Synthesis, molecular modelling studies of indolyl chalcone derivatives and their antimalarial activity evaluation

Article abstract of DOI:10.1080/14786419.2019.1696788

Twenty one chalcone derivatives were synthesized using Claisen-Schmidt condensation, their antimalarial activity against Plasmodium falciparum was determined and quantitative structure–activity relationship (QSAR) was developed. Condensation of substituted acetophenones with various aromatic aldehydes at room temperature gave chalcones in 75–96% yield. Chalcones are secondary metabolites of terrestrial plants, precursors for the biosynthesis of flavonoids and exhibit various biological activities. Antiplasmodial IC₅₀ (half-maximal inhibitory concentration) activity of a compound against malaria parasites in?vitro provides a good first screen for identifying the antimalarial potential of the compound. The most active compound was Trans-3-(1H-indol-3-yl)-1-(2’-hydroxyphenyl)-2-propen-1-one(1b) with IC₅₀ of 2.1 μM/L. Molecular mechanism was explored through in silico docking & ADMET studies for the active compounds.

Full text of DOI:10.1080/14786419.2019.1696788

Natural Product Research
Formerly Natural Product Letters
ISSN: 1478-6419 (Print) 1478-6427 (Online) Journal homepage: https://www.tandfonline.com/loi/gnpl20
Synthesis, molecular modelling studies of indolyl
chalcone derivatives and their antimalarial activity
evaluation
Jyoti, Rashmi Gaur, Yogesh Kumar, Harveer Singh Cheema, Deepak Singh
Kapkoti, Mahendra P. Darokar, Feroz Khan & Rajendra Singh Bhakuni
To cite this article: Jyoti, Rashmi Gaur, Yogesh Kumar, Harveer Singh Cheema, Deepak
Singh Kapkoti, Mahendra P. Darokar, Feroz Khan & Rajendra Singh Bhakuni (2019): Synthesis,
molecular modelling studies of indolyl chalcone derivatives and their antimalarial activity evaluation,
Natural Product Research, DOI: 10.1080/14786419.2019.1696788
To link to this article: https://doi.org/10.1080/14786419.2019.1696788
View supplementary material
Published online: 04 Dec 2019.
Submit your article to this journal
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at
https://www.tandfonline.com/action/journalInformation?journalCode=gnpl20

NATURAL PRODUCT RESEARCH
https://doi.org/10.1080/14786419.2019.1696788
Synthesis, molecular modelling studies of indolyl
chalcone derivatives and their antimalarial
activity evaluation
a
a†
b
c
Ã
Jyoti , Rashmi Gaur , Yogesh Kumar , Harveer Singh Cheema , Deepak Singh
Kapkoti, Mahendra P. Darokarc, Feroz Khanb and Rajendra Singh Bhakunia
aMedicinal Chemistry Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow,
b
India; Structural Biology Department, CSIR-Central Institute of Medicinal and Aromatic Plants,
c
Lucknow, India; Molecular Bio-Prospection Department Metabolic, CSIR-Central Institute of
Medicinal and Aromatic Plants, Lucknow, India
ABSTRACT
ARTICLE HISTORY
Received 19 June 2019
Accepted 14 November 2019
Twenty one chalcone derivatives were synthesized using
Claisen-Schmidt condensation, their antimalarial activity against
Plasmodium falciparum was determined and quantitative struc-
ture–activity relationship (QSAR) was developed. Condensation of
substituted acetophenones with various aromatic aldehydes at
room temperature gave chalcones in 75–96% yield. Chalcones are
secondary metabolites of terrestrial plants, precursors for the bio-
synthesis of flavonoids and exhibit various biological activities.
Antiplasmodial IC50 (half-maximal inhibitory concentration) activity
of a compound against malaria parasites in vitro provides a good
first screen for identifying the antimalarial potential of the
compound. The most active compound was Trans-3-(1H-indol-3-
yl)-1-(2’-hydroxyphenyl)-2-propen-1-one (1b) with IC50 of 2.1 mM/L.
Molecular mechanism was explored through in silico docking &
ADMET studies for the active compounds.
KEYWORDS
Chalcones; in-vitro;
antimalarial activity;
P. falciparum; QSAR
CONTACT Rajendra Singh Bhakuni
Both the authors contribute equally.
bhakunirs2000@gmail.com
Ã
#Present address: Natural Products Laboratory, International Joint Laboratory of Tea Chemistry and Health Effects,
State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, People’s Republic
of China.
Supplemental data for this article can be accessed at https://doi.org/10.1080/14786419.2019.1696788.
ß 2019 Informa UK Limited, trading as Taylor & Francis Group

2
JYOTI ET AL.
1. Introduction
Malaria, one of the most devastating infectious diseases, affects almost half of the glo-
bal population and poses a major socioeconomic hazard to humanity at large (World
Malaria Report 2018). The above grim scenario is further aggravated by the persistent
tendency of Plasmodium falciparum, the most common malaria parasite, to rapidly
develop resistance against any newly introduced drug (Klayman 1985; Luo and Shen
1987). In fact some recent reports have already indicated tolerance of this parasite
toward artemisinin and its derivatives (Naß and Efferth 2019), the current World
Health Organization reports the guidelines for treatment of chloroquine (CQ) resistant
malaria (Geneva: World Health Organization 2015).
Indole and its derivatives represent one of the most active class of compounds
possessing a wide spectrum of antiparasitic activities (Butcher et al. 2000; Enserink
2000; Gardner et al. 2000; Rastelli et al. 2000; Shrivastava and Chauhan 2001; Ursos
and Roepe 2002; Kumar et al. 2003a, 2003b). Some of the individual compounds
having nitrogen in their ring which is responsible for the antimalarial activity are
pyrimethamine (I) and apicidin (II) (Figure 1). Pyrimethamine is an antiparasitic
drug used for treating Toxoplasma gondii and other plasmodia infections. Indole
alkaloids as apicidin (II) have shown potent antimalarial activity against P. falcip-
arum. Apicidin is known to be a potent inhibitor of HDAC (histone deacetylase), a
nuclear enzyme that regulates gene transcription and the assembly of newly syn-
thesized chromatin. Apicidin reversibly induces histone hyperacetylation, causing
altered transcriptional regulation and ultimately cell death. Studies on apicidin have
suggested that the indole region is a key constituent of enzyme binding and HDAC
activity (Singh et al. 1996; Colletti et al. 2001). Compounds, which act on more than
one target sites are more liable to be active. Keeping in view all of the above facts
we have synthesized chalcone derivatives containing indole (HDAC inhibitor).
Antimalarial drugs as quinine, mefloquine, have piperidine nucleus and amopyro-
quine, cycloquine have pyrrolidine moiety. A large number of compounds having
piperidine, pyrrolidine, piperazine and morpholine moiety have shown potent anti-
malarial activity (Delarue et al. 2001; Ryckebusch et al. 2003; Brinner et al. 2005).
These results prompted us to synthesize compounds having indole moiety. As part
of our ongoing programme devoted to the synthesis of chalcone derivatives as anti-
diabetic (Gaur et al. 2014), antimicrobial (Gaur et al. 2015), anticancer (Gaur et al.
2015) and anti-TBagents (Gaur et al. 2015). This communication describes the syn-
thesis of substituted indoles 1a-1j, 2a-2k as antimalarial agents.
In continuation of our work published in Gaur et al. 2015, in the present study, we
have synthesized two different series (Figure 2) of novel indolyl chalcones 1a-1j
(Scheme 1) and 2a-2k (Scheme 2) and evaluated their in vitro antimalarial activity.
2. Results and discussions
General methods for the preparation of chalcones involve Claisen-Schmidt condensa-
tion of appropriate aryl methyl ketones and aldehydes in presence of acid or base
(Delarue et al. 2001; Ryckebusch et al. 2003; Brinner et al. 2005). We have prepared
both series of indolyl chalcones by using afore mentioned reference conditions in

NATURAL PRODUCT RESEARCH
3
I
II
Figure 1. Anti-malarial drugs having nitrogen ring: Pyrimethamine (I) aromatic nitrogen ring;
Apicidin (II) indole ring.
good yields. Indolyl chalcones 1a-j were prepared by the reaction of appropriate
acetophenone 4 with indol-3-carboxaldehyde 5 in the presence of NaOH at RT
(Scheme 1) (Bhagat et al. 2006; Srinivasan et al. 2009). Indolyl chalcones 2a-k were
prepared by the reaction of 3-acetylindole 6 with appropriate aldehyde 7 in the
presence of SOCl2 (Scheme 2) (Jeong et al. 2004; Gaur et al 2015). Acetophenones
(4d, 4e, 4h) for the preparation of the compounds 1d, 1e and 1h were prepared
by etherification of p-hydroxy (3d), m,p-hydroxy (3e) and p-hydroxy (3h) acetophe-
nones respectively with allyl bromide in the presence of KBr in acetone using
refluxing condition.
Among all the twenty one compounds tested, four compounds, 1b, 1d, 1e, 1f and
2k showed MIC below 3 mM/L and 1b was most active with IC50 2.1 mM/L, while five
compounds, 1a, 1c, 2b, 2d, 2e, have shown MIC below 6 mM/L. Only the compound
2k having thiophene ring showed MIC 2.8 mM/L. Most of the compounds of series 2
showed MIC more than 12 mM/L. All the compounds, of series 1 having electron
donating group in the ring showed better activity than compounds of series 2. These
results emphasize the better efficacy of series 1 compounds over series 2 compounds
in antimalarial activity (Supplementary material, Table S1).
All these indolyl chalcones were assayed for their in vitro antimalarial activity
against P. falciparum, NF54 strain. Varying the substituents on the phenyl ring of
series 2 chalcone derivatives in which ketone group of a,b-unsaturated chalcone is
near indole ring, have no significant effect on the activity, while substitution at the
second position of phenyl ring of series 1 chalcone derivatives plays a crucial role
in exerting antimalarial activity, in which double bond of a,b-unsaturated chalcone
is near indole ring. On introducing hydroxyl group at position 2 of phenyl ring of
1b showed good antimalarial activity with IC50 2.1 mM/L. On introducing ether group
with OH group activity dropped to 2.5 mM/L. On the removal of the hydroxyl group
the activity dropped to 2.6 mM/L. These results emphasize the better efficacy
of hydroxyl group over ether group in series 1 chalcone derivatives for antimalarial
activity.

4
JYOTI ET AL.
O
O
R
R
N
H
N
H
1
2
Series 1.
Series 2
Figure 2. Indole Chalcones skeleton; Series 1 and Series 2.
R1
R1
O allyl bromide/
acetone/600C/
O
CH3
CH3
reflux
3d. R1= p-OH
3e. R1= o,p-OH
3h. R1= m-OH
4d. R1= p-OCH2=CH2
4e. R1= o-OH, p-OCH2=CH2
4h. R1= p-OCH2=CH2
OHC
O
NH
+
R
N
H
R
CH
3
O
5
4
1
Scheme 1. Reagents and conditions: NaOH, methanol, 1–15 h, RT.
O
R
H3C
HN
RCHO
+
N
H
O
2
6
7
Scheme 2. Reagents and conditions: SOCl2, methanol, 1–2 h, RT.
2.1. Molecular docking study
During docking study a series of bioactive chalcone derivatives were screened for
the inhibitory effects in P. falciparum by targeting the best characterized plasmodium
cysteine protease (Falcipain-2) of papain family, consequently this family of enzymes
is a potential target for antimalarial drugs. Falcipain-2 is one of the key haemoglo-
binases of erythrocytic parasite, playing an essential role in the degradation of human

NATURAL PRODUCT RESEARCH
5
haemoglobin to provide nutrients for the pathogen (Rarey et al. 1996). The aim of
docking was to explore the binding site conformation of chalcone derivatives against
falcipain-2 and to inhibit the falcipain-2 activity, the results of docking studies suggest
that the compounds inhibit the activity of falcipain-2 by showing higher binding
energy as indicated by docking score. In this docking study, we explore the orienta-
tion and binding energy of active chalcone derivatives towards anti-malarial target
falcipain-2 (PDB: 2GHU). The binding energy of control drugs artemisinin and di-hydro
artemisinin (DHA) were obtained from docking study and compared with the studied
chalcone derivatives, the active derivatives were bound in the active binding site of
falcipain-2 and showed higher binding energy as comparable to artemisinin and DHA.
The binding energy of artemisinin and DHA were obtained by docking software was
À14.9698 and À13.8422 KJ/Mol, which was lower than studied chalcone derivatives
(1a, 1b, 1c, 1d,1e, 1f, 1g, 1h, 1i, 1j, 2a, 2b, 2c, 2d, 2e, 2f, 2g, 2h, 2i, 2j and 2k i.e.
À23.3609, À20.1176, À18.0378, À21.1530, À19.7242, À15.6122, À23.8243, À19.5057,
À18.1345, À34.7210, À23.2514, À20.1176, À22.7645, À19.929, À24.9142, À30.3430,
À27.6112, À30.5480, À32.2120, À 32.2012 and À28.0341 KJ/Mol and formed hydrogen
bonds with interacting residues respectively.
When we compared how the binding site pocket residues of falcipain-2 interact
with chalcone derivatives, we found that the compounds 1b, 1c, 1d, 1e, 1f, 1h, 1i, 2a,
2b, 2c, and 2d showed interaction with specific amino acids residues which were also
found conserved in artemisinin and DHA docking pose respectively. Although com-
pounds 2b, 2e and 1f do not have any single conserved residue with artemisinin or
DHA. During docking against falcipain-2, results showed similar binding site residues
for most favourable conformations of predicted active indole chalcones as well as
for DHA and artemisinin (Supplementary material, Table S2). Among the all studied
compounds, 1j showed higher binding energy with falcipain-2 and found to bind
in the active pocket of protein, although the bioactive chalcone derivatives were
showing higher binding energy as compared to artemisinin and DHA.
2.2. Screening through in-silico pharmacokinetics parameters
The chemical descriptors for the pharmacokinetic properties were calculated, to check
the compliance of studied compounds with the standard range. The ADMET properties
were calculated to check the failure of lead candidates, which may cause toxicity or
be metabolized by body into an inactive formor one unable to cross the intestinal
membranes. Results revealed that artemisinin and indole chalcones i.e. compound
1a–1j and 2a–2k follows Lipinski’s rule of five for oral bioavailability and follow rule of
5 violation i.e., 0 (Supplementary material, Tables S3 and S4). The bi-plot showed two
confidence ellipses of 95% and 99% for blood-brain barrier penetration and human
intestinal absorption models (Supplementary material, Figure S1). The polar surface
area (PSA) was showed to have inverse relationship with percent human intestinal
absorption and membrane permeability. Evaluation through standard ADMET
parameters showed that most of the studied compounds have low solubility level,
Blood-Brain Barrier (BBB) penetration level is very high which showed that studied
compounds can easily penetrate the BBB. On the other hand most of the compounds

6
JYOTI ET AL.
showed False Cytochrome (CYP- 2D6) binding parameter which showed, the
compounds have good inhibitory property with CYP 2D6, and compounds for hepato-
toxicity showed true parameter. All the studied compounds except 2d, 2k, artemisinin
and DHA, showed high plasma-protein binding (PPB), thus seems to be easily
distributed in the body. The bi-plot showed confidence ellipses of 95% and 99%
for the blood–brain barrier penetration and human intestinal absorption models
(Supplementary material, Figure S1). The polar surface area (PSA) was shown to have
an inverse relationship with percent human intestinal absorption and membrane
permeability. All the compounds were found inside the plot, which represent good
bioavailability and permeability. The toxic effect of all the studied compounds were
calculated in comparison to the standard drugs (Artemisinin, DHA) (Supplementary
material, Table S5). The computed toxicity results, showed that all the compounds
were non-mutagenic except 1a, 1j, 2f and 2k compound. Studied compounds 1f, 1g,
1c, 2b, 2d,2c, 1b, 1d, 1h, and 1e showed none skin irritancy while artemisinin, DHA,
1a, 1i, 1j, 2a, 2e, 2f, 2g, 2i, 2j and 2k showed mild skin irritancy. For ocular irritancy
only DHA, compound 1a, 1i, 2b, 2d, 2g and 2k showed severe irritancy rest of the
compounds showed either mild or none irritancy.
3. Experimental
For general experimental procedures of synthesis, extraction and isolation of indolyl
chalcones, antimalarial activity, in silico and NMR spectra of the synthesized
compounds (Supplementary material, Figure S2) see supplementary file Lecaille et al.
2002; Lipinski et al. 2001; Markler & Hinrich 1993; Pandey et al. 2005.
4. Conclusion
The present study suggested that the newly synthesized indole derivatives are new
lead in antimalarial chemotherapy. These molecules can be very useful for further
optimization work in malarial chemotherapy.
Acknowledgements
We acknowledge the Council of Scientific and Industrial Research (CSIR), New Delhi for financial
support through Emeritus project 21(1050)/18 EMR-II at the CSIR-Central Institute of Medicinal
and Aromatic Plants (CIMAP), Lucknow, India. We are also thankful to the Director, CSIR-CIMAP,
Lucknow for rendering essential research facilities and support.
Disclosure statement
The author(s) confirm that this article content has no conflicts of interest.
ORCID
Rajendra Singh Bhakuni
http://orcid.org/0000-0002-1423-8461

NATURAL PRODUCT RESEARCH
7
References
Bhagat S, Sharma R, Sawant DM, Sharma L, Chakraborti AKJ. 2006. LiOH.H2O as a novel dual
activation catalyst for highly efficient and easy synthesis of 1,3-diaryl-2-propenones by
Claisen-Schmidt condensation under mild conditions. J Mol Catal A Chem. 244(1-2):20.
Brinner KM, Powles MA, Schmatz DM, Ellman JA. 2005. Potent 4-aminopiperidine based antimal-
arial agents. Bioorg Med Chem Lett. 15(2):345–348.
Butcher GA, Sinden RE, Curtis C. 2000. Malaria: new ideas, old problems, new technologies.
Parasitol Today. 16(2):43.
Colletti SL, Myers RW, Darkin-Rattray SJ, Gurnett AM, Dulski PM, Galuska S, Allocco JJ, Ayer MB,
Li C, Lim J, et al. 2001. Broad spectrum antiprotozoal agents that inhibit histone deacetylase:
structure-activity relationships of apicidin. Part 2. Bioorg Med Chem Lett. 11(2):113–117.
Delarue S, Girault S, Maes L, Debreu-Fontaine MA, Labaeïd M, Grellier P, Sergheraert C. 2001.
Synthesis and in vitro and in vivo antimalarial activity of new 4-anilinoquinolines. J Med
Chem. 44(17):2827–2833.
Enserink M. 2000. Malaria researchers wait for industry to join fight. Science. 287(5460):1956.
Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M,
Weaver B. 2000. Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature.
419(6906):531–534.
Gaur R, Cheema HS, Kumar Y, Singh SP, Yadav DK, Darokar MP, Khan F, Bhakuni RS. 2015. In
vitro antimalarial activity and molecular modeling studies of novel artemisinin derivatives. RSC
Adv. 5(59):47959–47974.
Gaur R, Gupta VK, Pal A, Darokar MP, Bhakuni RS, Kumar B. 2015. Synthesis of novel chalcone
derivatives as potential inhibitor of multidrug resistance efflux pumps in clinical isolates of
methicillin resistant S. aureus: novel agents for combination therapy. RSC Adv. 5(8):5830–5845.
Gaur R, Thakur JP, Yadav DK, Kapkoti DK, Verma RK, Gupta N, Khan F, Saikia D, Bhakuni RS.
2015. Synthesis, antitubercular activity, and molecular modelling studies of analogues of isoli-
quiritigenin and liquiritigenin, bioactive components from Glycyrrhiza glabra. Med Chem Res.
24(9):3494–3503.
Gaur R, Yadav DK, Kumar S, Darokar MP, Khan F, Bhakuni RS. 2015. Molecular modelling based
synthesis and in vitro evaluation of anticancer activity of indolyl chalcones. Curr Top Med
Chem. 15(11):1003–1012.
Gaur R, Yadav KS, Verma RK, Yadav NP, Bhakuni RS. 2014. In vivo anti-diabetic activity of deriva-
tives of isoliquiritigenin and liquiritigenin. Phytomedicine. 21(4):415–422.
Geneva: World Health Organization. 2015. Strategy for malaria elimination in the GMS
(2015–2030). http://www.wpro.who.int/mvp/documents/strat_mal_elim_gms/en/.
Jeong T-S, Soon Kim K, An S-J, Cho K-H, Lee S, Song Lee W. 2004. Novel 3,5-diarylpyrazolines as
human acyl-CoA:cholesterolacyltransferase inhibitors. Bioorg Med Chem Lett. 14(11):2715.
Klayman DL. 1985. Qinghaosu (artemisinin): an antimalarial drug from China. Science. 228(4703):
1049–1055.
Kumar A, Katiyar SB, Agarwal A, Chauhan PMS. 2003a. Perspective in antimalarial chemotherapy.
Curr Med Chem. 10(13):1137.
Kumar A, Katiyar SB, Agarwal A, Chauhan PMS. 2003b. Current trends in antimalarial chemother-
apy. Drugs Fut. 28(3):243.
€
Lecaille F, Kaleta J, Bromme D. 2002. Human and parasitic papain-like cysteine proteases: their
role in physiology and pathology and recent developments in inhibitor design. Chem Rev.
102(12):4459–4488.
Lipinski CA, Lombardo F, Dominy B, Feeney P. 2001. Experimental and computational
approaches to estimate solubility and permeability in drug discovery and development set-
tings. Adv Drug Deliv Rev. 46(1-3):3–26.
Luo XD, Shen CC. 1987. The chemistry, pharmacology, and clinical applications of qinghaosu
(artemisinin) and its derivatives. Med Res Rev. 7(1):29–52.
Makler MT, Hinrichs D. 1993. Measurement of the lactate dehydrogenase activity of Plasmodium
falciparum as an assessment of parasitemia. Am J Trop Med Hyg. 48(2):205–210.

8
JYOTI ET AL.
Naß J, Efferth T. 2019. Development of artemisinin resistance in malaria therapy. Pharmacol Res.
146:104275.
Pandey KC, Wang SX, Sijwali PS, Lau AL, McKerrow JH, Rosenthal PJ. 2005. The Plasmodium
falciparum cysteine protease falcipain-2 captures its substrate, hemoglobin, via a unique
motif. Proc Natl Acad Sci USA. 102(26):9138–9143.
Rarey M, Kramer B, Lengauer T, Klebe G. 1996. A fast flexible docking method using an
incremental construction algorithm. J Mol Biol. 261(3):470–489.
Rastelli G, Sirawaraporn W, Sompornpisut P, Vilaivan T, Kamchonwongpaisan S, Quarrell R, Lowe
G, Thebtaranonth Y, Yuthavong Y. 2000. Interaction of pyrimethamine, cycloguanil, WR99210
and their analogues with Plasmodium falciparum dihydrofolate reductase: structural basis of
antifolate resistance. Bioorg Med Chem. 8(5):1117–1128.
Ryckebusch A, Deprez-Poulain R, Debreu-Fontaine M-A, Vandaele R, Mouray E, Grellier P,
Sergheraert C. 2003. Synthesis and antimalarial evaluation of new 1,4-bis(3-aminopropyl)
piperazine derivatives. Bioorg Med Chem Lett. 13(21):3783–3787.
Shrivastava SK, Chauhan PMS. 2001. Present trends and future strategy in chemotherapy
of malaria. Curr Med Chem. 8:1535.
Singh SB, Zink DL, Polishook JD, Dombrowski AW, Darkin-Rattray SJ, Schmatz DM, Goetz MA.
1996. Apicidins: novel cyclic tetrapeptides as coccidiostats and antimalarial agents from
Fusarium pallidoroseum. Tetrahedron Lett. 37(45):8077–8080.
Srinivasan B, Johnson TE, Lad R, Xing C. 2009. Structure-activity relationship studies of chalcone
leading to 3-hydroxy-4,3’,4’,5’-tetramethoxychalcone and its analogues as potent nuclear
factor kappa B inhibitors and their anticancer activities. J Med Chem. 52(22):7228.
Ursos LMB, Roepe PD. 2002. Chloroquine resistance in the malarial parasite, Plasmodium
falciparum. Med Res Rev. 22(5):465–491.
World Malaria Report. 2018.