M. Mohideen, N.A. Kamaruzaman, M.A. Hamali et al.
Journal of Molecular Structure 1243 (2021) 130771
Peganum harmala is a plant traditionally used as an abor-
tifacient agent and an emmenagogue for many years [8]. Pre-
viously, β-carboline compounds isolated from the seeds of Pe-
ganum harmala (Family: Zygophyllaceae) were reported to pos-
sess a planar tricyclic pyrido [3,4-β] indole ring system [9]. Pre-
vious studies have shown that the alkaloids in these seeds are
mostly β-carbolines (harmine, harmane, harmalol, and harma-
line) [10]. In addition to their occurrence in plants, β-carbolines
are also endogenously synthesized in mammals from tryptophan-
derived indoleamines and tryptophan [11]. These compounds’
pharmacological effects are varied and possess a broad range
of bioactivities, including anticonvulsant, hallucinogenic, antitu-
mor, antiviral, antibacterial, and antiparasitic [12,13]. In particu-
lar, these β-carboline molecules are known to induce apoptosis
and inhibit cancer cell proliferation [14] through multiple mech-
anisms of action such as inhibition of DNA-topoisomerase-I & -
II [15,16], cyclin-dependent kinases (CDKs) [17,18], Polo-like ki-
nases (PLKs) [19,20] and interaction with DNA, specifically by in-
tercalation with DNA or by binding through the minor groove
vapours to monitor the reactions’ progress to certify the purity of
the reaction products.
2.2. Synthesis
2.2.1. Procedure for the synthesis of intermediates 2 and 3
According to the previously published method, intermediate
2 was synthesized in good yield using Pictet-Spengler cycliza-
tion [34,35]. The reaction involved L-tryptophan (1) in the pres-
ence of the formaldehyde afforded the corresponding diastereoiso-
meric mixture 1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (2).
The synthesis of aromatic β-carbolines (3) involves
a simple
method using sequential decarboxylation and aromatization of
1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (2) with 10 mol%
of CuCl2 without any catalyst [36]. Thus, a convenient protocol for
the synthesis of aromatic β-carbolines (3) via copper(II)-mediated
decarboxylation and subsequent aromatization of tetrahydro-β-
carboline acid intermediate 2 in the absence of a ligand/catalyst
was developed. This sequence of reactions can be easily scaled up
to produce enough compounds for further transformations.
[
21–27]. In addition, recent reports indicated that these com-
pounds also inhibit protein synthesis translation and DNA pho-
tocleavage [28,29]. On top of this, due to the presence of aro-
matic planar tricyclic nucleus, β-carbolines could intercalate DNA
by stacking between DNA base pairs [21,24]. This capability has
further strengthened the rationale of targeting β-carbolines struc-
ture in discovering novel anticancer agents as doxorubicin and
dactinomycin, two well-known anticancer drugs for Hodgkin’s
sarcoma and Ewing’s sarcoma treatment, are DNA intercalating
agents [30].
2.2.2. General procedure for the synthesis of compounds 4a-h
Compounds 4a-h were synthesized according to the modified
reported procedure [37]. A mixture of β-carbolines (3, 0.2 g, 5.0
mmol) and anhydrous DMF (12.5 mL) was stirred at room temper-
ature for 10 minutes. 60% NaH (7.5 mmol) and substituted ben-
zyl bromide (10.0 mmol) were added. The mixture was heated
for 3 hrs at 60°C than continued with refluxed for 5 hrs. Upon
completion, the solution was poured into ice-cold water (H O,
2
In continuing our efforts in developing β-carbolines as signifi-
cant anticancer agents [31–33], the present study aimed to design
100 mL) and extracted with ethyl acetate (2 × 100 mL). The
combined organic layers were washed with water, brine, dried
over anhydrous sodium sulphate, filtered and evaporated to af-
ford compounds 4a-h as solid powder/crystals. Pure compounds
4a-h were obtained from recrystallization using ethanol. Phys-
ical properties, FT-IR, NMR, Mass and Elemental analysis data
for compounds 4a-h have been placed in the supplementary
file.
2
9
and synthesize a series of novel N ,N -bis(substituted benzyl)-β-
carbolineum bromides. Meanwhile, evaluation of their in-vitro cy-
totoxicity profile on selected human cancer or non-cancer cell lines
and comparison of their cytotoxicity profile with known anticancer
drugs were also conducted. In addition, we report for the first time,
single X-ray crystal structure of compound 4f and its orientation
that binds to the DNA complex. In order to understand the molec-
ular interaction of compound 4f with its macromolecular target,
the molecular docking technique was performed to provide a clear
view of molecular interaction between drug and DNA. The theoret-
ical results were compared with experimental data and are found
in good agreement.
2.3. Single-crystal X-ray diffraction (XRD) study of compound 4f
A supersaturated solution was prepared by dissolving com-
pound 4f in ethanol at ambient temperature. The prepared solu-
tion was slightly warmed and allowed to evaporate slowly at room
temperature. After seven days, good quality transparent crystal ap-
peared were allowed to grow to a maximum possible dimension
and then harvested. The single crystal obtained was used for X-ray
diffraction studies.
2. Materials and Methods
2
.1. General
A crystal of the compound 4f suitable for an X-ray diffrac-
tion study, with needle habit and having appropriate dimensions
of 0.25 mm × 0.17 mm × 0.10 mm, was glued to glass fiber
mounted on a Bruker APEX II Duo CCD diffractometer. The diffrac-
tion data were collected at temperature 100 K using graphite
All reagents used in this study were purchased from Aldrich
Co. Ltd. and used directly without further purifications. Melt-
ing point of synthesized compounds was determined using Stu-
art SMP 20 Melting Point B-545 apparatus and was uncorrected.
Fourier-transform infrared (FT-IR) spectra were recorded on a Nico-
let 6700 FT-IR spectrometer (Thermo Scientific, MA, USA) in the
˚
monochromated Mo-Kα radiation (λ = 0.71073 A) at a sample-
to-detector distance of
5 cm with APEX2 software [38]. The
data integration and reduction were carried out with SAINT soft-
ware, and the empirical absorption corrections were applied to
the collected reflections with SADABS program [38]. The com-
plex’s structure was solved by direct methods and refined us-
ing a full-matrix least-squares method on F2 using the SHELXTL
program [39]. All non-hydrogen atoms were refined anisotropi-
cally. All hydrogen atoms were placed in calculated positions with
mid-IR region (400-4,000 cm 1) using Attenuated Total Reflection
−
ATR) technique. 1D ( H- and 13C-) and 2D (DEPT90, DEPT135,
1
(
COSY, HSQC, HMBC) NMR spectra were recorded on Bruker AV 500
MHz and 125 MHz instruments in CDCl . The chemical shifts (δ)
3
were reported in ppm relative to the TMS as internal standard
and J values were reported in Hertz. The electrospray ionization
mass spectrometry (ESI-MS) was recorded on an LC-MS THERMO
QUEST Finnigan LCQ DUO system. Elemental analysis (CHN) was
conducted using Thermo Finnigan Flash EA 1112 elemental ana-
lyzer. Thin-layer chromatography (TLC) was performed on glass
plates coated with silica gel G254 (e-Merck) and exposed to iodine
˚
C–H = 0.93 and 0.97 A and refined using a riding model with
iso
U
(H) = 1.2Ueq(C). Data for publication were prepared by us-
ing SHELXTL [39] and PLATON [40]. Details of the data collections
condition and the parameters of the refinement process are sum-
marized in Table 1. Atomic coordinates, thermal parameters and
2
Hamali, Muhamad Azwan
