Exploration of piperidine 3D fragment chemical space: synthesis and 3D shape analysis of fragments derived from 20 regio- and diastereoisomers of methyl substituted pipecolinates

Fragment-based drug discovery is now widely adopted for lead generation in the pharmaceutical industry. However, fragment screening collections are often predominantly populated with flat, 2D molecules. Herein, we report the synthesis of piperidine-based 3D fragment building blocks – 20 regio- and diastereoisomers of methyl substituted pipecolinates using simple and general synthetic methods. cis-Piperidines, accessed through a pyridine hydrogenation were transformed into their trans-diastereoisomers using conformational control and unified reaction conditions. Additionally, diastereoselective lithiation/trapping was utilised to access trans-piperidines. Analysis of a virtual library of fragments derived from the 20 cis- and trans-disubstituted piperidines showed that it consisted of 3D molecules with suitable molecular properties to be used in fragment-based drug discovery programs.


Methyl (2R*,6R*)-1-benzyl-6-methylpiperidine-2-carboxylate cis-5d
BnBr (0.23 mL, 1.91 mmol, 3.0 eq.) was added dropwise to a stirred solution of a >95:5 mixture of piperidines cis-4d and trans-4d (100 mg, 0.64 mmol, 1.0 eq.) in saturated Na2CO3(aq) (2 mL) and CH2Cl2 (2 mL) at rt under Ar. The resulting solution was stirred at rt for 16 h. The two layers were separated, and the aqueous layer was extracted with CH2Cl2 (3 × 10 mL). The combined organics were dried (MgSO4) and evaporated under reduced pressure to give the crude product as a colourless oil. The stereochemistry of cis-5d was established through analysis of the coupling constants from the 1 H NMR spectrum. Proton at C-2 has 3 J HH coupling constant of 10.5 Hz and the proton at the C-6 has 3 J HH coupling constant of 13.0 Hz which suggests that the protons at the C-2 and C-6 position are axial and therefore confirms the cis relative stereochemistry.

benzyl-5-methylpiperidine-2-carboxylate trans-5e
PtO2 (83 mg, 0.37 mmol, 10 mol%) was added to a stirred solution of ester 3e (552 mg, 3.65 mmol, 1.0 eq.) in glacial acetic acid (10 mL). The reaction flask evacuated under reduced pressure and back filled with Ar three times. After a final evacuation, a balloon of hydrogen was added, and the reaction mixture was stirred vigorously at rt for 16 h. The mixture was filtered through Celite and washed with MeOH (30 mL), and the filtrate was evaporated under reduced pressure to give a 75:25 mixture of crude diastereomeric piperidines 4e·AcOH (1.14 g). Crude 4e·AcOH was dissolved in CH2Cl2 (10 mL) and sat. Na2CO3(aq.) (10 mL) and benzyl bromide (478 µL, 4.02 mmol, 1.1 eq.) were added. The resulting mixture was stirred at rt for 16 h. Then, water (30 mL) and CH2Cl2 (30 mL) were added, and the two layers were separated. The aqueous layer was extracted with CH2Cl2 (3 × 20 mL). The

Lab Book -JDF_B_170 and JDF_B_174
The stereochemistry of trans-5e was established through analysis of the coupling constants from the 1 H NMR spectrum. Proton at C-2 has 3 J HH coupling constants of 11.0 and 3.0 Hz and the proton at the C-5 has 3 J HH coupling constant of 11.0 and 3.0 Hz which suggests that the protons at the C-2 and C-5 position are axial and therefore confirms the trans relative stereochemistry.
Supporting Information S16
The aqueous layer was extracted with CH2Cl2 (3 × 10 mL). The combined organic layers were dried The solution was cooled to -78 °C and a solution of ester cis-5g (50 mg, 0.19 mmol, 1.0 eq.) in THF (2 mL) was added dropwise. The resulting solution was stirred at -78 °C for 2 h, then sat. NH4Cl(aq) (5 mL) was added, and the resulting mixture warmed to rt. Water (5 mL) and EtOAc (10 mL) were added Supporting Information S20 and the two layers were separated. The aqueous layer was extracted with EtOAc (3 × 10 mL). The combined organic layers were dried (MgSO4), filtered and evaporated under reduced pressure to give a 80:20 mixture of trans-5g and cis-5g. Purification by flash column chromatography on silica with 9:1 hexane-EtOAc as eluent gave piperidine trans-5g (33 mg, 65%) as a clear oil, RF ( Lab Book -JDF_B_157
Lab Book -PJ-05-98. 3-Dimensional structures of pyridines 3 were generated using RDKIT v4.5 in KNIME v4.4.1. A maximum of 50 conformers were generated for each molecule and the geometry of each was optimised using MMFF94 force field with 1000 iterations. Prior to calculation, salts were stripped and explicit hydrogens added. The lowest energy conformer of each molecule was selected and the three Principal Moments of Inertia calculated using Vernalis PMI KNIME nodes.
Principal moments of inertia (PMI) about the principal axes of a molecule were calculated according to the following rules: Supporting Information S37 1. The moments of inertia are computed for a series of straight lines through the centre of mass.
2. Distances are established along each line proportional to the reciprocal of the square root of I on either side of the centre of mass. The locus of these distances forms an ellipsoidal surface.
The principal moments are associated with the principal axes of the ellipsoid.

Virtual Library Enumeration and Lead-Likeness Analysis
To assess the suitability of our piperidines for the generation of lead-like compounds we used the open access tool LLAMA. 14,15 Using our deprotected piperidines (as amino acids) as scaffolds, LLAMA computationally decorated (once or twice) the amine and acid functionalities and analysed the resulting virtual molecules for their lead-likeness (for leading examples of lead-oriented synthesis see [16][17][18][19] ).
LLAMA generated 1599 virtual compounds from our 20 deprotected piperidines. The default set of capping groups was used, and of the standard decoration reactions, "Secondary amide alkylation" and "Secondary amide arylation" were disabled to prevent two diversification events occurring at the same diversification point of the scaffolds.
Of the 1599 virual compounds, 78% fell within lead-like space (defined as molecular weight between 200 and 350, and AlogP between -1 and 3) 14 ( Figure S2). For comparison, only 23% of the ZINC database of commercially available screening compounds fall within lead-like space. 14,17 LLAMA also generates a lead-likeness penalty (LLP) score for each molecule (the lower the better), considering the number of aromatic rings and the presence of unwanted structural features as well as molecular weight and AlogP. Our virtual library had a mean LLP of 1.02 (cf. 4.17 for ZINC) indicating that compounds derived from di-substituted piperidines 5 would be highly lead-like. Furthermore, analysis of the degree of saturation of the virtual library showed that it had a mean Fsp 3 of 0.62, whereas the mean value for the Zinc library is only 0.33.