Multi-Parameter Optimisation Chemical Reaction By Dr Giovanna There is often a divide between computational results and synthetic Tedesco and accessibility in the identification process of alternative compounds. Katriona Scoffin at Cresset However, there is now a way to produce results more quickly and precisely, and to ultimately accelerate the research process Bioisostere replacement is a popular minimised, while retaining or identify ideas for new dipeptidyl computational method for lead improving activity and potency. peptidase IV (DPP-IV) inhibitors, discovery. Accurate and fast scoring Switching to compounds that are using known inhibitors as starting functions make it possible to identify biologically similar, but structurally points (see Figure 1). DPP-IV promising alternative compounds different, is an efficient way to inhibitors have demonstrated that are likely to preserve activity. explore chemical space with a high that they are important agents in However, if there is a significant likelihood of retaining activity. treating type 2 diabetes. disconnect between computational results and synthetic accessibility, The interaction of a ligand with Alogliptin (A), omarigliptin (B) the suggested compounds will only a protein depends on three main and the experimental fluoro ever be of theoretical interest. This considerations: the reciprocity of olefin compound (C, PDB: 3C45), article explains how the intelligent electrostatic patterns, the matching represent some of the most use of reagent databases from of 3D shapes and the matching of ligand-efficient examples among available commercial sources can hydrophobicity patterns. To make known DPP-IV inhibitors. Two rank computational outcomes a realistic and useful computational experiments were performed according to synthetic tractability. assessment of biological similarity, using alogliptin and omarigliptin New ideas can be filtered to focus on these three factors must be encoded in in a simple scaffold hopping results that can be synthesised from such a way that they can be compared exercise. A final chemotype reagents, which are available to be over hundreds or thousands of merging experiment was also ordered online and delivered to the fragments and compounds. carried out using a truncated lab within days. omarigliptin, with fluoro olefin Field points (see Figure 1) are as a second template, to find Scaffold Hopping a computationally viable and molecules bridging the two series. chemically significant way of Bioisostere replacement – also encoding the biological effects This workflow is shown in Figure known as scaffold hopping – is of chemical changes. They 1, along with example outcomes a useful technology for lead condense electrostatics, shape that depict the diverse range of detection and optimisation. and hydrophobicity in such a way output suggestions provided Projects often start with promising that it becomes possible to scan for new chemistry. The results chemistry, but encounter large databases of compounds in a included examples which already challenges such as toxicity or reasonable amount of time in order have precedents in patents and patent issues. The path to a drug to usefully assess their biological literature, serving to validate can lead to many similarity, as demonstrated in the the method (1). Keywords dead ends as following case study. different scaffolds Fragment Reconnection Reagent databases and R-groups are Case Study 1: Finding modified, replaced or Bioisosteres of DPP-IV Bioisosteric replacement using Synthetic tractability discarded. The multi- Inhibitors fragment- and reagent-specific Field points parameter puzzle databases can be readily applied to Fragment growing requires unwanted A leading bioisostere replacement the popular discovery approaches side effects to be programme was employed to of fragment growing and linking. 16 Innovations in Pharmaceutical Technology Issue 57 iptonline.com Figure 1: The starting point is one or more Input: 3D structure Cresset Field points Output: rapid, feasible designs Expt. electrostatics Using bioisosteric fragments that are recognised as Alogliptin (A) replacements responsible for activity. Perhaps A to find new DPP-IV inhibitors. they have been isolated from other Hop Cyan represents projects, or it is known that they negative electrostatic field link with important elements of the Omarigliptin (B) and field points; B red represents protein binding site. The challenge positive field is to grow a compound from one Hop points; yellow represents steric fragment, or to identify linking field points; chemistry for two or more fragments. Fluoro olefin (C) and orange B and C represents Merge hydrophobic Uracil DNA glycosylase (UDG) is a field points potentially interesting target for both cancer and anti-viral therapies (2). Recent efforts to produce Figure 2: Active fragments synthetic inhibitors of this protein Accessible Chemistry originally relied on an active fragment tethered by a bis-oxime linker tethering approach, yielding In silico-generated ideas for R-group (disconnected for interesting bis-oxime linked active replacements become far more this experiment), shown ligands. This example describes practical when they are tied to embedded in UDG. In the an alternative method using available reagents. Chemistry being modelling scaffold hopping software for the chemistry, nothing can guarantee the origins of an R-group. For software, the protein reconnection of distant fragments. that a given compound can be example, an R-group could come is effectively readily synthesised – however, from a reagent that has undergone employed as an excluded volume To mimic a fragment linking narrowing the searches to accessible multiple steps before it ends up experiment with the software, the chemistry is one way to ensure that as an R-group. This method makes bis-oxime linker was excised from the bioisosteric replacements have it possible to encode chemistry an active ligand (PDB: 3FCI) (see the highest likelihood of being space, so that the choices being Figure 2). The two fragment synthesised in real life. made are realistic. atoms to be joined were selected and suitable fragments with Many attempts have been made to Focusing searches on R-group appropriate distance and encode all possible transformations libraries that are classified by geometry, which were capable of and reagents in order to score their specific chemistry provides a re-joining them, were inserted. synthetic accessibility; however, systematic way to rapidly exploit Fragments were sourced from the results have proven mixed, with a particular chemical reaction. databases such as ZINC and several exceptions which render ChEMBL. The resulting molecules decision-making difficult. An Case Study 2: Identifying were automatically constructed alternative is to come up with a set Optimisation Routes in situ, minimised and then scored of interpretable rules for chemistry against the parent compound space – a challenge that also The reagent databases (5) using a field-based 3D similarity proves to be quite hard. A more available with Spark (3) were used metric (3). powerful approach is to encode to identify alternative decorations Rank Rank Rank Figure 3: The example results (see Figure 3) (BIF %) Structure (BIF %) Structure (BIF %) Structure Example outputs from a show the diverse range of the fragment linking 3 16 32 experiment using output suggestions for new (38) (37) (34) scaffold hopping linking chemistry (4). Significantly, each of the new fragments not 60 76 174 only satisfies the geometry (34) (33) (29) and length requirements for their reconnection, but also has 196 203 860 features consistent with important (28) (28) (22) interactions within the protein. Innovations in Pharmaceutical Technology Issue 57 17 iptonline.com Figure 4: for a series of triazolopyridazine X-ray crystal structure of and 8-fluorotriazolopyridine compound C in selective inhibitors of the c-MET the active site of c-MET (PDB Arg 1208 kinase, developed by Amgen 3CD8), which as a potential treatment for elucidates four key interactions cancer (6,7). The use of databases (6) Asp 1222 derived from available reagents ensured that the results could be tethered to molecules that were readily synthetically accessible. Tyr 1230 The published X-ray crystal structure of an early lead compound D (6) bound to c-MET (PDB 3CD8) shows that this molecule adopts a ‘U-shaped’ binding mode into the active site. Four crucial interactions can be Met 1160 identified with key residues, which are highlighted in Figure 4. Based on this experimental information, researchers at Amgen Figure 5: R-groups E, 4nM F, 2nM G, 1nM associated with S Rank 1, S Rank 3, Rank 13, known active BIF %: 87 BIF %: 79 BIF %: 69 inhibitors of c-MET found by Spark S H, 3nM (analogue) I, 12nM S J, 11nM Rank 14, Rank 25, Rank 28, N BIF %: 69 BIF %: 66 N BIF %: 65 S N K, 4nM L, 29nM N M, 22nM N Rank 43, O Rank 45, Rank 149, S BIF %: 62 BIF %: 61 N BIF %: 48 N, 9nM O P Rank 448, N BIF %: 29 N O N O Q R S N N O N N N 18 Innovations in Pharmaceutical Technology Issue 57 iptonline.com speculated that modifications derivative as a starter molecule choice of fragments to explore of the C-6 phenyl group on on an expanded set of reagent in the successive rounds of the triazolopyridazine core databases (boronic acids and lead optimisation. would modulate the π-stacking aromatic halides), provided some interaction with Tyr1230, allowing interesting suggestions about References for increased potency. They alternative small heterocycles 1. Slater M, Scaffold hopping into new therefore started a chemical which could have been tried DPP-IV protease inhibitors, 2015. Visit: exploration based on the synthesis (O, P, Q, R, S). www.cresset-group.com/wp-content/ of aryl and heteroaromatic uploads/2015/05/Scaffold-hopping- analogues (6). The same strategy Available Synthetic Chemistry into-new-DPP-IV-protease-inhibitors_ was applied to the exploration Poster_APPROVED.pdf of 8-fluorotriazolopyridine It is possible to link the results of 2. Krosky, Nucleic Acids Research compounds (7). reagent searches to the eMolecules 34(20): pp5,872-5,879, 2006 site to enable a check of real time 3.