The Synthesis and Absolute Configuration of Enantiomeric Pure (R)- and (S)-3-(piperidin-3-yl)-1H-Indole Derivatives

This article describes the synthesis of new chiral 3-(piperidin-3-yl)-1H-indole derivatives (R)-10a-c and (S)-11a-c from the corresponding diastereomers: (3R, 2R) and (3S, 2R)-2-[3-(1H-indol-3-yl)-1-piperidyl]-2-phenyl-acetamides (3R, 2R)-4a, (3R, 2R)-6b, (3R, 2R)-8c and (3S, 2R)-5a, (3S, 2R)-7b, (3S, 2R)-9c. Diastereomers were obtained by N-alkylation of derivatives of racemic 3-(piperidin-3-yl)-1H-indoles 1a-c using (S)-2-(4-toluenesulfonyloxy)-phenylacetic amide (S)–II. The same method was applied to obtain (3R, 2S)-methyl-2-[3-(1H-indole-3-yl)-1-piperidyl]-2-phenylacetate (3R, 2S)-2a and (3S, 2S)-methyl-2-[3-(1H-indole-3-yl)-1-piperidyl]-2-phenylacetate (3S, 2S)-3a diastereomers by treating amine 1a with (R)-2-(4-toluenesulfonyloxy)-phenylacetic acid methylester (R)-I. Systematic studies via single crystal X-ray crystallography were used to determine the molecular structure of the racemates 1a-c and the absolute configuration of the enantiomers. The solid racemates 1b and 1c were “true racemates” crystallizing in a centrosymmetric space group, while 1a formed a racemic conglomerate of homoenantiomeric crystals. The absolute configuration was determined for the enantiomeric pairs (R)-10a/(S)-11a, (R)-10b/(S)-11b, and (R)-12c/(S)-13c, as well as for (3S,2S)-3a. Spectra of 1H, 13CNMR, HPLC, and HRMS for diastereomers and enantiomers were consistent with the determined structures.


Introduction
Analogs of 5-hydroxytryptamine and homotryptamine are a subject of research for new drugs that affect the central nervous system through the serotoninergic mechanism and that show multidirectional pharmacological activity [1][2][3][4]. Of particular interest are derivatives with a conformationally limited aminoethyl residue at the 3 position of the indole ring that also exhibit chiral centers in their structures, e.g., I-V, VII ( Figure 1). The conformational constraints of the side chain have been shown to be an effective tool to optimize both the activity and selectivity of numerous SERT serotonin transporter protein inhibitor compounds and the 5-HT 1A receptor [5,6].
The search for new and more effective drugs for the pharmacotherapy of migraine in the form of sumatriptan analogs (agonists of 5-HT 1A receptor) has yielded an analog with reduced conformational aminoethyl portion and an R-configuration, which has exhibited analgesic activity 10 4 times greater than sumatriptan ( Figure 2) [7].
An additional advantage of derivatives with a conformationally constrained aminoethyl constituent, in addition to their greater biological activity, is their higher stability in the first-pass phase of metabolic biotransformation processes [7,8]. Recently, there has been a significant increase in interest in new ligands with high binding to the 5-HT 6 receptor, due  An additional advantage of derivatives with a conformationally constrained aminoethyl constituent, in addition to their greater biological activity, is their higher stability in the first-pass phase of metabolic biotransformation processes [7,8]. Recently, there has been a significant increase in interest in new ligands with high binding to the 5-HT6 receptor, due to the role of this receptor in patho-mechanisms of depression, schizophrenia, Alzheimer's disease, and Parkinson's disease [9]. There are particularly high expectations for these molecules due to their influence on improving cognitive processes and memory [10].
A number of 5-hydroxytryptamine derivatives with constrained conformation of Narylsulfonyl constituent derivatives that show very high affinity to this receptor have been described (Figure 3) [11][12][13][14][15][16]. The search for new and more effective drugs for the pharmacotherapy of migraine in the form of sumatriptan analogs (agonists of 5-HT1A receptor) has yielded an analog with reduced conformational aminoethyl portion and an R-configuration, which has exhibited analgesic activity 10 4 times greater than sumatriptan ( Figure 2) [7]. An additional advantage of derivatives with a conformationally constrained aminoethyl constituent, in addition to their greater biological activity, is their higher stability in the first-pass phase of metabolic biotransformation processes [7,8]. Recently, there has been a significant increase in interest in new ligands with high binding to the 5-HT6 receptor, due to the role of this receptor in patho-mechanisms of depression, schizophrenia, Alzheimer's disease, and Parkinson's disease [9]. There are particularly high expectations for these molecules due to their influence on improving cognitive processes and memory [10].
The aim of this study was to synthesize and determine the absolute configuration for a number of chiral derivatives of (R)-3-(piperidin-3-yl)-1H-indole (R)-10a-c and (S)-3-(piperidin-3-yl)-1H-indole (S)-11a-c. Diastereomers used as substrates for their synthesis were obtained by the N-alkylation of racemic derivatives of 3-(piperidin-3-yl)-1H-indole 1a-c with the aid of a chiral reagent, (S)-2-(4-toluenesulfonyloxy)-phenylacetic amide S-II. The obtained mixture of diastereomers was chromatographically separated into analytically pure compounds: The hydrogenolysis of the diastereomers obtained above led to the pure enantiomers Finally, the absolute configuration was determined for representative compounds. This was preceded by a structural analysis of the solid-phase racemates 1a-c. Structural X-ray studies have shown that racemate 1b (Figure 4), as previously analyzed for 1c, are racemic compounds ("true racemates") crystallizing in a centrosymmetric space group [17,18].  These results are in contrast to racemate 1a, which was a racemic conglomerate; i.e., as a result of crystallization from methanol, the enantiomers spontaneously separated and produced a phase of a 1:1 mixture of homoenantiomeric crystals. Hence, compound 1a is a mixture of the crystalline compounds (R)-10a and (S)-11a. This was confirmed during measurements performed for a dozen or so crystals from mixture 1a. The absolute configuration was also determined for the pure enantiomers (R)-10a and (S)-11a obtained by applying the procedures described above ( Figure 5).  [17,18] and view of molecular structure of enantiomeric fluoro-derivatives.
These results are in contrast to racemate 1a, which was a racemic conglomerate; i.e., as a result of crystallization from methanol, the enantiomers spontaneously separated and produced a phase of a 1:1 mixture of homoenantiomeric crystals. Hence, compound 1a is a mixture of the crystalline compounds (R)-10a and (S)-11a. This was confirmed during measurements performed for a dozen or so crystals from mixture 1a. The absolute configuration was also determined for the pure enantiomers (R)-10a and (S)-11a obtained by applying the procedures described above ( Figure 5).  [17,18] and view of molecular structure of enantiomeric fluoro-derivatives.
These results are in contrast to racemate 1a, which was a racemic conglomerate; i.e., as a result of crystallization from methanol, the enantiomers spontaneously separated and produced a phase of a 1:1 mixture of homoenantiomeric crystals. Hence, compound 1a is a mixture of the crystalline compounds (R)-10a and (S)-11a. This was confirmed during measurements performed for a dozen or so crystals from mixture 1a. The absolute configuration was also determined for the pure enantiomers (R)-10a and (S)-11a obtained by applying the procedures described above ( Figure 5).  The obtained (R)-10a-c and (S)-11a-c compounds were chiral substrates for the synthesis of ligands with double-binding to the 5-HT 1A receptor and the SERT transporter protein as part of the search for new SSRI+ antidepressants within our research.

Synthesis
The synthesis of title compounds in the form of pure enantiomers ((R)-3-  Substrates for the synthesis were racemic 3-(piperidin-3-yl)-1H-indole 1a, 5-fluoro-3-(piperidin-3-yl)-1H-indole 1b and 5-methoxy-3-(piperidin-3-yl)-1H-indole 1c, which were obtained according to the formula provided by Gharagozloo [19] and the modifications introduced by prior work [17,18]. The chiral (R)-2-(4-toluenesulfonyloxy)-phenylacetic acid methylester (R)-I, which is essential as a reagent for the reaction, was obtained according to the formulation described by us earlier [20]. The obtained amine 1a was subjected to an N-alkylation reaction with a chiral (R)-I reagent to give a mixture of diastereomers: (3R,2S)-methyl-2-  Substrates for the synthesis were racemic 3-(piperidin-3-yl)-1H-indole 1a, 5-fluoro-3-(piperidin-3-yl)-1H-indole 1b and 5-methoxy-3-(piperidin-3-yl)-1H-indole 1c, which were obtained according to the formula provided by Gharagozloo [19] and the modifications introduced by prior work [17,18]. The chiral (R)-2-(4-toluenesulfonyloxy)-phenylacetic acid methylester (R)-I, which is essential as a reagent for the reaction, was obtained according to the formulation described by us earlier [20]. The obtained amine 1a was subjected to an N-alkylation reaction with a chiral (R)-I reagent to give a mixture of diastereomers: (3R,2S)methyl-2- To obtain a mixture of diastereomers with higher yields and stability, and which would be easier to separate, an alternative method was applied, where the chiral reagent, (S)-2-(4-toluenesulfonyloxy)-phenylacetic amide (S)-II, was used in the N-alkylation reaction of amines 1a-c; this process being described elsewhere in our paper. The (S)-II compound has been mentioned in prior works, but the respective authors did not provide important physicochemical data, such as melting point and optical rotation [21][22][23]. The reaction of N-alkylation of amines 1a-c with (S)-II led to a mixture of diastereomers in high yield, and the value of dr for these compounds was determined by HPLC method; results are given in Table 1 (Table 1).  For all entries, the reaction was performed by heating the mixture in 45 • C in acetonitrile; a isolated yield; b estimated by means of HPLC.
The chiral amines of the series (R)-10a-c and (S)-11a-c were obtained with good yields and their structure and purity were confirmed by 1 H i 13 C NMR, HRMS, HPLC, and X-ray structural analysis for (R)-10a, (R)-10b, (S)-11a, and (S)-11b.
After the isolation of amine (R)-10c and (S)-11c via concentration of the methanol solution, hydrogenolysis and acidification with methanolic HCl resulted in new compounds, in addition to amines (R)-10c and (S)-11c, that were observed in the TLC test. These compounds were isolated, and their structures were proposed via 1 H, 13 C NMR, HRMS, and ER using HPLC (Scheme 3). X-ray crystallography showed that tetracyclic structures (R)-12c and (S)-13c were formed as a result of intramolecular cyclocondensation reactions of starting compounds. Their absolute structure was then determined (Section 3).
TLC tests related to concentration of solution before addition of HCl/MeOH did not show creation of those new structures, nor did they when a weak acid, e.g., tartaric acid, had been used for acidification. Optical rotation measurements for these compounds showed a reverse polarity rotation with respect to the starting amines (R)-10c and (S)-11c. In the literature, one can find a description of obtaining 11-substituted teracycles of this type, which were obtained by the Pictet-Spengler reaction, where racemic amine 1a condensed with selected aldehydes was a substrate [24,25]. TLC tests related to concentration of solution before addition of HCl/MeOH did not show creation of those new structures, nor did they when a weak acid, e.g., tartaric acid, had been used for acidification. Optical rotation measurements for these compounds showed a reverse polarity rotation with respect to the starting amines (R)-10c and (S)-11c.
In the literature, one can find a description of obtaining 11-substituted teracycles of this type, which were obtained by the Pictet-Spengler reaction, where racemic amine 1a condensed with selected aldehydes was a substrate [24,25].
For example, for compounds (3R,2R)-4a and (3S,2R)-5a, chemical shifts were obtained as follows: 13  In turn, the proton and carbon spectra for the (R)-12c and (S)-13c enantiomers were the same and confirmed their structure.

General Remarks
Melting points were determined on an Electrothermal iA9200 apparatus with open capillary tubes and are uncorrected. The hydrogenolysis reactions were carried out in a Roth autoclave type 50 S. TLC was performed on 0. 25  The NMR spectra were recorded on Varian Unity Plus 500 MHz using CDCl 3 , D 2 O or CD 3 OD as solvents. NMR data are reported as follows: chemical shift (δ) (parts per million, ppm relative to tetramethylsilane used as the internal references), multiplicity; s (singlet), d (doublet), t (triplet), q (quartet), and br (broad); coupling constants (J) are given in Hertz (Hz). All NMR spectra can be found in Supplementary Materials. The HRMS spectra were obtained on a Thermo Q-Exactive mass spectrometer. The optical rotation was performed on a Perkin-Elmer 241 polarimeter at 20 • C. (R)-(-) methyl mandelate and (S)-(+)-mandelate amides were high-grade commercial products purchased from Aldrich and used without further purification.

X-ray Crystallography
The single crystal X-ray diffraction data were collected at either 293 K or 120 K on a SuperNova diffractometer with CuKα radiation. Some crystals disintegrated on cooling; therefore, their structural analysis was based on measurements at room temperature. The exception was crystal 10a, which underwent a phase transition to give a second polymorph at low temperature. Cell refinement and data collection as well as data reduction and analysis were performed with the CrysAlisPro [26]. Structures were solved with the use of SHELXS program and refined with the SHELXL−2018/3 [27]. All non-hydrogen atoms were refined with anisotropic displacement parameters. The hydrogen atoms were positioned either on the electron difference maps or were calculated from the geometry at idealized positions, depending on the quality of the crystal and diffraction data. The absolute configuration was determined using the Flack method [28,29]. The experimental details and final atomic parameters for all crystal structures have been deposited with the Cambridge Crystallographic Data Centre as supplementary material (ID CCDC No.: 2085100-2085108).  Table 2. The post-reaction mixture was concentrated dry at 45 • C under vacuum. The residue was pre-purified on a silica gel column using an eluent CH 2 Cl 2 /MeOH/TEA 98:2:0.1. A mixture of (3R,2S)-2a and (3S,2S)-3a diastereomers was separated by semipreparative HPLC. The remaining diastereomers were separated on a silica gel column using 50:50 acetone/cyclohexane eluent. Table 1 lists dr for mixtures; in Table 2, m.p., [α] and dr for diastereomers are given. Numbering system, which was used in NMR spectra interpretation of compounds (3R,2S)-2a and (3S, 2S)-3a is shown in Figure 6. Table 2. Physico-chemical data of diastereomers 2a, 3a, 4a, 5a, 6b, 7b, 8c, and 9c.

Compound Substrate 1a-c/Chiral Substrate (R)-I or (S)-II Reaction Time (h) m.p. (°C) Yield (%) a dr b [ α]
(   Numbering system, which was used in NMR spectra interpretation of compounds (3R,2R)-4a, (3S,2R)-5a, (3R,2R)-6b, (3S,2R)-7b, (3R,2R)-8c and (3S,2R)-9c is shown in Figure 8. Numbering system, which was used in NMR spectra interpretation of compounds (3R,2R)-4a, (3S,2R)-5a, (3R,2R)-6b, (3S,2R)-7b, (3R,2R)-8c and (3S,2R)-9c is shown in Figure 8.  compounds (3R,2R)-4a, (3S,2R)-5a,  (3R,2R)-6b, (3S,2R)-7b, (3R,2R)-8c and (3S,2R) compounds (3R,2R)-4a, (3S,2R)-5a,  (3R,2R)-6b, (3S,2R)-7b, (3R,2R)-8c and (3S,2R) An ampoule with the appropriate diastereomer (0.014m), Pd/C 10% 0.3 g catalyst, and 180 mL methanol were placed in the autoclave. The hydrogenolysis process was carried out at 30 • C under the pressure of 1-3 atm. The mixture was blended for 8 h. The catalyst was filtered off from the postreaction mixture and the filtrate was cooled down; after that, it was acidified with a methanolic HCl solution to a pH of about 2 and concentrated at 45 • C under vacuum until dry. After concentrating solutions of (R)-10a or (S)-11a compounds to dryness, 5 mL of absolute EtOH and Et2O were added to the remaining part to obtain a cloudy structure in the solutions, which were then placed in a refrigerator. As for the (R)-10-b, (S)-11-b enantiomers, after concentration to dryness, 10 mL of acetone was added to the residue, which was then placed in the refrigerator. In the case of (R)-10c and (S)-11c compounds, the solutions were concentrated to a volume of 10 mL and placed in a refrigerator, and the isolated crystals (R)-12-c or (S)-13c were filtered off. Then, 20 mL of acetone was added to the filtrate and placed in a refrigerator to obtain salt (R)-10c and (S)-11c. The reaction yield, melting temp, er, and [α] are given in Table 3. Numbering system, which was used in NMR spectra interpretation of compounds (R)-10a-c and (S)-11a-c is shown in Figure 9. carried out at 30 °C under the pressure of 1-3 atm. The mixture was blended for 8 h. The catalyst was filtered off from the postreaction mixture and the filtrate was cooled down; after that, it was acidified with a methanolic HCl solution to a pH of about 2 and concentrated at 45 °C under vacuum until dry. After concentrating solutions of (R)-10a or (S)-11a compounds to dryness, 5 mL of absolute EtOH and Et2O were added to the remaining part to obtain a cloudy structure in the solutions, which were then placed in a refrigerator. As for the (R)-10-b, (S)-11-b enantiomers, after concentration to dryness, 10 mL of acetone was added to the residue, which was then placed in the refrigerator. In the case of (R)-10c and (S)-11c compounds, the solutions were concentrated to a volume of 10 mL and placed in a refrigerator, and the isolated crystals (R)-12-c or (S)-13c were filtered off. Then, 20 mL of acetone was added to the filtrate and placed in a refrigerator to obtain salt (R)-10c and (S)-11c. The reaction yield, melting temp, er, and [α] are given in Table 3.
Numbering system, which was used in NMR spectra interpretation of compounds (R)-10a-c and (S)-11a-c is shown in Figure 9.