List 3 to give the amides (3) . Treatment with phosphorous oxychloride in pyridine gives the fused ring compounds (4) . The t-butyloxycarbonyl protecting group is then removed by treatment with acid to give the amines (5) .
The amines can either be alkylated with compounds selected from List 4, wherein # is a leaving group (especially halogen or sulphonate) , to give compounds where R4 = substituted alkyl or alkylated by reductive alkylation with compounds selected from List 5 to give compounds where R4 = substituted alkyl, or acylated with methane sulphonyl chloride or acetyl chloride to give compounds where R4 = #-S0Me or #-COMe, where # is the point of attachment .
Where R3 = H, amines (6) can then be further alkylated by reductive alkylation with aldehydes and ketones selected from List 6 to give compounds (6) where R3 = substituted alkyl.
The permitted substituents at positions Rl, R2 , R3 and R4 for compounds of Library 4 are shown below.
List 1
List 2
List 3
BOC
List 5
List 6
List 6 (Continued)
Methods for Synthesisisng Compounds of Library 4
General method for the synthesis of benzhydryl amines (2)
The cyano pyridine (0.1 mol) was dissolved in dry toluene (300 ml) and cooled to 0-5°C. The Grignard reagent (0.11 mol) was added dropwise over 30 minutes to give a thick creamy precipitate. The reaction was stirred for a further 30 minutes at 0-5°C then iso butanol (120 ml) was added dropwise keeping the temperature below 0-5°C to give a clear brown solution. The reaction was cooled to 0-5°C and sodium borohydride (0.14 mol) added portionwise and the whole stirred at RT overnight. The reaction was quenched with methanol/water and concentrated in vacuo to remove the toluene . The mixture was extracted with DCM and the organics dried over magnesium sulfate before
concentrating in vacuo. Purification was carried out by flash column chromatography on silica eluted with ethyl acetate and ethyl acetate/3% TEA mixtures. An alternative purification involved dissolving the residue in diethyl ether and extraction into dilute HC1. The acidic solution was washed three times with diethyl ether and then basified with IN sodium hydroxide and the product extracted with diethyl ether. The organics were dried over magnesium sulfate and concentrated in vacuo to yield the benzhydryl amine.
Examples of benzhydryl amines (2)
C- (4-Fluoro-phenyl) -C-pyridin-2-yl-methylamine Yellow δ.CDCl
3 °il 2.1 (2H, bs, NH
2) , 5.3 (1H, s.
CH) , 6.9-7.5 (7H, m, 7ArH) , 8.6 (1H, m, ArH)
C-Phenyl-C-pyrazin-2-yl-methylamine
Brown δ.CDCl
3 oil 2.2 (2H, bs, NH
a) , 5.3 (1H, m,
CH) , 7.2-7.4 (5H, m, 5ArH) , 8.4 (lH,.
'm, ArH), 8.5 (1H, m, ArH), 8.6 (1H, s, ArH)
4-Chloro-2- (2-methoxy-benzyl) -pyridine
Yellow δ.CDCl
3 oil 2.1 (2H, bs, NH
2) , 3.8 (3H, S,
OMe) , 5.5 (1H, s, CH) , 6.8-7.3
(6H, m, ArH) , 8.4 (1H, m, ArH)
C- (4 -Methyl -pyridin-2-yl) -C-phenyl-methylamine Brown δ.CDCl3 oil 2.1 (3H, bs, NH3.C1) , 2.3 (3H,
S, CH
3) , 5.2 (1H, S, CH) , 6.9-
7.5 (7H, m, ArH) , 8.4 (1H, m, ArH)
General method for the synthesis of amides (3)
The BOC protected amino acid (2, 15 mmol) was dissolved in dry DCM (25 ml) and CDI (15 mmol) added. The reaction was stirred for 30 minutes and then a solution of the benzhydryl amine (1, 15 mmol) in DCM (5 ml) was added. The whole was stirred overnight. The solution was washed with water, dried over magnesium sulfate and concentrated in vacuo to yield the desired amide. The amide was used without further purification.
Examples of amides (3)
4-{ [ (4-Fluoro-phenyl) -pyridin-2-yl-methyl] -carbamoyl}' piperidine-1-carboxylic acid tert-butyl ester
cream solid δ.CDCl31.4 (9H, s, fcBu) , 1.7 (2H, bm, 2xCH) , 1.9 (2H, bm,
2xCH) , 2.4 (IH, bm, CH) , 2.8
(2H, bm/ 2xCH) , 4.1 (2H, bm,
2xCH) , 6.1 (IH, m, CHNH) , 6.9 (IH, m, ArH), 7.2-7.3 (3H, m,
ArH+NH) , 7.6-7.8 (2H, m, ArH),
8.6 (IH, m, ArH)
C=0 1693, 1637
{3- [ (Phenyl-pyridin-2-yl-methyl) -carbamoyl] -propyl}-carbamic acid tert-butyl ester
δ.CDCl
31.4 (9H, m,
fcBu) , 2.5 (2H, m, CH
2) , 3.4 (2H, m, CH
2) , 5.4 (IH, m, NHBOC), 6.1 (IH, d, CH) , 7.2-7.4 (7H, m, ArH&NH) ,
7.6-7.7 (2H, m, ArH), 8.6 (IH, m, ArH)
s,
fcBu) , 2.1 (2H, m, 9 (IH, m, CH) , 3.3 (IH, 3.5-3.8 (3H, m, CH) ,
d, CHNH) , 6.9 (2H, m, ArH), 7.2-7.4 (3H, m, ArH), 7.6-7.7 (2H, m, ArH&NH), 8.5 (IH, m, ArH)
Cyclisation to give the bicyclic compounds (4)
a) For cyclic amino acids
POCl3 (8.5 mmol) was added dropwise to a cooled (ice/water) solution of the amide (7.2 mmol) and pyridine (44.5 mmol) in dry DCM (35 ml) . The mixture was stirred overnight at RT. The mixture was washed with water (2 x 10 ml) . The organics were dried over magnesium sulfate and concentrated in vacuo to yield the desired cyclised product. Purification was carried out by column chromatography on silica eluted with petrol: ethyl acetate
b) For open chain amino acids
The amide (2 mmol) was dissolved in dry DCM (10 ml) and pyridine (4 mmol) added. TFAA (2 mmol) was dissolved in dry DCM (2.5 ml) and added dropwise to the mixture at RT . The reaction was stirred for 1 h at RT. The mixture was washed with water (2 x 10 ml) . The organics were dried over magnesium sulfate and concentrated in vacuo to yield the desired cyclised product. Purification was carried out by column chromatography on silica eluted with petrol: ethyl acetate.
Examples of" bicyclic compounds (4)
4- [1- (4-Fluoro-phenyl) -imidazo [1, 5-a] pyridin-3-yl] -piperidine -1-carboxylic acid tert-butyl ester
0
1 (2H, m, ArH) , 7.7-7.9 (4H, m,
ArH)
C=0 1682
{2- [1- (3-Methoxy-phenyl) -imidazo [1, 5-a] yridin-3-yl] -ethyl} -carbamic acid tert-butyl ester yellow gum
(IH, m, ArH) , 7.3 (IH, m,
ArH) , 7.4-7.5 (2H, m, ArH) ,
7.7-7.8 (2H, m, ArH)
{2- [7-Chloro-l- (3-methoxy-phenyl) -imidazo [1, 5-a] yridin-3-yl] -ethyl} -carbamic acid tert-butyl ester
yellow solid .1- m, 3
(3H, m, ArH) , 7.8 (2H, m, ArH)
[2- (1-p-Tolyl -imidazo [1, 5-a] pyridin- 3 -yl) -ethyl] -carbamic acid tert-butyl ester
.2
[3- (1-Phenyl-imidazo [1, 5-a]pyridin-3-yl) -propyl] -carbamic acid tert-butyl ester
(IH, m, ArH) , 7.4 (2H, m,
ArH), 7.7-7.9 (4H, m, ArH)
- (1-Thiophen-2-yl-imidazo [1, 5-a] pyridin-3-yl) -pyrrolidine-1-carboxyl acid tert-butyl ester
m, 7- m, .1
ArH) , 7.4 (IH, m, ArH) 7.8- 7.9 (2H, m, ArH)
Removal of the tert-butyloxycarbonyl group to give the amines (5)
The BOC protected amine (8.86 mmol) was dissolved in 4N methanolic HC1 (15 ml) and stirred overnight at RT. The solvent was removed in vacuo and the solid residue triturated with diethyl ether. The solid was removed by filtration and dried to give the amine hydrochloride . The compounds were stored as the HC1 salt and then converted to the free base by aqueous sodium hydroxide for further reaction.
Examples of amines (5)
2- [1- (4-Fluoro-phenyl) -imidazo [1, 5-a] pyridin-3 -y] -ethylamine
.3
2
Free base
3-Pyrrolidin-3-yl-l-thiophen-2-yl-imidazo [1, 5-a] pyridine
CH) , 2.5-2.6 2-3.3 (IH, m, H, m, CH) , 3.6- , 4.2-4.3 (IH,
m, CH) , 6.0-7.0 (water from DMSO) , 6.8 (IH, m, ArH) , 6.9 (IH, m, ArH), 7.1 (IH, m, ArH), 7.4 (IH, m, ArH), 7.5 (IH, m, ArH), 7.8 (IH, m, ArH), 8.3 (IH, m, ArH), 9.5-10.0 (2H, bd, NH.HC1) D
20 shake - observe loss of NH
Alkylation of the amine ( 6) a) via displacement of a leaving group
The free amine (R3 = H) (0.2 mmol), alkylating agent (0.2 mmol) and Hunig's base (0.2 mmol) were heated in MIBK (2 ml) at 100°C for 5 hours. The reaction was cooled and water added. The mixture was extracted with ethyl acetate (2 x 1 ml) . The organics were dried over magnesium sulfate and concentrated in vacuo to yield the desired product. Purification was carried out by automated preparative HPLC.
Automated Preparative HPLC
The reaction mixture was dissolved in DMSO (~1.5ml). This solution was loaded onto a 10mm xtera MS C18 column at room temperature and eluted with the following gradient
Eluant A 0.05% diethlamine in water
Eluant B 0.05% diethlyamine in acetonitrile
Sample collection was triggered by U.V. absorbance, (thresholds set appropriated for the specific plates) . The collected samples were analysed by LC-MS to ascertain the identity and purity of the constituents.
The analytical conditions
1. Column: Waters xterra MS C18 100x4.6mm 5um packing (part No.186000486)
2. Temperature: ambient ~22°C
3. Eluant A: lOmM (NH4)HC03
Eluant B: Acetonitrile
4. Flow Rate during analysis: 2ml per min
5. Detection DAD window 210 - 400nm
6. Mass Spectra: APCI, M+l and possibly acetonitrile adducts present and coincident with the major uv peak
0.00 min - 95% A: 5% B 0.00 min - 70% A: 30% B
2ml/min 2ml/min
0.50 min - 95% A: 5% B 5.50 min - 5% A: 95% B
2ml/min 2ml/min
5.50 min - 5% A: 95% B 10.00 min - 5% A: 95% B
2ml/min 2ml/min
8.50 min - 5% A: 95% B 10.70 min - 70% A: 30% B
2ml/min 2ml/min
8.60 min - 95% A: 5% B 11.00 min - 70% A: 30% B
2ml/min 2ml/min
8.70 min - 95% A: 5% B
4ml/min
10.70 min - 95% A: 5% B
4ml/min
10.80 min - 95% A: 5% B
2ml/min
11.00 min - 95% A: 5% B
2ml/min
3-{l- [2- (4-Fluoro-phenoxy) -ethyl] -piperidin-4-yl} -1- (4-fluoro-phenyl) -imidazo [1, 5-a] pyridine
Purity Retention time 5.45 min 98% Method 1
3- (l-Allyl-piperidin-4-yl) -1-phenyl-imidazo [1, 5-a] pyridine
Purity Retention time 4.67 min 95% Method 1
l-{3- [4- (1-Phenyl-imidazo [1, 5-a] pyridin-3 -yl) -piperidin-1-yl] -propyl }-pyrrolidine-2 , 5-dione
Purity Retention time 4.71 min 91% Method 1
1- (2- {4- [1- (4-Chloro-phenyl) -imidazo [1, 5-a] pyridin-3-yl] -piperidin-1-yl}-ethyl) -pyrrolidine-2 , 5-dione
Purity Retention time 4.59 min 95% Method 1
h) via reductive amination
The free amine, aldehyde/ke one and sodium triacetoxyborohydride were mixed and shaken overnight at RT. The reaction was diluted with DCM, washed with 1M sodium bicarbonate solution and then water. The aqueous phase was back extracted with DCM. The organics were combined and concentrated. Purification was carried out by automated preparative HPLC.
(2-Methyl-3-phenyl-allyl) - [2- (l-thiophen-2-yl-imidazo [1, 5-a] pyridin-3-yl) -ethyl] -amine
tion time 5.35
d 1
3- [1- (2, 2-Diphenyl-ethyl) -pyrrolidin-3-yl] -1- (2-methoxy-phenyl) -imidazo [1, 5-a] pyridine tion time 6.04
d 1
3- [1- (l,2,3,4-Tetrahydro-naphthalen-2-yl) -pyrrolidin-3-yl] -1-m-tolyl-imidazo [1, 5-a] pyridine tion time 5.67
d 2
Acylation/sulfonylation of the amine (6)
The substituted amino imidazopyridine solution (0.175 m in THF 0.5 ml) and the triethylamine solution (0.175 m in THF 0.5 ml) were mixed together and then the solution of acetyl chloride (0.175 m in THF 0.5 ml) or methane sulphonyl chloride (0.175 m in THF 0.5 ml) added. The reaction mixture was shaken at room temperature overnight . Water 2ml was added and the mixture extracted with ethyl acetate (2 x 1 ml) and the extract concentrated in vacuo. The residue was purified by reverse phase HPLC.
1- {4- [1- (4-Fluoro-phenyl) -imidazo [1, 5-a] pyridin-3-yl] -piperidin-1-yl} -ethanone
Purity Retention time 4.28 min 83% Method 1
l-{4- [1- (2-Methoxy-phenyl) -imidazo [1, 5-a] pyridin-3 -yl] -piperidin-1-yl } -ethanone
Purity Retention time .04 min 93% Method 1
1- {4- [1- (4 -Trifluoromethyl-phenyl) -imidazo [1, 5-a] pyridin-3 -yl -piperidin-1-yl} -ethanone
Purity Retention time 4.80 min 94% Method 1
1- [4- (l-Benzo [1,3] dioxol-5-yl-7-chloro-imidazo [1, 5-a] pyridin-3-yl) -piperidin-1-yl] -ethanone
Purity Retention t me 4.55 min 95% Method 1
1- (4-Fluoro-phenyl) -3- (1-methanesulfonyl-piperidin-4-yl) -imidazo [1, 5-a] pyridine
Purity Retention time 4.68 min 91% Method 1
3- (l-Methanesulfonyl-piperidin-4-yl) -1- (2-methoxy-phenyl) -imidazo [1, 5-a] pyridine
Purity Retention time 4.42 min Method 1
3- (l-Methanesulfonyl-piperidin-4-yl) -1-m-tolyl -imidazo [1, 5-a] pyridine
Purity Retention time 4.85 min 93% Method 1
-Chloro-3- (1-methanesulfonyl-piperidin-4-yl) -1- (2-methoxy-phenyl) -imidazo [1, 5-a] pyridine
Purity Retention time 4.90 min 96% Method 1