Synthesis, antimicrobial activity and molecular docking of novel tetracyclic scaffolds incorporating a flavonoid framework with medium sized oxygen heterocycles

Article abstract of DOI:10.1016/j.bmcl.2014.12.066

A convenient approach for the synthesis of novel tetracyclic scaffolds incorporating a flavonoid framework with medium sized heterocyclic rings (eight-, nine-, ten- and eleven-membered rings) containing two oxygen atoms from flavonols through alkylation using different dibromoalkanes was described. The synthesized compounds were established based on the spectral data and X-ray crystal structure for 6c. The synthesized compounds were evaluated for their in vitro antimicrobial activity. Docking studies were carried out for most active two compounds 6f and 6i.

Full text of DOI:10.1016/j.bmcl.2014.12.066

Accepted Manuscript
Synthesis, antimicrobial activity and molecular docking of novel tetracyclic
scaffolds incorporating a flavonoid framework with medium sized oxygen het-
erocycles
Dongamanti Ashok, Aamate Vikas Kumar, Devulapally Mohan Gandhi, Gundu
Srinivas, Kotni Meena Kumari, Manga Vijjulatha, Sridhar Balasubramanian,
Prasad Ernala
PII:
S0960-894X(14)01374-2
DOI:
http://dx.doi.org/10.1016/j.bmcl.2014.12.066
BMCL 22311
Reference:
Bioorganic & Medicinal Chemistry Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
12 July 2014
8 December 2014
19 December 2014
Please cite this article as: Ashok, D., Kumar, A.V., Gandhi, D.M., Srinivas, G., Kumari, K.M., Vijjulatha, M.,
Balasubramanian, S., Ernala, P., Synthesis, antimicrobial activity and molecular docking of novel tetracyclic
scaffolds incorporating a flavonoid framework with medium sized oxygen heterocycles, Bioorganic & Medicinal
Chemistry Letters (2014), doi: http://dx.doi.org/10.1016/j.bmcl.2014.12.066
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Synthesis, antimicrobial activity and molecular docking of novel tetracyclic
scaffolds incorporating a flavonoid framework with medium sized oxygen
heterocycles
Dongamanti Ashok,a,* Aamate Vikas Kumar,a Devulapally Mohan Gandhi,a Gundu Srinivas,a
Kotni Meena Kumari,b Manga Vijjulatha,b Sridhar Balasubramanian,c and Prasad Ernalad
aDepartment of Chemistry, Osmania University, Hyderabad-500 007.
b Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College
of Science, Osmania University, Hyderabad-500 007.
cLaboratory of X-ray, CSIR-Indian Institute of Chemical Technology, Hyderabad-500 007.
dMedicinal Chemistry and Pharmacology Division, CSIR-Indian Institute of Chemical Technology,
Hyderabad-500 007.
∗ Corresponding author Tel.: +91-9391024769; e-mail: ashokdou@gmail.com.
A convenient approach for the synthesis of novel tetracyclic scaffolds incorporating a flavonoid
framework with medium sized heterocyclic rings ( eight-, nine-, ten- and eleven-membered rings )
containing two oxygen atoms from flavonols through alkylation using different dibromoalkanes was
described. The synthesized compounds were established based on the spectral data and X-ray crystal
structure for 6c. The synthesized compounds were evaluated for their in vitro antimicrobial activity.
Docking studies were carried out for most active two compounds 6f and 6i.
Keywords: Flavonoid framework, Medium sized rings, Antimicrobial activity, Molecular docking
Medium sized heterocyclic rings are commonly found structural units within the frame work of a
variety of natural products and is the main reason for the growing importance of such class of
compounds.1 In particular synthesis of medium sized heterocyclic rings bearing oxygen or nitrogen
atom(s) are important synthetic targets for organic chemists as they are integral parts of many
medicinally interesting synthetic compounds. However synthesis of medium sized heterocyclic rings
continues to be one of the fascinating endeavours in organic chemistry because of challenges involved
in their synthesis.2 Moreover for an equal number of atoms, cyclic analogues inherently possess a
lower number of rotatable bonds than their acyclic analogues. As a result cyclic counterparts are
more conformationally restricted than their acyclic analogues, which potentially can impart higher
target binding and selectivity and improved oral bioavailability.3 Flavonoid framework is medicinally
important structural organization present in many bioactive molecules showing various activities like
antiviral, antibacterial, antiprotozoal, oestrogenic, anti-inflammatory, mutagenic, antimutagenic and
antineoplastic activities, and is also capable of inhibiting many types of enzymes.4-6 Therefore there
has been increasing interest in the synthesis of diverse classes of compounds containing flavonoid
frame work.
Among numerous known heterocycles containing flavonoid framework, artelastocarpin and
carpelastofuran (Figure 1) have attractive frameworks because of their reported cytotoxic properties.7
1

Figure 1 Bioactive molecules of interest
Inspired by the growing importance of medium sized heterocyclic rings and the wide range of
biological importance of heterocycles containing flavonoid framework, we have devised a synthesis
for the construction of novel tetracyclic ring systems incorporating a flavonoid framework with
medium sized oxygen heterocycles and further evaluated their antimicrobial activity.
Figure 2 Proposed tetracyclic scaffolds
The retro-synthetic sequence of required tetracyclic medium sized heterocyclic rings is shown in
Scheme 1.
Scheme 1 Retro-synthetic strategy
2

Accordingly the required tetracyclic scaffolds were synthesized in three steps. Claisen-Schmidt
condensation of substituted 2-hydroxyacetophenones 1a-d and salicylaldehyde 2 in presence of
potassium hydroxide gave corresponding chalcones 3a-d (Scheme 2).8 Chalcones were converted to
corresponding flavonols 4a-d by treatment with alkaline hydrogen peroxide.9, 10
Scheme 2 Synthesis of 3-Hydroxy-2-(2-hydroxyphenyl)-4H-chrome-4-ones
Thus obtained substituted 3-Hydroxy-2-(2-hydroxyphenyl)-4H-chrome-4ones 4a-d were treated with
dibromoalkanes 5a-d in the presence of anhydrous potassium carbonate at 80oC for 8 hours in DMF
under N2 atmosphere provided required tetracyclic compounds 6a-p in moderate to good yields (58-
80%).
3

Scheme 3 Synthesis of tetracyclic compounds. aIsolated yields
All the compounds synthesized were well characterized by spectral (NMR, MS, IR) data, the
molecular structure of 6c was characterized by X-ray crystallography (CCDC 972844), 11 as shown in
Figure 3.
4

Figure 3 A view of AT78, showing the atom-labelling Scheme of compound 6c. Displacement
ellipsoids are drawn at the 30% probability level and H atoms are represented by circles of arbitrary
radii.
Scheme 4 Representative mechanism of ring closure reaction for synthesis of compound 612
5

The antibacterial activity of the precursor’s 4a-d and synthesized tetracyclic compounds 6a-p were
tested for their in vitro antibacterial activity against Bacillus subtilis (ATCC 6633), Staphylococcus
aureus (ATCC 25923), Escherichia coli (ATCC 10536), Pseudomonas aeruginosa (ATCC 10145)
and Klebsiella pneumonia (ATCC 10031). The results of the antibacterial screening were compared
with the standard antibacterial drug gentamicin sulfate. The minimum inhibitory concentrations
(MICs) and minimum bactericidal concentrations (MBCs) are reported in Table 1 and Table 2
respectively. As observed from Table 1, the inhibitory efficiency of tetracyclic compounds was
higher than their acyclic precursor’s. Among newly synthesized compounds, the inhibitory efficiency
of compound 6f against Gram-negative bacteria, Klebsiella pneumonia, compounds 6f, 6h and 6k
against Escherichia coli were close to those of standard (MIC = 0.025-0.032 µM). In the case of
Gram-positive bacteria, the inhibitory efficiency of compounds 6e and 6l against Bacillus subtilis,
compounds 6e and 6i against Staphylococcus aureus were close to those of standard (MIC = 0.027-
0.033 µM). It was observed that compound 6f exhibited broad spectrum of antibacterial activity as the
observed MIC values against all the tested strains were below 0.050 µM. All other compounds
showed slightly higher MIC values. The antibacterial activity study results revealed that tetracyclic
compounds with bromo substitution showed promising antibacterial activity compared to other
substituted tetracyclic compounds.
We have also tested the antifungal activity of these tetracyclic compounds against two fungal strains,
Candida albicans (ATCC 10231) and Candida tropicalis (ATCC 750). The results of the antifungal
screening were compared with standard antifungal drug fluconazol. However all the tetracyclic
compounds were ineffective against the tested fungal strains up to a concentration of 200 µg/mL.
6

Table 1 Antimicrobial activity (MICs in µMa)
a The MIC values are interpreted as an average of triplets. MIC: minimum inhibitory concentration
(the lowest concentration that inhibited the bacterial growth)
7

Table 2 Antimicrobial activity (MBCs in µM)
MBC: minimum bactericidal concentration (the lowest concentration at which no
bacterial growth was observed).
In order to give an explanation and understanding of the most potent compounds 6f against bacteria
Escherichia coli and 6i against bacteria Staphylococcus aureus, docking studies into the crystal
structure of Escherichia coli KAS III and Staphylococcus aureus KAS III was performed. β-ketoacyl
carrier protein synthase (KAS) III is a condensing enzyme that initiates fatty acid biosynthesis in most
bacteria and is a key target enzyme to overcome the antibiotic resistance problem. Molecular basis of
interactions between target enzyme and synthesized ligands can be understood with the help of
docking analysis and interactions as represented in figures 4 and 5. It is pertinent to note that the more
active compounds 6f and 6i showed good docking interactions figures 4 and 5 for Escherichia coli
KAS III and Staphylococcus aureus KAS III respectively. Glide predictions revealed that the
flavonoid derivatives are having greater binding affinity with the KAS III. These in silico findings are
well supported by results of antibacterial activity. The binding patterns of compound 6f in
Escherichia coli KAS III and compound 6i in Staphylococcus aureus KAS III were depicted in
figures 4 and 5 respectively and clearly revealed that the aliphatic ring with oxygens and the aromatic
moiety with –C=O showed binding interactions with Arg151 as seen for Escherichia coli KAS III
with compound 6f and the same aliphatic ring with oxygen of compound 6i showed binding
interaction with Ser152 of Staphylococcus aureus KAS III.
8

Figure 4 Binding pose of compound 6f within the Escherichia coli KAS III (1MZS) active site,
compound 6f shown in green colour with oxygens in red
Figure 5 Binding pose of compound 6i within the Staphylococcus aureus KAS III (1ZOW) active
site, compound 6i shown in orange colour with oxygens in red.
In summary, we have developed an easy synthetic strategy for the synthesis of novel tetracyclic
scaffolds incorporating a flavonoid framework with medium sized heterocyclic rings containing two
oxygen atoms with moderate to good yields. The reaction protocol requires cheap starting materials
and is carried out under mild conditions. The utility of this strategy has been demonstrated by
synthesizing a wide variety of tetracyclic derivatives. All the compounds were evaluated for their in
9

vitro antimicrobial activity, compounds 6e, 6f, 6h, 6i, 6k and 6l were found to be promising with MIC
values in the range of 0.027-0.033 µM indicating their potential as novel antibacterial agents. Fitness
of most active compounds 6f against bacteria Escherichia coli and 6i against bacteria Staphylococcus
aureus into the crystal structure of Escherichia coli KAS III and Staphylococcus aureus KAS III was
studied using in silico tools. Overall, the tetracyclic framework presented here could be an attractive
template for the identification of novel antibacterial agents.
Acknowledgements
The authors thank The Head, Department of Chemistry, Osmania University, Hyderabad for
providing laboratory facilities. AVK thank CSIR for PhD fellowship. We thank CFRD analytical team
for providing spectral analysis facilities.
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Synthesis, antimicrobial activity and molecular docking of novel
tetracyclic scaffolds incorporating a flavonoid framework with
medium sized oxygen heterocycles
Dongamanti Ashok,*a Aamate Vikas Kumar,a Devulapally Mohan Gandhi,a Gundu Srinivas,a Kotni
Meena Kumari,b Manga Vijjulatha,b Sridhar Balasubramanian,c and Prasad Ernalad
11