Discovery of N-indanyl benzamides as potent RORγt inverse agonists

Article abstract of DOI:10.1016/j.ejmech.2019.01.082

The retinoic acid receptor-related orphan receptor-gamma-t (RORγt) is a promising therapeutic target for treatment of Th17 cell-mediated autoimmune diseases. Based on a scaffold hopping/conformational restriction strategy, a series of N-indanyl benzamides as novel RORγt inverse agonists was discovered. Exploration of structure-activity relationship on the piperazine ring, benzoyl moiety and cyclopentyl moiety of N-indanyl benzamides 2a and 2d led to identification of potent RORγt inverse agonists. Compound 5c with (S)-enantiomer was found having an IC₅₀ of 153.7 nM in Fluorescence Resonance Energy Transfer (FRET) assay, and an IC₅₀ of 47.1 nM in mouse Th17 cell differentiation assay, which represents a promising starting point for developing potent small molecule RORγt inverse agonists. Binding modes of the two enantiomers 5c and 5d in RORγt ligand binding domain were also discussed.

Full text of DOI:10.1016/j.ejmech.2019.01.082

Accepted Manuscript
Discovery of N-Indanyl benzamides as potent RORγt inverse agonists
Jinlong Tian, Nannan Sun, Mingcheng Yu, Xianfeng Gu, Qiong Xie, Liming Shao, Jin
Liu, Li Liu, Yonghui Wang
PII:
S0223-5234(19)30101-1
DOI:
https://doi.org/10.1016/j.ejmech.2019.01.082
EJMECH 11089
Reference:
To appear in: European Journal of Medicinal Chemistry
Received Date: 13 December 2018
Revised Date: 27 January 2019
Accepted Date: 30 January 2019
Please cite this article as: J. Tian, N. Sun, M. Yu, X. Gu, Q. Xie, L. Shao, J. Liu, L. Liu, Y. Wang,
Discovery of N-Indanyl benzamides as potent RORγt inverse agonists, European Journal of Medicinal
Chemistry (2019), doi: https://doi.org/10.1016/j.ejmech.2019.01.082.
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Graphic Abstract

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Discovery of N-Indanyl Benzamides as Potent RORγt Inverse Agonists
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Jinlong Tiana, Nannan Suna, Mingcheng Yua, Xianfeng Gua, Qiong Xiea, Liming
Shaoa, Jin Liub, Li Liuc,*, Yonghui Wanga,*
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aDepartment of Medicinal Chemistry, School of Pharmacy, Fudan University, 826
Zhangheng Road, Shanghai 201203, China
bDepartment of Biology and Pharmacology, Shanghai ChemPartner CO., LTD., 998
Halei Road, Shanghai 201203, China
cState Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute
of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, 1111
Zhongshan North No. 1 Road, Shanghai, 200437, China
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*Corresponding authors:
Tel: +86-21-65053962, E-mail address: liulisipi@foxmail.com (L. Liu); Tel:
+86-21-51980118, E-mail address: yonghuiwang@fudan.edu.cn (Y. Wang)
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Abstract
The retinoic acid receptor-related orphan receptor-gamma-t (RORγt) is a promising
therapeutic target for treatment of Th17 cell-mediated autoimmune diseases. Based on
a scaffold hopping/conformational restriction strategy, a series of N-indanyl
benzamides as novel RORγt inverse agonists was discovered. Exploration of
structure-activity relationship on the piperazine ring, benzoyl moiety and cyclopentyl
moiety of N-indanyl benzamides 2a and 2d led to identification of potent RORγt
inverse agonists. Compound 5c with (S)-enantiomer was found having an IC50 of
153.7 nM in Fluorescence Resonance Energy Transfer (FRET) assay, and an IC50 of
47.1 nM in mouse Th17 cell differentiation assay, which represents a promising
starting point for developing potent small molecule RORγt inverse agonists. Binding
modes of the two enantiomers 5c and 5d in RORγt ligand binding domain were also
discussed.
Keywords: N-indanyl benzamides; RORγt inverse agonists; Th17 cells;
autoimmune diseases; binding modes
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1. Introduction
The retinoic acid receptor-related orphan receptor-gamma-t (RORγt), an isoform
of RORγ restrictedly expressed in the thymus, is a key transcriptional factor in Th17
cell differentiation[1-6]. Th17 cells produce inflammatory cytokines (IL-17A, IL-17F,
etc.), which play a central role in the pathogenesis of various autoimmune diseases
such as psoriasis, rheumatoid arthritis, and multiple sclerosis[7-14]. Recently,
accumulated clinical efficacy of the biologics has confirmed importance of the Th17
pathway as a viable clinical target for the treatment of psoriasis, rheumatoid arthritis,
ankylosing spondylitis and uveitis[15-20]. Given the crucial role of RORγt in the
differentiation of Th17 cells, RORγt has been considered as a promising therapeutic
target for treatment of Th17 cell-mediated autoimmune diseases[21]
.
Since the identification of digoxin[22], SR1001[23] and ursolic acid[24] as small
molecule RORγt inhibitors, quite a number of small molecule RORγt inhibitors have
been reported[21,25-28]. Among them, a few compounds such as VTP-43742,
GSK-2981278, AZD-0284, ESR-114, ARN-6069, AUR-101, RTA-1701 and others
have been progressed into clinical trials (Figure 1)[29]. However, some of these
front-runners have failed in clinical trials due to compound toxicities or lack of
efficacy. Thus, the development of more and better RORγt inhibitors with diverse
structure types for therapeutic use remains in need.
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Figure1. Structures of RORγt inhibitors in clinical trials and benzyl piperazine 1
Previously, we have reported the discovery of RORγt inhibitors such as
carbazole carboxamides[30], thiazole/thiophene ketone amides[31], thiazole ether
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amides[32], indole amides[33] and biaryl amides[34]. Recently, GlaxoSmithKline (GSK)
disclosed a series of benzyl piperazines as novel RORγt inhibitors in their PCT
patents[35-38]. Subsequently, a few RORγt inhibitors based on the benzyl piperazine
scaffold were disclosed by Pfizer[39], Novartis[40] and LEO Pharm[41]. In light of
benzyl piperazine representing a unique structure type and displaying reasonable
RORγt activities, it was chosen as our starting scaffold for further structural
modification. Compound 1, a typical GSK patent compound with the benzyl
piperazine scaffold, displayed low RORγt activity (IC50 of 8.2 µM) in our FRET assay
(Figure 1). We hypothesized that cyclization of the benzyl core using a scaffold
hopping/conformational restriction strategy could rigidify the molecule and improve
its RORγt activity. In this paper, we report the design, synthesis, structure-activity
relationship (SAR) of a series of indane-containing compounds as novel RORγt
inhibitors. The binding modes of two indane enantiomers in the RORγt ligand binding
domain (LBD) were also discussed.
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2. Results and discussion
2.1 Compound design
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First, the analogs of benzyl piperazine 1 with different bicyclic cores (2a-2g)
were designed with aid of computer modeling and docking, trying to identify new
bicyclic cores that could maintain RORγt inhibitory activity. Then, with the best
indane cores (2a and 2d) identified, some compounds with modification on piperazine
moiety (3a-3d and 4a-4d) were designed and evaluated. Finally, SARs of
left-hand-side (LHS) benzoyl moiety and right-hand-side (RHS) cyclopentyl moiety
were investigated on two different indane cores (5a-5i and 6a-6g) to optimize the
N-indanyl benzamide compounds with better RORγt activity (Figure 2).
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Figure 2. Target compounds with modifications on benzyl core (2a-g), piperazine
moiety (3a-d and 4a-d), cyclopentyl moiety (5a-5e and 6a-6c) and benzoyl moiety
(5f-5i and 6d-6g) of benzyl piperazine 1
2.2 Chemistry
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A general procedure for the synthesis of N-indanyl benzamide compounds is
described in Scheme 1. The commercially available 1-indanone (7) reacted with
KNO3 in the presence of H2SO4 to produce compound 8a or 8b, which then reacted
with Boc-protected piperazine analogues in the presence of sodium cyanoborohydride
to obtain compounds 9a or 9b. After N-deprotection of 9a or 9b, the resulting amines
subsequently reacted with the corresponding carboxylic acids or acyl chlorides to
afford the compounds 10a or 10b. Then, the anilines 11a or 11b were obtained by the

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reduction of the nitro group on 10a or 10b. Finally, the target compounds (2a, 2d,
3a-3d, 4a-4d, 5a, 5b, 5e-5i, 6a-6g) were obtained via acylation with the
corresponding carboxylic acids or urea formation with anilines/amines. Enantiomers
(S)-5c and (R)-5d were obtained by chiral HPLC separation of 5b. The absolute
structures of 5c and 5d were determined by the optical rotation values of 5c and 5d
compared with that of (1R)-1-Aminoindane in the literature.
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Scheme 1. Synthesis of compounds 2a, 2d, 3a-3d, 4a-4d, 5a-5i and 6a-6ga
aReagents and conditions: (a) H2SO4, KNO3, 0 to rt, 1h; (b) Boc-YH, NaBH3CN,
CH3OH, AcOH, 0 to rt, overnight; (c) CF3COOH, DCM, rt, 4h; (d) R1CO2H or
R1COCl, DIPEA, DCM, 0 to rt, 2h; (e) Fe, AcOH, rt, overnight; (f) R2CO2H, HATU,
DIPEA, DCM, rt, overnight, or N-(3-cyanophenyl)-1H-imidazole-1- carboxamide,
ZrCl4, THF, reflux; (g) Chiral supercritical-fluid chromatography (SFC), 25% MeOH
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(0.2% Methanol ammonia): 5c (42%), 5d (56%).
Synthetic procedures of compounds 2b, 2c, 2e-2g, the detailed chiral separation
and absolute structure determination of 5c and 5d were described in the supporting
information.
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2.3 Structure-activity relationship
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The first set of compounds with different bicyclic cores (2a-2g) were designed,
synthesized and evaluated in the RORγ FRET assay (Table 1). Cyclization of the
methylene carbon of benzyl piperazine 1 to the 4-position of central phenyl ring
resulting in indane compound 2a improved the RORγt potency by 10-fold (830.0 nM
in 2a vs. 8242.0 nM in 1), while replacing indane ring in 2a with indoline ring (2b) or
indole ring (2c) lowered the RORγt activity (1574.5 nM in 2b and 4897.5 nM in 2c,
respectively). Interestingly, when cyclization of the methylene carbon of benzyl
piperazine 1 to the 2-position of central phenyl ring, the resulting indane-containing
compound 2d exhibited a 17-fold improvement in RORγt activity (464.9 nM in 2d vs.
8242.0 nM in 1). Replacing indane ring in 2d with N-methylindole ring (2e) or
indoline ring (2g) dramatically decreased the activity and replacing with indole ring
(2f) completely aborted the activity. Thus, the indane compounds 2a and 2d which
possessed the best RORγt activity among the bicyclic compounds were subject to
further optimization.
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Table 1. SAR exploration of benzyl core in 1.
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RORγ
FRET IC50 (nM)a
Compd
Y
X
N
(% max. inhibition)b
1
8242.0 ± 2387.0 (135.9)
2a
N
830.0 ±19.3 (107.7)

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2b
2c
2d
2e
2f
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C
N
C
C
C
1574.5 ± 163.3 (156.2)
4897.5 ± 102.5 (137.8)
464.9 ± 10.1 (149.0)
6149.0 ± 562.9 (108.7)
N/Ac
2g
5575.0 ± 927.7 (129.7)
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aIC50 value was expressed as mean ± SD, n=2.
bPercent max. inhibition measured against activation by the surrogate agonist.
cN/A represents no activity.
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The SAR of the piperazine moiety of the indanes 2a and 2d was then
explored, and the results were summarized in Table 2. Replacing the piperazine
moiety in 2a with (S)-3-methylpiperazine (3a) improved RORγt activity (193.6
nM in 3a vs. 830.0 ± 19.3 nM in 2a), while replacing piperazine moiety with
(R)-3-menthylpiperazine (3b) lowered RORγt activity (1674.5 nM in 3b vs.
830.0 nM in 2a), indicating the importance of the chirality in methylpiperazine.
Subsequently,
we
replaced
the
piperazine
moiety
with
(3S,
5R)-2,6-dimethylpiperazine moiety (3c), resulting in equipotent RORγt activity
compared to 2a. Conformation restriction by bridging two methyl groups in 3c
to form 3d improved the RORγt activity (207.9 nM in 3d vs. 925.1 nM in 3c)
and the maximum inhibition (147.4% in 3d vs. 122.3% in 3c). We used the same
strategy to modify the piperazine moiety of the indane 2d (Table 2). Interestingly,
the RORγt inhibitory potency (IC50) and the maximum inhibition (%) of the
methyl substituted piperazines (4a-4d) were not dramatically affected by the
methyl conformation or conformation restriction on piperazine ring, indicating

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that the substituent groups on piperazine moiety might play an insignificant role
on biological activities of 2d. For example, compound 4d exhibited a slightly
improved RORγt activity with an IC50 of 287.2 nM relative to 2d with an IC50 of
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464.9 nM.
Table 2. SAR exploration of the piperazine moieties.
R
RORγ FRET IC50 (nM)a
(%max.inhibition)b
RORγ FRET IC50 (nM)a
(%max.inhibition)b
Compd
Compd
2a
830.0 ± 19.3 (107.7)
193.6 ± 81.9 (118.3)
1674.5 ± 27.6 (124.0)
925.1 ± 197.8 (122.3)
207.9 ± 17.9 (147.4)
2d
464.9 ± 10.1 (149.0)
384.7 ± 12.4 (151.8)
399.9 ± 68.0 (146.4)
270.3 ± 14.8 (148.9)
287.2 ± 23.6 (144.3)
3a
3b
3c
3d
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4b
4c
4d
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aIC50 value was expressed as mean ± SD, n=2.
bPercent max. inhibition measured against activation by the surrogate agonist.
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We next explored the SAR of RHS (R1) and LHS (R2 and R3) of the
ethylene-bridged piperazines (3d) and (4d). SAR data were summarized in
Tables 3 and 4. Firstly, fixing the R2 and R3 moiety as 3-cyano-benzamido, we
explored SAR of R1 in 3d. Changing the cyclopentyl in 3d to cyclobutyl (5a),
cyclohexyl (5b) or cyclobutylmethyl (5e) could essentially maintain the RORγt
activity. Fixing R1 as cyclopentyl, replacing the LHS 3-cyano-phenyl in 3d with
pyridine derivatives either maintained (5h) or mildly decreased (5f) the RORγt
activity, but with a 4-methyltetrahydro-2H-pyran (5g), the RORγt activity
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LHS. Replacing the amide linker in 3d with a urea linker (5i) slightly decreased
the RORγt activity. Chiral separation of racemic 5b led to its two respective
enantiomers 5c and 5d. The (S)-enantiomer 5c displayed higher RORγt activity
compared to 5b (153.7 nM in 5c vs. 264.9 nM in 5b), whereas the
(R)-enantiomer 5d displayed no activity at all in the RORγ FRET assay. This
result can be explained by the binding mode differences of the compound 5c and
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5d in RORγt LBD (see section 2.4).
Table 3. SAR explorations of LHS and RHS in 3d.
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RORγ FRET IC50 (nM)a
(% Max inhibition)b
Compd
R1
R2
R3
3d
207.9 ± 17.9 (147.4)
5a
5b
333.2 ± 27.6(141.6)
264.9 ± 163.2 (119.2)
153.7 ± 4.7 (137.3)
N/Ac
5c (S)
5d (R)
5e
366.7 ± 6.2 (148.9)
717.9 ± 1.8 (148.1)
8410.0 ± 1971.0 (140.1)
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5h
5i
288.4 ± 6.4 (141.5)
357.7 ± 45.6 (134.2)
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aIC50 value was expressed as mean ± SD, n=2.
bPercent max. inhibition measured against activation by the surrogate agonist.
cN/A represents no activity.
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The SAR of the R1, R2 and R3 in 4d was explored in a similar way (Table 4).
Fixing the R2 and R3 moiety as 3-cyano-benzamido, changing the cyclopentyl
ring in 4d with cyclobutyl (6a), cyclohexyl (6b) or cyclobutylmethyl (6e)
resulted in a marked drop in RORγt activity. With identification of cyclopentyl
as the best RHS substituent in 4d, we continued to explore the SAR of R2 and R3
in LHS. When 3-cyano-phenyl was replaced by either pyridines (6d and 6f) or
4-methyltetrahydro-2H-pyran (6e), the RORγt activity was greatly reduced.
Similarly, replacing the amide linker in 4d with a urea linker (6g) also decreased
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the RORγt activity.
Table 4. SAR exploration of LHS and RHS in 4d.
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RORγ FRET IC50(nM)a
(% Max inhibition)b
Compd
R1
R2
R3
4d
287.2 ± 23.6 (144.3)
6a
6b
6c
6d
873.4 ± 329.0 (144.3)
1692.5 ± 415.1 (166.7)
569.3 ± 124.9 (146.4)
2442.5 ± 466.0 (156.5)

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6e
6f
> 10000 (92.8)
1512.5 ± 352.8 (142.3)
1589.5 ± 1132.0 (114.1)
6g
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aIC50 value was expressed as mean ± SD, n=2.
bPercent max. inhibition measured against activation by the surrogate agonist.
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We further evaluated the representative N-indanyl benzamides 2a, 2d, 3d, 4d,
5b-5d in the mouse Th17 cell differentiation assay (Table 5). The results revealed that
compound 2a and 2d containing the piperazine moiety possessed relatively weak
Th17 cellular activity. Replacing piperazine ring with ethylene-bridged piperazines
(3d, 4d and 5b) could improve the Th17 cellular activity greatly. Compound 5c with
(S)-enantiomer showed excellent activity with an IC50 of 47.1 nM in the Th17 cell
differentiation assay while the compound 5d with (R)-enantiomer had no activity at
all. The activities of the compounds tested in the Th17 cellular assay were essentially
consistent with those in the FRET assay.
Table 5. Results in mouse Th17 cell differentiation assay
Compd
2a
mTh17 IC50 (nM)a
2661.4 ± 2385.2
1782.5 ± 436.3
422.6 ± 39.3
384.6 ± 83.4
105.5 ± 15.9
47.1 ± 4.8
2d
3d
4d
5b
5c
N/Ab
5d
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aIC50 value was expressed as mean ± SD, n=2.
bN/A represents no activity.
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2.4 Binding mode study
The activity differences between piperazine ring and ethylene-bridged piperazine
ring as well as between the two indane enantiomers such as 5c and 5d draw our
intention, so docking studies on a few N-indanyl benzamide compounds in RORγt

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LBD were carried out to understand the mode of actions (MOAs). Docking of 2a (S
and R enantiomers), 3d (S and R enantiomers) and 5b (5c and 5d) into RORγt LBD
revealed the binding mode of a typical indane-based RORγt inverse agonist, which
was similar to the reported indole benzamide’s binding mode[39]. As illustrated in
Figure 3A, in the LHS of N-indanyl benzamide 5c, the benzoyl moiety provides
preferred π-π cluster interactions with His323 and Phe377, and the cyano substituent
can form a hydrogen bond with the backbone Leu287. The linker amide beside the
indane core can form hydrogen bond interaction with the backbone of Phe377. In the
RHS of 5c, the cyclohexyl ring occupies an existed vacant cavity between H11 and
H11’, and formed intermolecular interactions with surrounding hydrophobic residues
in the hydrophobic site near His479. Overlay of 5c with the reported indole
benzamide co-crystal structure in RORγt LBD (PDB ID: 6CN6) reveals a similar
overall binding mode (Figure 3B).
Besides the common binding mode, it was also noted that a key hydrogen bond
between His479 and the carbonyl group in the RHS of all indane (S)-enantiomers is
associated with the inverse agonism of RORγt. In the binding modes of (S)-
enantiomers of 2a, 3d and 5b, the carbonyl group was apt to form hydrogen bonds
with His479, breaking the hydrogen bond of His479 and Tyr502, thus made the
H11-H12 bridging force weak (Figure 4A). The loose interaction within the triplet
residues His479-Tyr502-Phe506 resulted in the disorder of H12, and the unwinding
H12 could not recruit co-activator, making these compounds as RORγt inverse
agonists. On the contrary, in the binding modes of (R)-enantiomers of 2a, 3d and 5b,
the carbonyl group is not easily to form hydrogen bond with His479, which might be
the reason why (S)-enantiomer 5c is quite active but the (R)- enantiomer 5d not.
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B
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Figure 3. Binding mode of indane derivative 5c. A: Zoomed-in view of 5c (shown in

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lime) in the binding pocket of RORγt LBD; B: overlay of 5c with the reported indole
benzamide in co-crystal structure (shown in white, PDB ID: 6CN6).
Another note from the binding mode study is that the confirmation of the
piperazine moiety constrained by the ethylene bridge can enhance the formation of
hydrogen-bond between the carbonyl group and His479 (Figure 4B). Thus, 3d
(S)-enantiomer is more preferred to form hydrogen bond with His479 than 2a
(S)-enantiomer, which is critical for the secondary structure of H12 as mentioned
above. The conformational restriction of the bridged piperazines such as in 3d is
reflected in an activity enhancement as observed not only in the RORγ FRET assay
but also in the mouse Th17 cell differentiation assay.
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B
Figure 4. Binding modes of S and R enantiomers. A: Binding modes of 2a, 3d and
5b; B: overlay of (S)-enantiomers of 2a and 3d, and (R)-enantiomers of 2a and 3d.
(2a (S)-enantiomer colored in yellow, 2a (R)-enantiomer colored in orange, 3d

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(S)-enantiomer colored in cyan, 3d (R)-enantiomer colored in blue, 5c colored in lime,
5d colored in green)
3. Conclusions
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In summary, we discovered a series of N-indanyl benzamides as novel RORγt
inhibitors through cyclization of the benzyl piperazines using a scaffold hopping
/conformational restriction strategy. The exploration of structure-activity relationship
on the benzyl core, the piperazine ring, the LHS aryl and the RHS cyclopentyl of the
benzyl piperazine 1 led to the identification of potent RORγt inhibitors. The indane
compound 5c with (S)-enantiomer was found having decent RORγt inhibitory activity
with an IC50 of 153.7 nM in RORγ FRET assay and 47.1 nM in mouse Th17 cell
differentiation assay, and represented a promising starting point for developing potent
small molecule RORγt inverse agonists with the potential for treatment of
autoimmune diseases. The binding mode study of the N-indanyl benzamides in RORγt
LBD using a molecular docking method revealed the rationales that why the bridged
piperazines are more potent than piperazine and the (S)-enantiomer compared to
(R)-enantiomer was preferred in RORγt activity. Further optimization of the
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N-indanyl benzamide lead series is ongoing and will be reported in due course.
4. Experimental
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4.1. Materials and methods
All the reagents used were commercially available and were used without further
purification unless otherwise indicated. All of the reactions were monitored by thin
layer chromatography (TLC) using silica gel plates (fluorescence F254, UV light).
The intermediate and the final target compound was purified by column
chromatography on silica gel 200~300 GF254 (Qingdao Haiyang Chemical Co., Ltd.,
Qingdao, Shandong Province, China). Melting point was recorded by WRS-1B digital
1
instrument. H NMR spectra was recorded on a Bruker 400 MHz spectrometer,
Coupling constants (J values) were given in hertz (Hz). 13C NMR spectra was
recorded at 600 MHz. Chemical shifts (δ) were reported in parts per million (ppm)

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(using TMS as an internal control). Signals were described as singlet (s), doublet (d),
triplet (t), quartet (q), multiplet (m), and broad (br). Mass spectroscopy was carried
out on Electrospray ionization (ESI) instruments or MALDI-TOF (Bruker).
4.2. Synthesis
4.2.1. General procedure for the synthesis of indane analogues (2a, 2d, 3a-3d, 4a-4d,
5a-5i and 6a-6g)
Step 1: To a solution of 2,3-dihydro-1H-inden-1-one (1.0 eq) in sulfuric acid stirred
at 0oC was added KNO3 (1.05 eq) in several portions over 15 mins and the reaction
mixture was stirred for 1 hr at this temperature. After the reaction completed, the
mixture was poured into ice-water, and extracted with AcOEt. The organic phase was
washed with water and saturated NaHCO3 solution, dried over anhydrous sodium
sulfate, filtered and the filtrate was concentrated under reduced pressure to afford the
crude product, which was purified by column chromatography (silica gel, eluent:
AcOEt/Pet 0-25%, v/v) to give the 6-nitro-2,3-dihydro-1H-inden-1-one intermediate
8a and 4-nitro-2,3-dihydro-1H-inden-1-one intermediate 8b.
Step 2: To a solution of 6-nitro-2,3-dihydro-1H-inden-1-one intermediate 8a (1.0 eq)
or 4-nitro-2,3-dihydro-1H-inden-1-one intermediate 8b (1.0 eq) and Boc-protection
piperazine analogues (1.5 eq) in methanol was added acetic acid (1.5 eq) and
NaBH3CN (2.0 eq) at room temperature and the reaction mixture was heated to reflux
overnight. When the starting material was consumed completely, the mixture was
cooled to room temperature, and saturated NH4Cl solution was added to the mixture
to quench the reaction. The mixture was concentrated under reduced pressure and
extracted with AcOEt. The organic phase was washed with water and saturated
NaHCO3 solution, dried over anhydrous sodium sulfate, filtered and the filtrate was
concentrated under reduced pressure to afford the crude product, which was purified
by column chromatography (silica gel, eluent: PE/DCM 0-50%, v/v) to give the
6-nitro-indanyl analogue 9a or 4-nitro-indanyl analogue 9b.
Step 3: To a solution of 6-nitro-indanyl analogue 9a (1.0 eq) or 4-nitro-indanyl
analogue 9b (1.0 eq) in DCM (4 mL) was added trifluoroacetic acid (2.0 mL) at 0oC

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and the reaction mixture was stirred at this temperature for 3 hours. When the starting
material was consumed completely, the mixture was concentrated under reduced
pressure to remove the solvent. The resulting residue was dissolved with DCM and
Et3N (3.0 eq). Different acid chloride (1.05 eq) was dropwise to the mixture for 10min.
Then the reaction mixture was stirred for another 1 hour. Methanol was added to the
reaction mixture to quench the reaction. The mixture was concentrated under reduced
pressure to remove the solvent. The crude product was purified by column
chromatography (silica gel, eluent: PE/DCM 0-100%, v/v) to give the compound 10a
or compound 10b.
Step 4: To a solution of compound 10a (1.0 eq) or compound 10b (1.0 eq) in
methanol (5.0 mL) was added Pd/C (5%, 0.2 eq, M/M) at room temperature under H2
atmosphere and the reaction mixture was stirred at this temperature overnight. When
the starting material was consumed completely, the mixture was filtered and the
filtrate was concentrated under reduced pressure to to give the crude compound 11a
or compound 11b which was used directly in the next step.
Step 5a: The mixture of the crude compound 11a (1.0 eq) or compound 11b (1.0 eq),
HATU (1.5 eq), different acid (1.1 eq) and DIPEA (3.0 eq) in DCM was stirred at
room temperature overnight under N2 atmosphere. When the starting material was
consumed completely, the mixture was washed with saturated NaHCO3 solution and
water, dried over anhydrous sodium sulfate, filtered and the filtrate was concentrated
under reduced pressure to afford the crude product, which was purified by column
chromatography to afford the target compounds (2a, 2d, 3a-3d,4a-4d, 5a, 5b, 5e-5h
and 6a-6f). Enantiomers (S)-5c and (R)-5d were obtained by chiral HPLC separation
of 5b.
Step 5b: The mixture of the crude compound 11a (1.0 eq) or compound 11b (1.0 eq),
ZrCl4 (1.0 eq), N-(3-cyanophenyl)-1H-imidazole-1- carboxamide (1.2 eq) in THF was
heated to reflux and stirred at this temperature for 8 hour under N2 atmosphere. When
the starting material was consumed completely, the reaction mixture was filtered and
the filtrate was concentrated under reduced pressure, the resulting residue was

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purified by flash column chromatography on silica gel to afford the desired product
(5i and 6g).
4.2.1.1
3-Cyano-N-(3-(4-(cyclopentanecarbonyl)piperazin-1-yl)-2,3-dihydro-1H inden -5-yl)
benzamide(2a) as white solid (55.4%); mp 229.6-230.4°C.1H NMR (400 MHz,
DMSO-d6) δ 10.38 (s, 1H), 8.41 (s, 1H), 8.25 (d, J = 8.0 Hz, 1H), 8.06 (d, J = 7.7 Hz,
1H), 7.80-7.73 (m, 2H), 7.63 (d, J = 8.2 Hz, 1H), 7.22 (d, J = 8.1 Hz, 1H), 4.34 (t, J =
6.9 Hz, 1H), 3.48 (m, 3H), 3.42 (m, 1H), 2.94 (m, 1H), 2.84 (m, 1H), 2.73 (m, 1H),
13
2.45 (m, 2H), 2.34 (m, 2H), 2.01 (q, J = 7.1 Hz, 2H), 1.73-1.49(m, 8H). C NMR
(151 MHz, DMSO-d6) δ 173.11, 163.21, 142.74, 139.14, 136.97, 135.85, 134.71,
132.33, 131.08, 129.64, 124.37, 119.80, 118.19, 116.92, 111.32, 69.00, 48.47, 47.98,
45.23, 41.53, 29.76, 29.44, 29.40, 25.49, 24.13. MS (ESI) m/z: 443.3[M+H]+. HRMS
(ESI+) m/z calcd for C27H30N4O2 [M+H]+ : 443.2442; found: 443.2445.
4.2.1.2
3-Cyano-N-(1-(4-(cyclopentanecarbonyl) piperazin-1-yl)-2,3-dihydro-1H-inden -4-yl)
359
benzamide(2d) as white solid (35.6%); mp 78.5-80.5°C. 1H NMR (400 MHz, DMSO-
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d6) δ 10.14 (s, 1H), 8.39 (s, 1H), 8.24 (d, J = 7.6 Hz, 1H), 8.08 (d, J = 7.1 Hz, 1H),
7.75 (t, J = 8.7 Hz, 1H), 7.36 (d, J = 6.6 Hz, 1H), 7.25 (t, J = 7.1 Hz, 1H), 7.18 (d, J =
6.8 Hz, 1H), 4.37 (m, 1H), 3.49 (m, 2H), 2.89 (m, 2H), 2.74 (m, 1H), 2.38 (m, 4H),
1.98 (m, 2H), 1.61 (m, 10H). 13C NMR (151 MHz, DMSO-d6) δ 173.10, 163.12,
143.61, 138.27, 135.46, 134.82, 133.75, 132.36, 131.22, 129.68, 126.45, 123.19,
122.10, 118.16, 111.39, 69.17, 48.62, 47.95, 45.21, 41.50, 29.43, 28.57, 25.48, 23.66.
MS (ESI) m/z: 443.2[M+H]+
443.2442; found: 443.2434.
4.2.1.3
.
HRMS (ESI+) m/z calcd for C27H30N4O2 [M+H]+:
3-Cyano-N-(3-((S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl)-2,3-dihydro
-1H -inden-5-yl) benzamide (3a) as white solid (45.2%); mp 114.2-115.6°C. 1H NMR
(400 MHz, DMSO-d6) δ 10.39 (s, 1H), 8.40 (d, J = 10.0 Hz, 1H), 8.24 (t, J = 7.8 Hz,
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1H), 8.06 (d, J = 7.8 Hz, 1H), 7.81-7.73 (m, 2H), 7.67-7.53 (m, 1H), 7.21 (d, J = 7.3
Hz, 1H), 4.54 (m, 1H), 4.35-4.17 (m, 2H), 3.77 (m, 1H), 3.29-3.13 (m, 1H), 2.86 (m,
2H), 2.73 (m, 2H), 2.38-2.15 (m, 2H), 1.99 (s, 2H), 1.69-1.49(m, 8H), 1.35-1.13(m,
3H). 13C NMR (151 MHz, DMSO-d6) δ 173.13, 163.28, 142.97, 138.98, 136.97,
135.89, 134.69, 132.34, 131.08, 129.63, 124.34, 119.70, 118.18, 116.89, 111.32, 68.97,
54.61, 51.04, 46.59, 43.98, 40.63, 36.60, 29.52, 25.47, 24.07, 16.88, 15.35. MS (ESI)
m/z: 457.3[M+H]+. HRMS (ESI+) m/z calcd for C28H32N4O2 [M+H]+ : 457.2598;
found: 457.2606.
4.2.1.4
3-Cyano-N-(3-((R)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl)-2,3-dihydro-1H
382
-inden-5-yl)benzamide(3b) as white solid (30.2%); mp 178.3-179.4°C.1H NMR (400
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MHz, DMSO-d6) δ 10.39 (s, 1H), 8.40 (d, J = 10.0 Hz, 1H), 8.24 (t, J = 7.4 Hz, 1H),
8.06 (d, J = 7.4 Hz, 1H), 7.81 (s, 1H), 7.75 (t, J = 7.5 Hz, 1H),7.68-7.53 (m, 1H), 7.21
(d, J = 7.1 Hz, 1H), 4.54 (m, 1H), 4.35-4.16 (m, 2H), 3.77 (m, 1H), 3.26 (m, 1H), 2.86
(m, 2H), 2.73 (m, 2H), 2.34-2.19 (m, 2H), 1.98 (s, 2H), 1.69-1.49 (m, 8H), 1.33-1.13
13
(m, 3H). C NMR (151 MHz, DMSO-d6) δ 173.07, 163.28, 142.98, 138.91, 137.01,
135.96, 134.68, 132.34, 131.08, 129.63, 124.32, 119.70, 118.18, 116.77, 111.33, 68.97,
51.04, 47.83, 46.59, 43.75, 40.64, 30.52, 29.52, 29.05, 25.46, 20.02, 16.81, 15.23. MS
(ESI) m/z: 457.3[M+H]+. HRMS (ESI+) m/z calcd for C28H32N4O2 [M+H]+ :
457.2598; found: 457.2599.
4.2.1.5
3-Cyano-N-(3-((3S,5R)-4-(cyclopentanecarbonyl)-3,5-dimethylpiperazin-1-yl)-2,3-dih
1
394
-ydro-1H-inden-5-yl)benzamide(3c) as white solid (46.7%); mp 184.7-185.8°C. H
395
396
397
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400
NMR (400 MHz, DMSO-d6) δ 10.39 (s, 1H), 8.39 (s, 1H), 8.24 (d, J = 7.4 Hz, 1H),
8.06 (d, J = 7.5 Hz, 1H), 7.84 (s, 1H), 7.75 (t, J = 7.7 Hz, 1H), 7.61 (d, J = 8.1 Hz, 1H),
7.21 (d, J = 8.0 Hz, 1H), 4.37 (m, 2H), 4.09 (m, 1H), 2.85 (m, 2H), 2.72 (m, 2H), 2.42
(m, 1H), 2.32 (m, 2H), 2.08 – 1.94 (m, 2H), 1.78 – 1.49 (m, 8H), 1.38-1.19 (m, 6H)..
13C NMR (151 MHz, DMSO-d6) δ 174.00, 163.29, 138.94, 137.05, 135.96, 134.69,
132.35, 131.08, 129.63, 124.33, 119.73, 118.18, 116.80, 111.33, 69.29, 55.38, 50.77,

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30.52, 29.59, 25.60. MS (ESI) m/z: 471.3[M+H]+. HRMS (ESI+) m/z calcd for
C29H34N4O2 [M+H]+:471.2755; found:471.2750.
4.2.1.6
3-Cyano-N-(3-(8-(cyclopentanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3-
405
dihydro-1H-inden-5-yl) benzamide(3d) as white solid (66.7%); mp 105.6-106.2°C.
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1H NMR (400 MHz, DMSO-d6) δ 10.38 (s, 1H), 8.39 (s, 1H), 8.24 (d, J = 8 Hz, 1H),
8.06 (d, J = 8 Hz, 1H), 7.75 (m, 2H), 7.59 (d, J = 8 Hz, 1H), 7.19 (d, J = 8 Hz, 1H),
4.48 (m, 1H), 4.34 (m, 2H), 2.78-2.69 (m, 4H), 2.29 (m, 2H), 1.97 (m, 5H), 1.72-1.50
(m, 10H). 13C NMR (151 MHz, DMSO-d6) δ170.91, 163.33, 143.00, 138.79, 137.11,
135.99, 134.69, 132.35, 131.10, 129.63, 124.32, 119.61, 118.19, 116.61, 111.33,
68.08, 55.68, 54.09, 51.36, 40.79, 29.77, 29.62, 28.39, 28.24, 26.70, 26.58, 25.64,
24.09, 23.90. MS (ESI) m/z: 469.3[M+H]+. HRMS (ESI+) m/z calcd for C29H32N4O2
[M+H]+: 469.2598; found:469.2597.
4.2.1.7
3-Cyano-N-(1-((S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl)-2,3-dihydro-1H
416
-inden-4-yl)benzamide(4a) as yellow solid (46.9%); mp 103.6-105.8°C.1H NMR (400
417
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MHz, DMSO-d6) δ 10.14 (s, 1H), 8.39 (s, 1H), 8.24 (d, J = 8.0 Hz, 1H), 8.08 (d, J =
7.6 Hz, 1H), 7.75 (t, J = 8.0 Hz, 1H), 7.36 (d, J = 5.5 Hz, 1H), 7.26 (t, J = 7.6 Hz, 1H),
7.22-7.15 (m, 1H), 4.57-4.51 (m, 1H), 4.42-4.32 (m, 1H), 4.26-4.16 (m, 1H),
3.81-3.70 (m, 1H), 3.33-3.13 (m, 1H), 2.95-2.81 (m, 2H),2.77- 2.67 (m, 2H),
2.44-2.15 (m, 2H), 1.96 (m, 2H), 1.69-1.50 (m, 8H), 1.35-1.06 (m, 3H). 13C NMR
(151 MHz, DMSO-d6) δ 173.13, 163.12, 143.81, 138.08, 135.46, 134.82, 133.75,
132.36, 131.21, 129.68, 126.48, 123.15, 122.03, 118.16, 111.39, 69.12, 50.96, 49.78,
47.77, 43.71, 30.53, 30.31, 29.42, 29.04, 28.53, 28.40, 25.56, 25.46. MS (ESI) m/z:
457.3[M+H]+. HRMS (ESI+) m/z calcd for C28H32N4O2 [M+H]+: 457.2598;
found:457.2589.
4.2.1.8
3-Cyano-N-(1-((R)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl)-2,3-dihydro-1H
-inden-4-yl)benzamide(4b) as yellow solid (28.5%); mp 91.9-92.4°C.1H NMR (400

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MHz, DMSO-d6) δ 10.15 (s, 1H), 8.39 (s, 1H), 8.26 (m, 1H), 8.09 (m, 1H), 7.76 (m,
1H), 7.36 (m, 1H), 7.26-7.17 (m, 2H), 4.56 (m, 1H), 4.37 (m, 1H), 4.19 (m, 1H),
3.83-3.70 (m, 1H), 3.31-3.10 (m, 1H), 2.89 (m, 2H), 2.75 (m, 2H), 2.27(m, 2H), 1.98
(m, 2H), 1.70-1.57 (m, 8H), 1.35-1.12 (m, 3H). 13C NMR (151 MHz, DMSO-d6) δ
173.12, 163.13, 143.88, 138.15, 135.46, 134.82, 133.75, 132.36, 131.21, 129.68,
126.48, 123.17, 121.73, 118.16, 111.39, 69.23, 50.39, 47.77, 46.63, 43.98, 30.52,
29.04, 28.53, 25.56, 23.49, 22.85, 16.73, 15.36. MS (ESI) m/z: 457.3[M+H]+. HRMS
(ESI+) m/z calcd for C28H32N4O2 [M+H]+ : 457.2598; found:457.2596.
4.2.1.9
3-Cyano-N-(1-((3S,5R)-4-(cyclopentanecarbonyl)-3,5-dimethylpiperazin-1-yl)-2,3-dih
1
ydro-1H-inden-4-yl)benzamide(4c) as white solid (28.5%); mp 101.6-102.7°C. H
NMR (400 MHz, DMSO-d6) δ 10.13 (s, 1H), 8.39 (s, 1H), 8.25 (d, J = 8.0 Hz, 1H),
8.08 (d, J = 7.7 Hz, 1H), 7.76 (t, J = 7.8 Hz, 1H), 7.37 (d, J = 7.1 Hz, 1H), 7.27 (t, J =
8 Hz, 1H), 7.23 (d, J = 7.3 Hz, 1H), 4.42 (m, 2H), 4.10 (m, 1H), 2.89-2.83 (m, 2H),
2.79-2.73 (m, 2H), 2.45 (m, 1H), 2.28-2.23 (m, 2H), 1.98 (m, 2H), 1.78-1.50 (m, 8H),
1.39-1.16 (m, 6H). 13C NMR (151 MHz, DMSO-d6) δ 174.01, 163.12, 144.05, 138.09,
135.47, 134.82, 133.75, 132.36, 131.21, 129.68, 126.51, 123.19, 121.84, 118.16,
111.39, 69.43, 55.58, 50.49, 47.80, 44.18, 30.94, 29.53, 28.45, 25.60, 22.85, 22.03,
21.62, 20.55, 20.16. MS (ESI) m/z: 471.3 [M+H]+. HRMS (ESI+) m/z calcd for
C29H34N4O2 [M+H]+ : 471.2755; found:471.2745.
4.2.1.10
3-Cyano-N-(1-(8-(cyclopentanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3-
dihydro-1H-inden-4-yl) benzamide(4d) as white solid (60.4%); mp 115.3-116.4°C.
1H NMR (400 MHz, DMSO-d6) δ 9.99 (s, 1H), 8.26 (s, 1H), 8.11 (d, J = 7.3 Hz, 1H),
7.95 (d, J = 7.4 Hz, 1H), 7.62 (t, J = 7.5 Hz, 1H), 7.23 (d, J = 7.5 Hz, 1H), 7.13 (t, J =
7.4 Hz, 1H), 7.04 (d, J = 7.2 Hz, 1H), 4.34-4.13(m, 3H), 2.71 (m, 2H), 2.59 (m, 2H),
13
2.32 (m, 1H), 2.17-2.12 (m, 2H), 1.84 (m, 2H), 1.75-1.36 (m, 12H). C NMR (151
MHz, DMSO- d6) δ 170.85, 163.12, 143.79, 138.03, 135.47, 134.82, 133.74, 132.36,
131.21, 129.68, 126.51, 123.14, 121.89, 118.16, 111.39, 68.21, 56.94, 54.44, 51.69,

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50.24, 40.81, 29.77, 29.61, 28.53, 28.32, 26.63, 25.64, 25.56, 23.60. MS (ESI) m/z:
469.3[M+H]+. HRMS (ESI+) m/z calcd for C29H32N4O2 [M+H]+ : 469.2598; found:
469.2593.
4.2.1.11
3-Cyano-N-(3-(8-(cyclobutanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3-
dihydro-1H-inden-5-yl) benzamide(5a) as white solid (55.0%); mp 114.6-115.8°C.
1H NMR (400 MHz, DMSO-d6) δ 10.38 (s, 1H), 8.39 (s, 1H), 8.24 (d, J = 8.0 Hz, 1H),
8.06 (d, J = 7.5 Hz, 1H), 7.86-7.68 (m, 2H), 7.67-7.56 (m, 1H), 7.19 (d, J = 8.0 Hz,
1H), 4.42 (dd, J = 5.6 Hz, 27.9 Hz, 1H), 4.29 (t, J = 7.0 Hz, 1H), 4.08, (dd, J = 5.0 Hz,
29.1 Hz, 1H), 3.28 (m, 1H), 2.81 (m, 1H), 2.72 (m, 2H), 2.45 (m, 1H), 2.47-2.17 (m,
13
4H), 2.09-1.63 (m, 10H). C NMR (151 MHz, DMSO-d6) δ 169.31, 163.33, 142.97,
138.74, 137.08, 135.99, 134.68, 132.34, 131.09, 129.62, 124.31, 119.60, 118.18,
116.58, 111.32, 68.08, 57.07, 55.67, 54.01, 51.35, 36.46, 29.59, 28.18, 26.72, 24.63,
24.17, 23.89, 17.48. MS (ESI) m/z: 455.3[M+H]+. HRMS (ESI+) m/z calcd for
C28H30N4O2 [M+H]+ : 455.2442; found:455.2433.
4.2.1.12
3-Cyano-N-(3-(8-(cyclohexanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3-
dihydro-1H-inden-5-yl) benzamide(5b) as white solid (45.6%); mp 242.8-243.2°C.1H
NMR (400 MHz, DMSO-d6) δ 10.39 (s, 1H), 8.40 (s, 1H), 8.25 (d, J = 7.8 Hz, 1H),
8.07 (d, J = 7.8 Hz, 1H), 7.76 (m, 2H), 7.60 (d, J = 7.7 Hz, 1H), 7.19 (d, J = 8.0 Hz,
1H), 4.44 (dd, J = 25.3 Hz, 6.5 Hz, 1H), 4.35-4.22 (m, 2H)., 2.79-2.68 (m, 3H), 2.45
(m, 2H), 2.35-2.21 (m, 2H), 1.98 (m, 2H), 1.89 (m, 2H), 1.67-1.23 (m, 12H). 13C
NMR (151 MHz, DMSO-d6) δ 170.96, 163.32, 142.96, 138.78, 137.08, 135.98,
134.68, 132.34, 131.09, 129.63, 124.32, 119.61, 118.18, 116.62, 111.32, 68.05, 57.24,
55.66, 54.07, 51.20, 40.21, 29.60, 29.23, 29.05, 28.45, 26.68, 25.39, 25.05, 24.94,
24.10. MS (ESI) m/z: 483.3[M+H]+. HRMS (ESI+) m/z calcd for C30H34N4O2
[M+H]+ : 483.2755; found:483.2744.
4.2.1.13

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3-Cyano-N-((3S)-3-(8-(cyclohexanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3
- dihydro-1H-inden-5-yl) benzamide (5c) as white solid (42.0%); mp 110.2-112.5°C.
ee: 100%, [α]D23 +122° (c 0.37, CHCl3). 1H NMR (400 MHz, DMSO-d6) δ 10.39 (s,
1H), 8.40 (s, 1H), 8.25 (d, J = 7.8 Hz, 1H), 8.07 (d, J = 7.8 Hz, 1H), 7.76 (m, 2H),
7.60 (d, J = 7.7 Hz, 1H), 7.19 (d, J = 8.0 Hz, 1H), 4.44 (dd, J = 25.3 Hz, 6.5 Hz, 1H),
4.35-4.22 (m, 2H)., 2.79-2.68 (m, 3H), 2.45 (m, 2H), 2.35-2.21 (m, 2H), 1.98 (m, 2H),
1.89 (m, 2H), 1.67-1.23 (m, 12H). 13C NMR (151 MHz, DMSO-d6) δ 170.96, 163.32,
142.96, 138.78, 137.08, 135.98, 134.68, 132.34, 131.09, 129.63, 124.32, 119.61,
118.18, 116.62, 111.32, 68.05, 57.24, 55.66, 54.07, 51.20, 40.21, 29.60, 29.23, 29.05,
28.45, 26.68, 25.39, 25.05, 24.94, 24.10. MS (ESI) m/z: 483.3[M+H]+. HRMS (ESI+)
m/z calcd for C30H34N4O2 [M+H]+ : 483.2755; found:483.2744.
4.2.1.14
3-Cyano-N-((3R)-3-(8-(cyclohexanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)
-2,3 -dihydro-1H-inden-5-yl) benzamide (5d) as white solid (56.0%); mp
23
1
112.6-113.8°C. ee:100%, [α]D -122° (c 0.37, CHCl3). H NMR (400 MHz,
DMSO-d6) δ 10.39 (s, 1H), 8.40 (s, 1H), 8.25 (d, J = 7.8 Hz, 1H), 8.07 (d, J = 7.8 Hz,
1H), 7.76 (m, 2H), 7.60 (d, J = 7.7 Hz, 1H), 7.19 (d, J = 8.0 Hz, 1H), 4.44 (dd, J =
25.3 Hz, 6.5 Hz, 1H), 4.35-4.22 (m, 2H)., 2.79-2.68 (m, 3H), 2.45 (m, 2H), 2.35-2.21
(m, 2H), 1.98 (m, 2H), 1.89 (m, 2H), 1.67-1.23 (m, 12H). 13C NMR (151 MHz,
DMSO-d6) δ 170.96, 163.32, 142.96, 138.78, 137.08, 135.98, 134.68, 132.34, 131.09,
129.63, 124.32, 119.61, 118.18, 116.62, 111.32, 68.05, 57.24, 55.66, 54.07, 51.20,
40.21, 29.60, 29.23, 29.05, 28.45, 26.68, 25.39, 25.05, 24.94, 24.10. MS (ESI) m/z:
483.3[M+H]+. HRMS (ESI+) m/z calcd for C30H34N4O2 [M+H]+: 483.2755;
found:483.2744.
4.2.1.15
3-Cyano-N-(3-(8-(2-cyclobutylacetyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)- 2,3-
dihydro-1H-inden-5-yl) benzamide(5e) as white solid (42.4%); mp 100.8-101.4°C. 1H
NMR (400 MHz, DMSO-d6) δ 10.39 (s, 1H), 8.40 (s, 1H), 8.24 (d, J = 7.2 Hz, 1H),
8.06 (d, J = 6.3 Hz, 1H), 7.75 (m, 2H), 7.60 (s, 1H), 7.19 (d, J = 7.4 Hz, 1H),

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4.44-4.18(m, 3H), 2.76-2.50 (m, 5H), 2.43-2.25 (m, 5H), 1.99-1.63 (m, 11H). 13C
NMR (151 MHz, DMSO- d6) 166.92, 163.33, 142.94, 138.80, 137.08, 135.98, 134.70,
132.35, 131.09, 129.63, 124.33, 119.62, 118.19, 116.62, 111.33, 68.07, 56.79, 55.50,
54.66, 51.38, 31.98, 29.62, 28.38, 27.80, 27.71, 26.70, 26.66, 24.21, 18.04. MS (ESI)
m/z: 469.3 [M+H]+. HRMS (ESI+) m/z calcd for C29H32N4O2 [M+H]+ : 469.2598;
found: 469.2592.
4.2.1.16
N-(3-(8-(Cyclopentanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3-dihydro-
1H-inden-5-yl)-6-methylnicotinamide(5f) as white solid (38.4%); mp 228.3-231.2°C.
1H NMR (400 MHz, DMSO-d6) δ 10.31 (s, 1H), 9.00 (s, 1H), 8.19 (d, J = 7.0 Hz, 1H),
7.78 (d, J = 9.2 Hz, 1H), 7.59 (brs, 1H), 7.42 (d, J = 7.5 Hz, 1H), 7.18 (d, J = 7.5 Hz,
1H), 4.49-4.29(m, 3H), 2.84-2.69 (m, 5H), 2.56 (s, 3H), 2.32 (m, 2H), 1.98-1.50 (m,
14H). 13C NMR (151 MHz, DMSO-d6) δ 170.88, 163.67, 160.81, 148.03, 142.94,
138.57, 137.25, 135.48, 127.78, 124.27, 122.50, 119.59, 116.58, 68.06, 57.00, 55.65,
54.58, 54.09, 51.37, 50.93, 40.79, 29.77, 29.62, 28.40, 26.70, 25.66, 25.58, 24.10,
23.94. MS (ESI) m/z: 459.3 [M+H]+. HRMS (ESI+) m/z calcd for C28H34N4O2
[M+H]+ : 459.2755; found: 459.2753.
4.2.1.17
N-(3-(8-(Cyclopentanecarbonyl)-3,8-diazabicyclo
octan-3-yl)-2,3-dihydro-1H-
[3.2.1]
inden-5-yl)-2-(tetrahydro-2H-pyran-4-yl) acetamide (5g) as white solid (55.6%); mp
89.5-90.2°C. 1H NMR (400 MHz, DMSO-d6) δ 9.83 (s, 1H), 7.60 (d, J = 14.7 Hz, 1H),
7.40 (t, J = 9.5 Hz, 1H), 7.09 (d, J = 8.1 Hz, 1H), 4.44 (dd, J = 5.9 Hz, 26.2 Hz, 1H),
4.34-4.22 (m, 2H), 3.82 (m, 2H), 3.30 (m, 2H), 2.89-2.62 (m, 4H), 2.43 (m, 1H),
2.31-2.22 (m, 4H), 1.98-1.93 (m, 2H), 1.90-1.50 (m, 14H), 1.27-1.19(m, 3H). 13C
NMR (151 MHz, DMSO-d6) δ 170.76, 169.52, 142.87, 137.55, 124.20, 118.33,
115.33, 68.03, 66.72, 56.94, 55.52, 54.74, 54.46, 54.09, 51.36, 50.93, 50.06, 43.49,
40.79, 32.29, 31.90, 29.77, 29.61, 28.37, 26.67, 25.57, 24.12. MS (ESI) m/z: 466.3
[M+H]+. HRMS (ESI+) m/z calcd for C28H39N3O3 [M+H]+ : 466.3064; found:

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4.2.1.18
N-(3-(8-(Cyclopentanecarbonyl)-3,8-diazabicyclo[3.2.1]octan-3-yl)-2,3-dihydro -1H
- inden-5-yl)-5-fluoro-6-methylnicotinamide(5h) as white solid (56.9%); mp
109.2-110.6°C. 1H NMR (400 MHz, DMSO-d6) δ 10.36 (s, 1H), 8.86 (s, 1H), 8.13 (d,
J = 10.4 Hz, 1H), 7.78 (d, J = 9.2 Hz, 1H), 7.58 (s, 1H), 7.19 (d, J = 8.2 Hz, 1H), 4.45
(dd, J = 6.5 Hz, 27 Hz, 1H), 4.34 (m, 2H), 2.90-2.78 (m, 2H), 2.75-2.68 (m, 2H), 2.53
(s, 3H), 2.45 (m, 1H), 2.33-2.25 (m, 2H), 1.99 (m, 2H), 1.92 (m, 2H), 1.72-1.50(m,
10H). 13C NMR (151 MHz, DMSO-d6) δ 170.78, 162.32, 157.46, 155.77, 143.82,
143.01, 138.83, 136.99, 130.20, 124.33, 121.46, 119.62, 116.60, 68.05, 57.00, 55.67,
54.08, 51.37, 40.79, 29.62, 28.40, 28.24, 26.70, 26.58, 25.64, 24.09, 23.90, 17.79. MS
(ESI) m/z: 477.3[M+H]+. HRMS (ESI+) m/z calcd for C28H33FN4O2 [M+H]+ :
477.2660; found: 477.2656.
4.2.1.19
1-(3-Cyanophenyl)-3-(3-(8-(cyclopentanecarbonyl)-3,8-diazabicyclo[3.2.1] octan-3
-yl)-2,3-dihydro-1H-inden-5-yl)urea(5i) as white solid (46.9%); mp 139.5-141.2°C.1H
NMR (400 MHz, DMSO-d6) δ 8.93 (s, 1H), 8.80 (s, 1H), 7.94 (m, 1H), 7.64 (d, J =
8.2 Hz, 1H), 7.46 (t, J = 7.9 Hz, 2H), 7.40 (t, J = 8.7 Hz, 1H), 7.26-7.16 (m, 1H), 7.09
(d, J = 8.0 Hz, 1H), 4.42 (dd, J = 5.3 Hz, 23.7 Hz, 1H), 4.32-4.22 (m, 2H), 2.85-2.79
(m, 2H), 2.74-2.63 (m, 2H), 2.40 (m, 1H), 2.30-2.22 (m, 2H), 1.95 (m, 2H),
13
1.87-1.47(m, 12H). C NMR (151 MHz, DMSO-d6) 170.79, 152.29, 143.08, 140.62,
137.53, 136.94, 130.00, 125.00, 124.45, 122.65, 120.52, 118.74, 117.91, 114.74,
111.42, 68.05, 56.95, 54.74, 54.11, 51.34, 50.10, 40.81, 29.81, 29.60, 28.37, 26.66,
25.64, 24.23. MS (ESI) m/z: 484.3[M+H]+. HRMS (ESI+) m/z calcd for C29H33N5O2
[M+H]+ : 484.2707; found: 484.2710.
4.2.1.20
3-Cyano-N-(1-(8-(cyclobutanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3-
dihydro-1H-inden-4-yl) benzamide(6a) as white solid (38.1%); mp 105.9-106.7°C.

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1H NMR (400 MHz, DMSO-d6) δ 10.11 (s, 1H), 8.38 (s, 1H), 8.24 (d, J = 7.7 Hz, 1H),
8.07 (d, J = 7.7 Hz, 1H), 7.75 (t, J = 7.8 Hz, 1H, 1H), 7.36 (d, J = 7.7 Hz, 1H), 7.25 (t,
J = 7.6 Hz, 1H), 7.16 (d, J = 7.2 Hz, 1H), 4,41 (dd, J = 5.5 Hz, 26.2 Hz, 1H), 4.32 (t, J
= 6.9 Hz, 1H), 4.08 (dd, J = 4.3 Hz, 29.6 Hz, 1H), 3.27 (m, 1H), 2.83 (m, 1H),
2.74-2.67 (m, 2H), 2.46-2.38 (m, 1H), 2.27-2.10 (m, 4H), 2.03-1.64 (m, 10H). 13C
NMR (151 MHz, DMSO-d6) δ 169.34, 163.11, 143.72, 138.01, 135.46, 134.81,
133.72, 132.35, 131.21, 129.68, 126.51, 123.13, 121.87, 118.15, 111.39, 68.21, 55.39,
53.60, 51.31, 50.15, 36.47, 28.50, 28.17, 26.64, 24.68, 24.13, 23.55, 17.48. MS (ESI)
m/z: 455.3[M+H]+. HRMS (ESI+) m/z calcd for C28H30N4O2 [M+H]+ : 455.2442;
found:455.2442.
4.2.1.21
3-Cyano-N-(1-(8-(cyclohexanecarbonyl)-3,8-diazabicyclo [3.2.1] octan-3-yl)-2,3 -
dihydro-1H-inden-4-yl) benzamide (6b) as white solid (46.5%); mp 118.1-119.6°C.
1H NMR (400 MHz, DMSO-d6) δ 10.11 (s, 1H), 8.38 (s, 1H), 8.24 (d, J = 7.5 Hz, 1H),
8.07 (d, J = 7.6 Hz, 1H), 7.75 (t, J = 7.6 Hz, 1H, 1H), 7.36 (d, J = 7.7 Hz, 1H), 7.26 (t,
J = 7.3 Hz, 1H), 7.17 (d, J = 6.7 Hz, 1H), 4,43 (dd, J = 4.8 Hz, 25.3 Hz, 1H), 4.36
-4.20 (m, 2H), 2.83 (m, 1H), 2.78-2.67 (m, 2H), 2.43 (m, 2H), 2.34-2.25 (m, 2H),
1.97-1.62 (m, 11H), 1.38-1.10 (m, 5H). 13C NMR (151 MHz, DMSO-d6) δ 170.91,
163.11, 143.76, 138.06, 135.47, 134.82, 133.73, 132.36, 131.21, 129.68, 126.51,
123.14, 121.91, 118.16, 111.39, 68.20, 57.12, 55.50, 54.41, 54.06, 51.14, 50.70, 40.21,
29.23, 28.56, 28.37, 26.62, 25.38, 25.05, 23.66. MS (ESI) m/z: 483.3[M+H]+. HRMS
(ESI+) m/z calcd for C30H34N4O2 [M+H]+ : 483.2755; found:483.2759.
4.2.1.22
3-Cyano-N-(1-(8-(2-cyclobutylacetyl)-3,8-diazabicyclo[3.2.1]octan-3-yl)-2,3-dihydro
1
-1H-inden-4-yl)benzamide (6c) as white solid (56.5%); mp 187.4-189.1°C. H NMR
(400 MHz, DMSO-d6) δ 10.11 (s, 1H), 8.38 (s, 1H), 8.24 (d, J = 7.7 Hz, 1H), 8.07 (d,
J = 7.6 Hz, 1H), 7.75 (t, J = 7.8 Hz, 1H), 7.36 (d, J = 7.8 Hz, 1H), 7.25 (t, J = 7.5 Hz,
1H), 7.17 (d, J = 7.0 Hz, 1H), 4.42 (dd, J = 4.7 Hz, 24.6 Hz, 1H), 4.33 (t, J = 6.9 Hz,
1H), 4.22 (dd, J = 4.5 Hz, 31.3 Hz, 1H), 2.82 (m, 1H), 2.74 (m, 1H), 2.68 (m, 1H),

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2.58 (m, 1H), 2.47-2.24 (m, 6H), 2.00-1.59 (m, 11H). 13C NMR (151 MHz, DMSO-d6)
δ 166.88, 163.11, 143.73, 138.02, 135.53, 134.81, 133.72, 132.35, 131.21, 129.68,
126.50, 123.13, 121.89, 118.15, 111.39, 68.22, 55.43, 54.26, 51.27, 50.87, 32.01,
28.51, 28.31, 27.80, 26.64, 23.65, 18.04. MS (ESI) m/z: 469.3[M+H]+. HRMS (ESI+)
m/z calcd for C29H32N4O2 [M+H]+ : 469.2598; found:469.2594.
4.2.1.23
N-(1-(8-(Cyclopentanecarbonyl)-3,8-diazabicyclo[3.2.1]octan-3-yl)-2,3-dihydro-1H-i
1
nden-4-yl)-6-methylnicotinamide(6d) as white solid (44.5%); mp 99.0-101.2°C. H
NMR (400 MHz, DMSO-d6) δ 10.02 (s, 1H), 8.99 (s, 1H), 8.18 (d, J = 8.1 Hz, 1H),
7.41 (t, J = 8.1 Hz, 1H), 7.36 (d, J = 7.7 Hz, 1H), 7.25 (t, J = 7.5 Hz, 1H), 7.16 (d, J =
7.3 Hz, 1H), 4.44 (dd, J = 6.1 Hz, 26.0 Hz, 1H), 4.35-4.26 (m, 2H), 2.85 (m, 2H),
2.72 (m, 2H), 2.55 (s, 3H), 2.44 (t, J = 8 Hz, 1H), 2.32-2.25 (m, 2H), 1.97 (m, 2H),
1.90-1.78 (m, 2H), 1.73-1.49(m, 10H). 13C NMR (151 MHz, DMSO-d6) δ 170.80,
163.46, 160.98, 148.12, 143.68, 138.00, 135.52, 133.88, 127.24, 126.47, 123.17,
122.55, 121.73, 68.23, 55.46, 54.07, 51.32, 50.24, 40.81, 29.61, 28.52, 28.32, 26.63,
25.56, 23.94, 23.60. MS (ESI) m/z: 459.3 [M+H]+. HRMS (ESI+) m/z calcd for
C28H34N4O2 [M+H]+ : 459.2755; found:459.2751.
4.2.1.24
N-(1-(8-(Cyclopentanecarbonyl)-3,8-diazabicyclo[3.2.1]octan-3-yl)-2,3-dihydro-1H-i
nden-4-yl)-2-(tetrahydro-2H-pyran-4-yl)acetamide(6e) as white solid (46.5%); mp
85.6-86.0°C. 1H NMR (400 MHz, DMSO-d6) δ 9.28 (s, 1H), 7.44 (d, J = 8.2 Hz, 1H),
7.19-7.11 (m, 1H), 7.04 (d, J = 6.2 Hz, 1H), 4.41 (m, 1H), 4.33-4.16 (m, 2H), 3.82 (m,
2H), 3.29 (m, 2H), 2.84-2.71 (m, 2H), 2.66-2.63 (m, 2H), 2.43-2.39 (m, 1H),
2.26-2.21 (m, 4H), 1.95 (m, 2H), 1.84-1.50 (m, 14H), 1.29-1.19(m, 3H). 13C NMR
(151 MHz, DMSO-d6) δ 170.83, 169.57, 143.46, 135.70, 134.33, 126.39, 121.46,
120.63, 68.21, 66.73, 56.96, 56.88, 55.49, 54.42, 51.30, 50.90, 42.86, 40.80, 32.24,
29.61, 28.31, 26.62, 25.63, 23.53. MS (ESI) m/z: 466.3 [M+H]+. HRMS (ESI+) m/z
calcd for C28H39N3O3 [M+H]+ : 466.3064; found: 466.3068.
4.2.1.25

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octan-3-yl)-2,3-dihydro-1H-
[3.2.1]
inden-4-yl)-5-fluoro-6-methylnicotinamide(6f) as white solid (46.5%); mp
107.8-108.9°C. 1H NMR (400 MHz, DMSO-d6) δ 10.11 (s, 1H), 8.86 (s, 1H), 8.10 (d,
J = 10.2 Hz, 1H), 7.35 (d, J = 6.9 Hz, 1H), 7.26 (t, J = 7.8 Hz, 1H), 7.17 (d, J = 6.9
Hz, 1H), 4.43 (m, 1H), 4.33-4.26 (m, 2H), 2.82 (m, 2H), 2.75-2.68 (m, 2H), 2.53 (s,
3H), 2.45 (m, 1H), 2.29-2.25 (m, 2H), 1.97 (m, 2H), 1.88 (m, 2H), 1.71-1.49(m, 10H).
13C NMR (151 MHz, DMSO-d6) 170.80, 162.13, 157.49, 155.76, 149.08, 143.86,
138.06, 133.59, 129.69, 126.53, 123.18, 121.95, 121.49, 71.19, 68.20, 56.93, 55.45,
54.06, 51.31, 50.25, 40.80, 29.61, 28.53, 28.32, 26.62, 25.56, 23.62, 17.80. MS (ESI)
m/z: 477.3[M+H]+. HRMS (ESI+) m/z calcd for C28H33FN4O2 [M+H]+ : 477.2660;
found: 477.2653.
4.2.1.26
1-(3-Cyanophenyl)-3-(1-(8-(cyclopentanecarbonyl)-3,8 –diazabicyclo [3.2.1] octan -3
-yl)-2,3-dihydro-1H-inden-4-yl) urea(6g) as white solid (66.5%); mp 142.7-143.4°C.
1H NMR (400 MHz, DMSO-d6) δ 9.34 (s, 1H), 8.19 (s, 1H), 8.03 (s, 1H), 7.83 (s, 1H),
7.64 (s, 1H), 7.51 (s, 1H), 7.45 (s, 1H), 7.19 (s, 1H), 6.99 (s, 1H), 4.42 (m, 1H),
4.32-4.22 (m, 2H), 2.85-2.79 (m, 2H), 2.74-2.63 (m, 2H), 2.45 (m, 1H), 2.29 (m, 2H),
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1.99 (m, 2H), 1.74-1.52(m, 12H). C NMR (151 MHz, DMSO-d6) 170.84, 152.14,
143.31, 140.47, 135.08, 132.51, 130.08, 126.84, 125.12, 122.51, 120.36, 118.91,
118.70, 117.92, 111.51, 68.29, 56.80, 54.74, 54.07, 51.30, 40.80, 29.75, 28.31, 27.81,
26.63, 25.64, 23.51. MS (ESI) m/z: 484.3[M+H]+. HRMS (ESI+) m/z calcd for
C29H33N5O2 [M+H]+ : 484.2707; found: 484.2703.
4.3. Biological assays
4.3.1. RORγ FRET assay
The assays were performed in an assay buffer consisting of 50 mM NaF, 50 mM
3-(N-morpholino)propanesulfonic acid, pH 7.4, 0.05 mM 3-[(3-cholamidopropyl)
dimethylammonio]propanesulfonate, 0.1 mg/mL bovine serum albumin, and 10 mM