Synthesis, biological evaluation and molecular docking studies of indeno [1, 2-c] pyrazol derivatives as inhibitors of mitochondrial malate dehydrogenase 2 (MDH2).

Hypoxia inducible factor-1 (HIF-1) is a pivotal transcription factor, which is strongly correlated with the induction of angiogenesis, tumor survival, metastasis, and cell proliferation, making it a pivotal therapeutic target for solid tumor therapeutic agents. Herein, a new series of multi-functional chemical probes were designed including principal groups, viz. adamantyl and indene, at various locations of the parent compound LW6. Molecular docking studies were performed on the designed compounds and their relationship with HIF-1α and malate dehydrogenase 2 (MDH2). Inhibition of MDH2 by our compounds was expected to decrease the NADH level. Indeed, treatment of the breast cancer cell line 4T1 led to a strong reduction of the NADH concentration. The greatest reduction in NADH production in mitochondria was observed with (E)-3-(4-((3r, 5r, 7r)-adamantan-1-yl) phenoxy)-N-(5-(piperidine-1-carbonyl)-1, 4-dihydroindeno [1, 2-c] pyrazol-3-yl) acrylamide (18: IC50 = 59 nM), and has the best inhibitory potential under hypoxic conditions (MCF-7: IC50 = 57 nM). This compound also gave one of the highest docking "higher than the score obtained with LW6 in parallel (-31.63 kcal/mol) in the initial docking runs (PDB Code: 4WLO). Other related compounds with good yields were also synthesized from docking results, and all the synthesized compounds (14, 18, 22, 26, 29, 30) were evaluated in vitro on human adenocarcinoma cell lines.

2-[(Z)-4,7-Dichloro-3,3-dimethyl-2,3-dihydro-1H-indol-2-yl-idene]-3-oxopropane-nitrile.

In the title compound, C(13)H(10)Cl(2)N(2)O, the ring N atom and its three attached atoms are essentially coplanar with angles adding to 359.8°, indicating conjugation with the 2-formyl-acrylonitrile subunit. The aldehyde group is oriented to place the carbonyl O atom 2.02 (3) Šfrom the N-H hydrogen atom. Intra-molecular N-H⋯O and C-H⋯Cl inter-actions occur. The geometry of the exocyclic double bond is Z. In the crystal, weak C-H⋯N hydrogen bonds link the mol-ecules into chains along [1[Formula: see text]0].

2-(4-Chloro-3,3,7-trimethyl-2,3-dihydro-1H-indol-2-yl-idene)-2-cyano-acetamide.

Reaction of 2-(4-chloro-3,3,7-trimethyl-2,3-dihydro-1H-indol-2-yl-idene)propane-dial with hydroxyl-amine gives the title compound, C(14)H(14)ClN(3)O, in which the ring N atom is essentially planar [sum of angles around the ring N atom = 361°], indicating conjugation with the 2-cyano-acryl-amide unit. The orientation of the acetamide group arises from intra-molecular hydrogen bonding between the indole N-H and carbonyl groups. In the crystal, inversion-related acetamide groups form N-H⋯O hydrogen-bonded dimers in graph-set R(2) (2)(8) motifs, whilst dimers are also formed by pairs of amine-nitrile N-H⋯N hydrogen bonds in R(2) (2)(12) motifs. These inter-actions together generate ribbons that propagate along the b-axis direction.

1-[(E)-4-(5-Bromo-1H-indol-3-yl)-1-methyl-2,5,6,7-tetra-hydro-1H-azepin-2-yl-idene]propan-2-one.

In the title compound, C(18)H(19)BrN(2)O, the seven-membered azepine ring adopts a twist-boat conformation: the bond angles about the azepine N atom are indicative of sp(2) hybridization. The dihedral angle between the plane of the carbon-carbon double bond of the enone unit and the mean plane of the indole ring is 27.8 (1)°. In the crystal, an N-H⋯O hydrogen bond links the mol-ecules into chains along the b axis.

3-(1-Methyl-pyrrolidin-2-yl-idene)-3H-indole sesquihydrate.

The asymmetric unit of the title compound, C(13)H(14)N(2)·1.5H(2)O, contains two similar mol-ecules of 3-(1-methyl-pyrrolidin-2-yl-idene)-3H-indole, (I), and three water mol-ecules. (I) is the product of reacting indole with 1-methyl-pyrrolidin-2-one in the presence of phospho-rus oxychloride. Both organic molecules are almost completely planar; the maximum distances above and below the least-squares plane through all the atoms of mol-ecule 1 are 0.050 (8) and -0.045 (8) Å, respectively, and the deviations for mol-ecule 2 are 0.096 (8) and -0.059 (8) Å, respectively. In the crystal, the two crystallographically different mol-ecules alternate in π-stacked columns [centroid-centroid distances = 3.729 (5) and 3.858 (5) Å], which are linked by O-H⋯N hydrogen bonds to a network of hydrogen-bonded water mol-ecules. O-H⋯O inter-actions are also present.

7-Chloro-2-[1-(4-methoxy-phen-yl)pyrazol-4-yl]-3,3-dimethyl-3H-indole.

In the title compound, C(20)H(18)ClN(3)O, the dihedral angle between the pyrazole and the 3H-indole components is only 13.28 (6)°, indicating that there is conjugation between the two heterocyclic subunits. The N-methoxy-phenyl unit makes a dihedral angle of 25.10 (7)° with the pyrazole ring.