A recent publication from AstraZeneca provides a really interesting overview of the approach that they took to optimise the solubility of a series of GPR119 agonists. The initial lead compound 2 was only poorly soluble but, by obtaining small molecule x-ray structures of this and subsequent compounds, the AZ team were able to identify H-bonding networks within the crystal lattice and to target molecular features with the potential to disrupt these and other intermolecular interactions, thus lowering the melting point and increasing aqueous solubility. The paper describes this process in some detail and also highlights other key strategies that were used to progress from compound 2 through to 42, a clinical candidate for treating type II diabetes. The paper also serves to illustrate and build upon the concepts described in the review that we blogged previously.
The successful development of inhibitors of protein-protein interactions remains a formidable challenge for medicinal chemists. An excellent review highlights some successes in this field and ascribes the low tractability of these targets to:
- The large contact surfaces between proteins (~1,500–3,000 Å2).
- The flat and relatively featureless nature of these surfaces as compared to the active-sites on more traditional targets.
- The lack of a natural small molecule ligand to use as a lead molecule.
However, as the authors go on to discuss, it is often found that a small number of amino acid residues contribute disproportionately to the binding interaction between proteins. Targeting these so-called hot-spots represents an approach to tackling these targets. The review provides a nice analysis of six examples of the successful discovery of inhibitors of protein-protein interactions.
Recently, scientists at the Universities of Newcastle and Oxford have published the optimisation of a series of isoindolinone inhibitors of the interaction between Murine Double Minute 2 (MDM2) and p53. The tumor suppressor protein p53 acts as a signalling node and is involved in the response of cells to a range of stresses. Inactivation of p53 is often involved in the development and subsequent progression of cancer. Inhibitors of the MDM2-p53 interaction have been proposed as anti cancer agents. The same team has previously reported isoindolinone 49 that has an IC50 for the MDM2-p53 interaction of 15.9 μM. This paper outlines the optimisation of this compound to generate 74a with an IC50 of 0.17 μM. Ideally the optimisation would have been supported by X-ray crystallography, however the team were unable to obtain co-crystals of the series bound to their target, the MDM2 protein. Instead a combination of NMR studies and docking were used to predict binding modes for the inhibitors.
Through the preparation and testing of analogues of 49 it was established that increases in potency were achievable through the introduction of a para nitro substituent on the N-benzyl group and by steric restriction of the 3-carbon chain through introduction of a cyclopropyl group. Despite considerable efforts to find a suitable replacement for the nitro-group the team were unable to find a similarly active replacement. Separation and testing of the enantiomers of 74 showed that the (R) form, 74a, is primarily responsible for the MDM2-p53 inhibition.
The authors go on to demonstrate cellular activity for 74a in a range of assays. This paper provides nice evidence of the inroads that medicinal chemists are making into the challenging protein-protein interaction target class.
A recently published letter from scientists at Boehringer Ingelheim nicely summarizes recent advances in our understanding of G protein-coupled receptor (GPCR) structure and function. X-ray structures of the inactive forms of bovine rhodopsin (2000), β2 adrenergic receptor (2007 – with antibody and as a T4-lysozyme fusion), A2a adenosine receptor (2008), CXCR4 chemokine receptor (2010), and dopamine D3 receptor (2010) have all been published and despite low sequence homology all of these were shown to have transmembrane (TM) regions with high levels of 3D structural similarity. The main structural differences in proximity to the ligand binding sites were noted in extracellular loop regions and modeling these motifs (as well as the ligand binding mode) has proved to be challenging. With no reliable template available for homology modeling of the active states, the recent publication of the crystal structure of long acting agonist, BI-167107 (in yellow below), to β2 in what appears to be an activated form, is of particular note. Surprisingly, the ligand binding site in this structure is very similar to that modeled for a related agonist bound to an inactive form (in green below).
The authors postulate the following on the basis of these findings:
- Inactive structures of GPCRs are sufficiently good templates for activated state models (also see recent structures of β1 and β2 with agonists bound in the inactive state).
- The molecular switching between inactive and active receptor forms appears to be controlled by significant residue movements (and disruption of a hydrophobic network) one turn beyond the so-called “toggle switch” (W286 in β2). This information could enable better modeling of ligand-induced activation.
- The high similarity of binding sites in inactive and active receptors may make in silico discrimination between agonists and antagonists extremely difficult, if not impossible.
However, they emphasize the importance of obtaining additional structural data for activated GPCR complexes in order to establish the generality of these early observations and to elucidate the best methods for incorporating these findings into computational approaches to predicting ligand activity. It’ll be interesting to see how this area develops as additional structures become available.
Posted in Computational Methods, GPCR ligands
Tagged A2A adenosine receptor, b2 adrenergic receptor, Boehringer Ingelheim, computational method, CXCR4, dopamine D3 receptor, gpcr, rhodopsin, Structure Based Design, toggle switch, X-ray data
Following on from his earlier papers (e.g. ADMET rules of thumb for candidate drug design), Gleeson’s most recent publication in Nature Reviews|Drug Discovery details a now familiar tale of physicochemical woe associated with the failure of many medicinal chemistry programmes to focus adequately on properties other than target affinity. Once again arguing that an over-reliance on targeting high potency in order to minimize the clinical dose and risk of toxicity related attrition (see now classic papers & citing works by Leeson and Hann) has continually seduced medicinal chemists away from ‘drug-like space’. These are points which in themselves are worthy of further emphasis, but of particular interest in this case is the origin of the data in the ChEMBL database, a publicly accessible database of targets and drugs compiled by the European Bioinformatics Institute (EBI). Whilst some of the available data are incomplete (and the authors acknowledge the limitations in their analyses) this database is an important and often under-utilized source of information and is worthy of wider attention. In contrast to many of the physicochemical analyses published to date, all the ChemBL source information is freely accessible for others to validate and/or challenge. The database contains over half a million compounds (stored as 2D structures), with accompanying in vitro biological data and calculated properties.
For this analysis, the authors calculated an ADMET score (i.e. the deviation from oral drug space as defined by AlogP and molecular mass) to characterize the data set. The plot below shows 1791 oral drugs colour-coded according to their ADMET score (on the left), and then (on the right) the same drugs compared with the scores for the total content of the ChEMBL database (approximately 200k compounds). A greater deviation from oral drug space is observed in the latter case (14% of drugs have ADMET scores >2 compared with 39% of ChEMBL molecules).
Further detailed graphics and analyses are also presented to arrive at the following conclusions:
- Average oral drug potency is approx 50 nM (Another clear observation was that 8% of oral drugs have both mol mass > 400 and AlogP > 4, compared to 30% of all ChEMBL molecules and 41% of ChEMBL molecules with nanomolar potency).
- The majority of oral drugs have off-target pharmacological activities (This analysis was clearly complicated by any intentional poly-pharmacology). The graphic below shows, for 392 oral drugs, N = number of off-target hits with reported potencies ≤ 1 µM (i.e. only 29% in the N=0 segment are totally selective) :
- There was no clear relationship between in vitro potency and therapeutic dose (which is perhaps unsurprising given the numerous additional factors involved).
Whilst the points made in the paper mainly serve to reinforce the conclusions of earlier publications, they nonetheless highlight the importance, and usefulness, of open-source information sources and the prospect of their more widespread utility in future.
Neurotherapeutic agents generally illicit their effects by acting on receptors in the central nervous system (CNS) and a short review in Expert Opin. Drug Discov. highlights the current best practices and recent developments in targeting molecules to the brain. The key areas covered in this concise overview are:
- Design strategies for optimizing unbound brain concentration in the CNS. Recent publications (e.g. Wager, et.al., Defining Desirable Central Nervous System Drug Space…; and the earlier Hitchcock, et.al., Structure−Brain Exposure Relationships) have highlighted the key physicochemical property space within which CNS drugs are located and to which drug discovery efforts ought to ostensibly be aligned in order to achieve the required balance of efficacy and safety. However, the authors stress that optimizing unbound brain and plasma concentration ratios (or brain availability) by adopting a more holistic, multi-parameter approach is crucial to success (and they refer back to another of their own recent publications in this vein). Structural elements associated with blood-brain barrier (BBB) penetration and computational approaches to predicting BBB permeability are also discussed briefly.
Physicochemical property space - CNS drugs and candidates (click to enlarge)
- Screening strategies to optimise brain availability. This section looks at the role of transporters (e.g. P-gp) in controlling molecular access to the CNS and at in-vitro and in-vivo screening approaches to addressing this issue in drug discovery. The recent publication of the mouse P-gp x-ray crystal structure (PDB3G60) and it’s implications are also discussed.
- Brain Delivery Approaches. Molecules with properties that fall outside the property space of known CNS drugs (e.g. antibodies, siRNA, peptides) offer novel approaches to the treatment of CNS disease and numerous innovative approaches to the delivery of such agents are under investigation. The final section summarizes progress in this area.
An excellent J.Med.Chem. perspective titled ‘Synopsis of Some Recent Tactical Applications of Bioisosteres in Drug Design‘ has just published (The article is based on a short course presented at an ACS Prospectives conference in 2009). The author gives a brief introduction to the concept of biosisosterism (classical and non-classical) but concentrates on pulling together numerous recent examples which together illustrate the use of bioisosteres to address a diverse range of issues that are commonly encountered in the process of drug discovery. Whilst he expressly states the intention to avoid compiling a comprehensive catalogue of bioisosteres the paper does, nonetheless, cover a wide range of isosteres and it includes a lot of data and primary references that will serve as key resource material for medicinal chemists. A really nice paper and highly recommended reading material.
Click here to see a list of the topics covered in this review
Sulfonyl pyridines have utility both as constituents of bioactive molecules and as synthetic intermediates. Typical methods for their preparation have suffered from the use of odiferous thiols, capricious oxidation steps, poor atom economy, and production of significant amounts of hazardous waste. Scientists in process research at Merck recently published a nice, straightforward, and one-pot approach which addresses all of these issues.Their method involves direct displacement of chloropyridines (they do also demonstrate that the methodology applies equally to other halides and triflates) with sulfinic acid salts in the presence of tetrabutylammonium chloride (TBACl). [The TBACl is postulated to enhance the solubility of the sulfinic acid salt in the solvent used (Dimethylacetamide, DMAc)]. The method works equally well for electron-deficient, electron-neutral, and electron-rich chloropyridines and is operationally straightforward (See examples above – an equivalent of HCl is required to protonate, and hence activate, the pyridine in the case of the latter two classes of substrate). The products are isolated in high yield simply by quenching with water and filtration of the resulting slurry.