Indole Research Articles

Synthesis and cytotoxicity evaluation of novel 5-fluorinated indoles

We report herein the synthesis of a small 28-membered library of novel 5-fluorinated indole phytoalexins. Target compounds were designed by a structure-based bioisosterism strategy. The newly prepared compounds were screened in vitro for cytotoxic activity against seven human cancer cell lines. The cytotoxic evaluation revealed that the 2’-(3,4-dichlorophenylamino) analogue of 5-fluorospirobrassinin was the most active against cancer cell lines without causing toxicity to HUVEC cells. Overall, 5-fluoro analogues of indole phytoalexins did not show improved anti-cancer activity compared to the lead compounds. The preliminary structure-activity relationship (SAR) study revealed that placing fluoro substituent at C-5 position of the indole ring is not crucial for inducing cytotoxicity against a cancer cell line.

Engineered RebH Halogenase Variants Demonstrating a Specificity Switch from Tryptophan towards Novel Indole Compounds.

Activating industrially important aromatic hydrocarbons by installing halogen atoms is extremely important in organic synthesis and often improves the pharmacological properties of drug molecules. To this end, tryptophan halogenase enzymes are potentially valuable tools for regioselective halogenation of arenes, including various industrially important indole derivatives and similar scaffolds. Although endogenous enzymes show reasonable substrate scope towards indole compounds, their efficacy can often be improved by engineering. Using a structure‐guided semi‐rational mutagenesis approach, we have developed two RebH variants with expanded biocatalytic repertoires that can efficiently halogenate several novel indole substrates and produce important pharmaceutical intermediates. Interestingly, the engineered enzymes are completely inactive towards their natural substrate tryptophan in spite of their high tolerance to various functional groups in the indole ring. Computational modelling and molecular dynamics simulations provide mechanistic insights into the role of gatekeeper residues in the substrate binding site and the dramatic switch in substrate specificity when these are mutated.

Structural and biophysical characterization of the Burkholderia pseudomallei IspF inhibitor L-tryptophan hydroxamate

The enzyme 2-methylerythritol 2,4-cyclodiphosphate synthase, IspF, is essential for the biosynthesis of isoprenoids in most bacteria, some eukaryotic parasites, and the plastids of plant cells. The development of inhibitors that target IspF may lead to novel classes of anti-infective agents or herbicides. Enantiomers of tryptophan hydroxamate were synthesized and evaluated for binding to Burkholderia pseudomallei (Bp) IspF. The L-isomer possessed the highest potency, binding BpIspF with a KD of 36 µM and inhibited BpIspF activity 55% at 120 µM. The high-resolution crystal structure of the L-tryptophan hydroxamate (3)/BpIspF complex revealed a non-traditional mode of hydroxamate binding where the ligand interacts with the active site zinc ion through the primary amine. In addition, two hydrogen bonds are formed with active site groups, and the indole group is buried within the hydrophobic pocket composed of side chains from the 60 s/70 s loop. Along with the co-crystal structure, STD NMR studies suggest the methylene group and indole ring are potential positions for optimization to enhance binding potency.

Mechanistic Insights into the P450 TleB-Catalyzed Unusual Intramolecular C-N Bond Formation Involved in the Biosynthesis of Indolactam V.

Indolactam V, a known biosynthetic precursor of indolactam alkaloids, is the main pharmacophore of this family and exhibits potential protein kinase C activation. A key step in the biosynthesis of indolactam V is the formation of an indole-fused nine-membered lactam core by intramolecular C-N bond formation. In this work, we report a computational study of the unique cytochrome P450 TleB enzyme-catalyzed direct and selective C-H bond amination reaction that can generate indolactam V from the dipeptide N-methylvalyl-tryptophanol. By performing molecular dynamics simulations and quantum-mechanical/molecular-mechanical calculations, we revealed that the C-H bond amination involves one step of proton transfer from N1-H of the indole ring to the FeIV═O unit, one step of hydrogen abstraction of N13-H in the side chain of the substrate by the FeIV-OH unit, and diradical coupling, in which two conformational changes of the side chain of the substrate are necessary. In the enzyme-substrate complex of TleB, the N-H bond of the indole ring of the substrate forms a strong hydrogen bond with the FeIV═O unit in compound I, and the porphyrin radical cation accepts an electron from the substrate to form the closed-shell electronic configuration. Thus, compound I in the enzyme-substrate complex cannot be described as FeIV═O coupled to a porphyrin radical cation, which is different from those of other P450 enzymes. Besides, two stages of conformational changes of the side chains of the substrate may increase the relative energies of reaction intermediates by 10-12 kcal/mol. From the structure point of view, it is the rotatable long side chain of the substrate and the large flexible active pocket of TleB that make the intramolecular diradical coupling feasible. Our findings may provide useful information to further understand the Tleb-catalyzed intramolecular C-H bond amination and the other bio-catalyzed intramolecular diradical coupling.

Double Arylation of the Indole Side Chain of Tri- and Tetrapodal Tryptophan Derivatives Renders Highly Potent HIV-1 and EV-A71 Entry Inhibitors†.

We have recently described a new generation of potent human immunodeficiency virus (HIV) and EV-A71 entry inhibitors. The prototypes contain three or four tryptophan (Trp) residues bearing an isophthalic acid moiety at the C2 position of each side-chain indole ring. This work is now extended by both shifting the position of the isophthalic acid to C7 and synthesizing doubly arylated C2/C7 derivatives. The most potent derivative (50% effective concentration (EC50) HIV-1, 6 nM; EC50 EV-A71, 40 nM), 33 (AL-518), is a C2/C7 doubly arylated tetrapodal compound. Its superior anti-HIV potency with respect to the previous C2-arylated prototype is in consonance with its higher affinity for the viral gp120. 33 (AL-518) showed comparable antiviral activities against X4 and R5 HIV-1 strains and seems to interact with the tip and base of the gp120 V3 loop. Taken together, these findings support the interest in 33 (AL-518) as a useful new prototype for anti-HIV/EV71 drug development.

Enantioselective Total Synthesis of (+)‐Nordasycarpidone, (+)‐Dasycarpidone, and (+)‐Uleine

AbstractThe structure of uleine type alkaloids is characterized by the presence of a bridged tetracyclic hexahydro‐1H‐1,5‐methanoazocino[4,3‐b]indole ring system 1. Various strategies have been developed to access this polycyclic structural motif. We report herein a one‐step conversion of appropriately functionalized 1,3,4‐trisubstituted cyclopent‐1‐ene to 1 by way of an integrated oxidation/reduction/cyclization (iORC) process. This domino sequence, initiated by oxidative cleavage of cyclopentene ring, generated subsequently a cyclohexenone, an indole and a 1,3‐bridged piperidine ring through formation of one C−C and two C−N bonds. Compound 1 is subsequently converted to nordasycarpidone, dasycarpidone and uleine. The chirality of the molecule was introduced by enzymatic desymmetrization of commercially available meso cis‐3,5‐diacetoxy‐1‐cyclopentene.

Bisindole [3]arenes—Indolyl Macrocyclic Arenes Having Significant Iodine Capture Capacity

Bisindole [3]arenes—Indolyl Macrocyclic Arenes Having Significant Iodine Capture Capacity

Dithiolated peptides incorporating bis(tryptophan)s for cooperative mercury(II) binding

The indole side chain of tryptophan is a versatile π-donor that can participate in various types of cation-π interactions. An understanding of how it may contribute as an auxiliary binding group in mercury(II) complexes can provide valuable insights toward the design of effective chelators for optimal mercury immobilization. In this study, we investigate how the incorporation of two tryptophan residues in model dicysteinyl peptides might participate in peptide-mercury(II) complex stabilization. Two pentapeptides consisting of a Cys-Trp-Cys sequence motif containing a second tryptophan residue at the N-terminal (BT1) or C-terminal (BT2) were designed. An analogous cyclohexapeptide (BT3) was included to evaluate how tryptophan residues, restricted in constrained peptidic turn motifs, might take part in mercury(II) complexation. Their interactions with mercury(II) were investigated by spectroscopic methods and computational modeling. UV–vis studies indicate the formation of 1:1 dithiolated mercury(II) complex, which is corroborated by ESI-MS analysis. Spectroscopic studies reveal that the tryptophan indole group(s) in BT1 and BT3 can participate in mercury(II) cation-π interactions. Optimized 1:1 mercury(II)-BT3 structures indicate that both indole rings are very close to the mercury(II) coordination site and could stabilize it by shielding it from ligand exchange. These findings provide some useful insights toward use of aromatic donor groups as hydrophobic shields in designing more effective metal chelating agents.

Palladium-Catalyzed Aminocyclization-Coupling Cascades: Preparation of Dehydrotryptophan Derivatives and Computational Study.

Dehydrotryptophan derivatives have been prepared by palladium-catalyzed aminocyclization-Heck-type coupling cascades starting from o-alkynylaniline derivatives and methyl α-aminoacrylate. Aryl, alkyl (primary, secondary, and tertiary), and alkenyl substituents have been introduced at the indole C-2 position. Further variations at the indole benzene ring, as well as the C-2-unsubstituted case, have all been demonstrated. In the case of C-2 aryl substitution, the preparation of the o-alkynylaniline substrate by Sonogashira coupling and the subsequent cyclization–coupling cascade have been performed in a one-pot protocol with a single catalyst. DFT calculations have revealed significant differences in the reaction profiles of these reactions relative to those involving methyl acrylate or methacrylate, and between the reactions of the free anilines and their corresponding carbamates. Those calculations suggest that the nature of the alkene and of the acid HX released in the HX/alkene exchange step that precedes C–C bond formation could be responsible for the experimentally observed differences in reaction efficiencies.

Propargylamines in Pd/Cu-catalyzed tandem coupling-cyclization-N-deprotection in a single pot: Construction of N-unsubstituted vs N-sulfonyl indole ring

The Pd/Cu-catalyzed tandem coupling–cyclization-N-deprotection in a single pot (Method a) vs sequential coupling–cyclization under similar conditions (Method b) has been studied using propargylamine as a terminal alkyne under environmentally friendly conditions. The first sequence (Method a) was followed to afford the N-unsubstituted indoles when 2,2,2-trifluoro-N-(2-iodophenyl)acetamides were employed as halides whereas N-sulfonyl indoles were obtained following the second path (Method b) when 2-iodo sulfanilides were used as halides. A number of compounds based on either the framework indolo[2,3–b]quinoxaline-indole or a similar framework possessing a sulfonyl group at the indole nitrogen were obtained in good yield employing the Method a or b, respectively. While the study was carried out with the goal of accessing a library of indolo[2,3–b]quinoxaline-indole based small molecules of potential biological interest (especially as anti-tubercular agents) the generality/scope of Method a was expanded further via the synthesis of simpler indole derivatives using various other propargylamines as terminal alkynes.

Spirocyclizative Remote Arylcarboxylation of Nonactivated Arenes with CO 2 via Visible-Light-Induced Reductive Dearomatization

Spirocyclizative Remote Arylcarboxylation of Nonactivated Arenes with CO ₂ via Visible-Light-Induced Reductive Dearomatization

Enantioselective C–H Rutheniation for the Preparation of Tetrahydrocarbazoles and Cyclohepta[b]indoles

Key words ruthenium catalysis - chiral carboxylic acid - tetrahydrocarbazoles - C–H activation

New synthetic cannabinoids carrying a cyclobutyl methyl side chain: Human Phase I metabolism and data on human cannabinoid receptor 1 binding and activation of Cumyl-CBMICA and Cumyl-CBMINACA.

Synthetic cannabinoids (SCs) represent a large group of new psychoactive substances (NPS), sustaining a high prevalence on the drug market since their first detection in 2008. Cumyl-CBMICA and Cumyl-CBMINACA, the first representatives of a new subclass of SCs characterized by a cyclobutyl methyl (CBM) moiety, were identified in July 2019 and February 2020. This work aimed at evaluating basic pharmacological characteristics and human Phase I metabolism of these compounds. Human Phase I metabolites were tentatively identified by liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QToF-MS) of urine samples and confirmed by a pooled human liver microsome (pHLM) assay. The basic pharmacological evaluation was performed by applying a competitive ligand binding assay and a functional activation assay (GTPγS) using cell membranes carrying the human cannabinoid receptor 1 (hCB1 ). Investigation of the human Phase I metabolism resulted in the identification of specific urinary markers built by monohydroxylation or dihydroxylation. Although Cumyl-CBMICA was primarily hydroxylated at the indole ring, hydroxylation of Cumyl-CBMINACA mainly occurred at the CBM moiety. Both substances acted as agonists at the hCB1 receptor, although substantial differences could be observed. Cumyl-CBMINACA showed higher binding affinity (Ki = 1.32 vs. 29.3 nM), potency (EC50 = 55.4 vs. 497 nM), and efficacy (Emax = 207% vs. 168%) than its indole counterpart Cumyl-CBMICA. This study confirms that substitution of an indole by an indazole core tends to increase in vitro potency, which is potentially reflected by higher in vivo potency. The emergence and disappearance of SCs distributed via online shops carrying a CBM moiety once more demonstrate the "cat-and-mouse" game between manufacturers and legislation.

Structural understanding of 5-(4-hydroxy-phenyl)-N-(2-(5-methoxy-1H-indol-3-yl)-ethyl)-3-oxopentanamide as a neuroprotectant for Alzheimer’s disease

In our continuing efforts to develop novel neuroprotectants for Alzheimer’s disease (AD), a series of analogs based on a lead compound that was recently shown to target the mitochondrial complex I were designed, synthesized and biologically characterized to understand the structure features that are important for neuroprotective activities. The results from a cellular AD model highlighted the important roles of the 4-OH on the phenyl ring and the 5-OCH3 on the indole ring of the lead compound. The results also demonstrated that the β-keto moiety can be modified to retain or improve the neuroprotective activity. Docking studies of selected analogs to the FMN site of mitochondrial complex I also supported the observed neuroprotective activities. Collectively, the results provide further information to guide optimization and development of analogs based on this chemical scaffold as neuroprotectants with a novel mechanism of action for AD.

BMS Derivatives C7-Linked to β-Cyclodextrin and Hyperbranched Polyglycerol Retain Activity against R5-HIV-1NLAD8 Isolates and Can Be Deemed Potential Microbicides.

Amides from indole-3-glyoxylic acid and 4-benzoyl-2-methylpiperazine, which are related to entry inhibitors developed by Bristol-Myers Squibb (BMS), have been synthesized with aliphatic chains located at the C7 position of the indole ring. These spacers contain an azido group suitable for the well-known Cu(I)-catalyzed (3+2)-cycloaddition or an activated triple bond for the nucleophilic addition of thiols under physiological conditions. Reaction with polyols (β-cyclodextrin and hyperbranched polyglycerol) decorated with complementary click partners has afforded polyol-BMS-like conjugates that are not cytotoxic (TZM.bl cells) and retain the activity against R5-HIV-1NLAD8 isolates. Thus, potential vaginal microbicides based on entry inhibitors, which can be called of 4th generation, are reported here for the first time.

SH-1028, An Irreversible Third-Generation EGFR TKI, Overcomes T790M-Mediated Resistance in Non-Small Cell Lung Cancer.

SH-1028 is an irreversible third-generation EGFR TKI. Both SH-1028 and osimertinib have a pyrimidine structure (a typical mutant-selective EGFR TKI structure). Compared with osimertinib, SH-1028 is modified on the indole ring, thus resulting in a more stable 6,7,8,9-tetrahydro-pyrrolo [1, 2-a] indol structure. In this study, we explored the anti-tumor effect of SH-1028 in vitro and in vivo, the inhibition of cell signal, such as EGFR and ERK phosphorylation, and verified the relationship between the pharmacokinetics and pharmacodynamic responses. Firstly, SH-1028 selectively inhibited EGFR sensitive and resistant mutations, with up to 198-fold more effective compared with wild-type EGFR cells. Then, in mouse xenograft models, oral administration of SH-1028 at a daily dose of 5 mg/kg significantly inhibited proliferation of tumor cells with EGFR sensitive mutation (exon 19 del) and resistant mutation (T790 M) for consecutive 14 days, with no TKI-induced weight loss. Moreover, SH-1028 exhibited good bioavailability, and was distributed extensively from the plasma to the tissues. The main metabolite of SH-1028, Imp3, was tested and showed no wild-type EGFR inhibition or off-target effects. In conclusion, SH-1028 is a new third-generation EGFR inhibitor that exhibits potent activity against EGFR sensitive and resistant (T790 M) mutations.

Au(I)-Catalyzed Pictet-Spengler Reactions All around the Indole Ring.

Au(I) complexes catalyze iso-Pictet-Spengler reactions. Ethylamine or methylamine chains were introduced at C2, C4, or the nitrogen atom of the indole ring, and the corresponding substrates were reacted in the presence of aldehydes and catalytic amounts of Au(I) complexes, leading to a variety of polycyclic scaffolds. Selectivity could be achieved in the course of a double iso-Pictet-Spengler reaction involving two successive aldehydes, leading to highly complex molecules.

Supersized Indoles by Gold-Catalyzed [8+2]-Cycloadditions

Supersized Indoles by Gold-Catalyzed [8+2]-Cycloadditions

Crystal structure of (R)-6-(benzo[b]thiophen-5-yl)-2-methyl-2,6-dihydrobenzo [5,6] silino[4,3,2-cd]indole, C23H17NSSi

Abstract C23H17NSSi, orthorhombic, P212121 (no. 19), a = 7.7862(5) Å, b = 9.0728(6) Å, c = 25.3797(16) Å, V = 1792.9(2) Å3, Z = 4, R gt (F) = 0.0301, wR ref (F 2) = 0.0778, T = 100.0 K.

Synthesis of 5-[(1H-indol-3-yl)methyl]-1,3,4-oxadiazole-2(3H)-thiones and their protective activity against oxidative stress.

A small library of 2-[(1H-indol-3-yl)methyl]-5-(alkylthio)-1,3,4-oxadiazoles was prepared, starting from indole-3-acetic acid methyl ester and its 5-methyl-substituted derivative. The synthetic route involved the formation of intermediate hydrazides, their condensation with carbon disulfide, and intramolecular cyclization to corresponding 5-[(1H-indol-3-yl)methyl]-1,3,4-oxadiazole-2(3H)-thiones. The latter were then S-alkylated, and in case of ester derivatives, they were further hydrolyzed into corresponding carboxylic acids. All 5-[(1H-indol-3-yl)methyl]-1,3,4-oxadiazole-2(3H)-thiones and their S-alkylated derivatives were then screened for their protective effects in vitro and in vivo. Methyl substitution on the indole ring and propyl, butyl, or benzyl substitution on sulfhydryl group-possessing compounds were revealed to protect Friedreich's ataxia fibroblasts against the effects of glutathione depletion induced by the γ-glutamylcysteine synthetase inhibitor, buthionine sulfoximine. Two of the active compounds also reproducibly increased the survival of Caenorhabditis elegans exposed to juglone-induced oxidative stress.