HELICENES AND THEIR IMPORTANCE AS APPLIED TO BIOLOGICAL ACTIVITY
A research Proposal Submitted to “OSDD Chemistry Outreach Program"
CSIR-Central Drug Research Institute
Council of Scientific & Industrial Research
Government of India
Dr. J. Narasimha Moorthy
Professor, Department of Chemistry
Indian Institute of Technology
Kanpur 208 016
2
3
HELICENES AND THEIR IMPORTANCE AS APPLIED TO BIOLOGICAL ACTIVITY
Jarugu Narasimha Moorthy
Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016
I. Introduction
During the last two decades, enormous advancement has been accomplished in understanding the
chemistry of helicenes, which have been tremendously exploited in a variety of domains. A
remarkable progress has also been achieved in harvesting exceptional enantiodifferentiating
potential of helicenes for applications in asymmetric catalysis.1 Today, helical core effectively
forms a design element in the development of chiroptical materials,2 photochromic materials,
3
sensors,4 molecular level devices,
5 organic electronics,
6 NLO materials,
7 etc. The most
astounding feature is that helicenes−by virtue of their inherent chirality−are obvious choices for
eliciting certain biological activities. In particular, investigation of the interactions of nucleic
acids with small molecules is an active area of research insofar as the drug design in anticancer
therapy is concerned.8,9
In this regard, molecules capable of structure-selective binding to nucleic
acids are of paramount importance, since they may influence biological functions of genetic
material.10
The condensed poly(hetero)aromatic compounds are usually regarded as renowned
DNA intercalators, especially if they possess electron-deficient or charged aromatic rings.11
Helical molecules in this respect represent unique category of molecular systems as DNA-
binding ligands for anticancer therapy.
Incidentally, remarkable applications of helicenes for drug development are beginning to be
explored only now. Thus, there is a sudden surge of interest in chiral helicenes with unique
properties and in the investigation of novel synthetic protocols to access them. In the
contemporary research on helical organic molecules, diverse chiral helicenes with ingenious
designs have been reported aimed at biological activities such as mutagenesis to bacterial cells,12
high tumor-initiating activity,12
chiral recognition13
and selectivity in DNA binding and
intercalation14-16
and enantioselectivity in telomerase inhibition.17
In the following, we have
4
consolidated a few most noteworthy instances, where helicenes have been exploited in various
ways to a significant extent to influence biological properties.
Amin and co-workers12
in 1990 reported the synthesis and biological activity of benzo[c]-
phenanthrene-3,4-diol 1,2-epoxide (BcPhDE), which is a tetrahelical molecule. This helicene-
like molecule exists as a pair of diastereoisomers: syn-BcPhDE (1) and anti-BcPhDE (2). Both of
these diastereoisomers are exceptionally mutagenic to bacteria and Chinese hamster V79 cells,
and can show remarkably high tumor-initiating activity on mouse skin cells. Seemingly, in the
newborn mouse tumor model, the anti- isomer 2 is more persuasive an agent than the syn-isomer
1. In particular, the helical diol epoxides 1 and 2 were shown to covalently bind with calf thymus
DNA at exocyclic nitrogen atoms of guanine and adenine almost equally. Likewise, these diol
epoxides are also capable of binding DNA in embryo cell cultures of mouse, hamster and rat.
Yamaguchi and co-workers13
in 2002 first reported the chiral recognition between
helicenediamine 3 and B-DNA. Perceptible changes in the UV and CD spectra caused by the
addition of calf thymus DNA to the solutions of (P)- and (M)-3 were interpreted to result in the
formation of DNA–helicene complex. The binding constant of (P)-helicene turns out to be
slightly larger than that of the (M)-enantiomer as suggested by isothermal titration calorimetry.
On the other hand, the chiral recognition whereby (P)-3 favors right-handed helicity is seemingly
driven by entropy.
5
In 2004, Sugiyama and co-workers14
reported that (P)-helicene 4 can bind Z-DNA selectively
and convert B-DNA into Z-DNA. The binding constant of the (P)-enantiomer was five times
greater than that of its (M)-enantiomer although the latter exhibited selective binding with Z-
DNA. The importance of protonated amino-substituents in binding Z-DNA was exemplified by
the fact that the structural selectivity vanished when the amino groups were replaced by hydroxyl
groups.
Ihmels and co-workers15
in 2007 reported a variety of helical-shaped diazoniaanthra[1,2-
a]anthracenes, e.g., 5a-c, and studied their interaction behavior with calf thymus DNA. This
series of helical diazoniapolycyclic salts were shown to bind both the duplex and triplex DNA by
intercalation with a high affinity (Kapp ~ 5 × 106 M
–1). DNA thermal denaturation studies
revealed that these helical dicationic species have pronounced influence on the thermal stability
of the triple-helical DNA. It was envisaged that this behavior was most probably due to the
favorable match of the shape of the chromophore, which allows a partial intercalation into the
duplex as well as into the triplex DNA. In particular, the helical diazoniapolycyclic salts provide
a relatively larger overlap area between the intercalator and the two DNA base pairs that
constitute the intercalation pocket.
ZXQ
Y
2 BF4
Q X Y Z
5a C C N N
5b N N C C
5c C N N C
6
Latterini and co-workers16
in 2009 reported the effect of counter ion in the DNA binding
behavior of helicenes using the same organic azahelicenium moiety with different anions such as
I–, NO3
–, and CF3CO2
–. The counter ions were shown to have great impact on the interaction;
e.g., 6c with CF3CO2– anion had the highest association binding constant, while 6b with NO3
–
ions had the highest number of binding sites. Circular dichroism and AFM studies were
suggestive of a mixed mechanism to be operative in the intercalation and external binding with
the azahelicenium salts.
Telomerase inhibition has emerged as a new technique for cancer therapy. Sugiyama and co-
workers17
in 2010 described the first example of a bridged helicene molecule as a chiral wedge to
block the approach of telomerase enzyme to telomeres by organization with G-quadruplex
structures. They employed quadruplex dimers to investigate the enantioselective recognition by
means of two different TTA linkers as the substrates, e.g., ODN 1,
(AGGG(TTAGGG)3TTAGGG-(TTAGGG)3), connected by one TTA repeat and ODN 2,
(AGGG(TTAGGG)3(TTA)6-GGG(TTAGGG)3), in which the linker is elongated to six TTA
repeats. Consequently, three differently-bridged thiahelicenes 7, 8 and 9 were designed as
telomerase inhibitors. Among all the three bridged thiahelicene molecules, only (M)-7 with an
appropriate dihedral angle was shown to display an efficient interaction with the substrates due
apparently to better shape complementarity with the chiral pocket between the two G-
quadruplexes.
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II. Work Plan
1. Research in Our Laboratories
As evident from the foregoing discussion, it is clear that helicenes offer tremendous excitement
in the context of biological activity. The importance of chiral helicenes with ingenious designs
continues to be explored in pursuit of remarkable selectivity in interaction with DNA–the basic
unit of life.
In fact, there has been a considerable interest in our laboratories to exploit helicity aimed at
developing novel materials and catalysts.18
Among various protocols available for the synthesis
of helicenes, dehydro-photocyclization of certain diarylethylenes turns out to be the most widely
exploited.19,20
We have been involved in the synthesis of helicenes that contain heterocyclic
systems using dehydro-photocyclization as a key synthetic protocol, cf. Scheme 1.
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Scheme 1
O Ph
Ph
PPh3
O O
R
NBS
O O
R
O O
CCl4, reflux24 h
dry benzene,reflux,14 h
(ii) 50% NaOH,0 ºC, 30 40 min
(i)
cis + trans
R
46
7
O
R
a : R = Hb : R = Mec : R = Cld : R = OMe
O
(67%) (74%)
(78 90%)
O O
R
46
7
cis + trans
(64 85%)
(ii) 50% NaOH,0 ºC, 40 50 min
(i)
CHO
CHO
H3C BrH2C Ph3PH2C
Br
O O
h
R
O O
R
I2/O2, Benzene
i) PhMgBr (excess)THF, rt, 2 3 h
ii) H+, 3 h
(60-95%)
(65-94%)
h
I2/O2, Benzene
(73-95%)
O Ph
Ph
RR
Moorthy, J. N. et al. Org. Lett. 2006, 8, 4891.
i) PhMgBr (excess)THF, rt, 2 3 h
ii) H+, 3 h
(60-95%)
Pentahelical Chromene Tetrahelical Chromene
Pentahelical Coumarin Tetrahelical Coumarin
9
We believe that a variety of helicenes that incorporate key structural fragments responsible for
biological activities may be readily developed to provide access to a range of new molecular
systems, whose biological properties can be very promising.
2. Literature on Structural Features of Molecules that are Relevant to the Activity Against
Tropical Diseases
In Chart 1 are shown some of the commercial drugs and literature-reported compounds active
against tropical diseases like malaria and tuberculosis. Based on these structural features, we
have identified certain moieties that are seemingly responsible for biological activities. They are
quinoline, guanidine, phenanthrene-based amino alcohol, triazine, salicyclic acid derivative, 1,4-
naphthquinone, coumarin, chromene, benzimidazole, etc.
Chart 1. Drugs/Biologically-Active Molecules Against Malaria/Tuberculosis
Quinoline-Based Compounds
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Nitrogen-Containing Compounds−guanidines, phenanthrene-based amino alcohols and triazines
Cl
HN
NH
HN
NH
HN
CH3
CH3
Proguanil
Nature 1951, 168, 1080.
Cl
Cl
CF3
OH
N
Halofantrine
J. Inorg. Chem. 2008, 102,1660.
N
HN
Cl
HN
N N
N R1
R2
Med. Chem. Commun. 2012, 3, 71.
Triazine
Salicylic acid Derivatives
1,4-Naphthoquinone Derivatives
11
Coumarin Derivatives
O
O
OH
OH
OH
HO
HO
O
O
OHOHO
OHO O
HO
OH
OH
J. Nat. Prod. 2005, 68, 537.
OO
O
O
HO
HO
OMe
OH
OO
O
O
OH
OH
OH
OMe
J. Nat. Prod. 2006, 69, 346.
Chromene Analogs
12
Benzimidazole Derivatives
3. Objectives (Proposed Molecular Systems)
Here in, we propose to synthesize helicenes that incorporate the above-mentioned moieties as a
part of a helical scaffold to develop a wide spectrum of new helical systems, which may be
explored for the design of potential drugs with activity against tropical diseases like malaria and
tuberculosis. Shown in Chart 2 are the structures of helicenes that we propose to synthesize. It
would be interesting as well exciting to evaluate their biological activity against the tropical
diseases.
13
Chart 2. Helical Systems Proposed to be Synthesized
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4. Synthetic Scheme Proposed to be Followed
Shown in Scheme 2a-f, are the synthetic protocols that are proposed to be employed for the
preparation of the helicenes (Target-1 – Target-10). We wish to capitalize on the oxidative
photocyclization of diarylolefins that has been immensely exploited in our research group.
i) Scheme 2a
ii) Scheme 2b
iii) Scheme 2c
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iv) Scheme 2d
iv) Scheme 2e
16
v) Scheme 2f
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III. Time Schedule
We wish to have the proposed molecular systems synthesized within the next 2 years. As the
synthetic protocols are already well established in our laboratories, we believe that the
suggested duration is reasonable. We hope to have 25-30 molecules prepared within the first
one year and ca. 30-40 molecules in the next year.
As some of the molecules are also part of our on-going photochemistry investigations, we
believe that the proposed number of molecules will be easily realized.
IV. Budget Requirements
Nonconsumables: INR 5,00,000
Consumables: INR 2,00,000
Total: INR 7,00,000
Justification:
We request that Rs. 1.0 lac be granted per year towards the chemicals and solvents required
for the synthesis.
Rs. 5.0 lacs is requested for small equipments such as the following, which we are badly in
need of:
1.Digital Balance (Mettler/Sartorious) up to the sensitivity of 4th
decimal point: Rs. 1.2 lacs
2.Rotary Evaporator with a vacuum pump and a chiller: Rs. 2.8 lacs
3.Digital Melting Point Apparatus: Rs. 1.0 lac
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Dalton Trans. 2012, 41, 8238.
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7. Verbiest, T.; Elshocht, S. V.; Persoons, A.; Nuckolls, C.; Phillips, K. E.; Katz, T. J.
Langmuir 2001, 17, 4685.
8. Neidle, S.; Waring, M. In Molecular Aspects of Anticancer Drug-DNA Interactions; CRC
Press, Boca Raton, FL, 1993.
9. D’Incalci, M.; Sessa, C. Expert Opin. Invest. Drugs 1997, 6, 875.
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U.K., 2006.
11. Hannon, M. J. Chem. Soc. Rev. 2007, 36, 280.
12. Misra, B.; Amin, S. J. Org. Chem. 1990, 55, 4478.
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15. Basili, S.; Bergen, A.; Dall’Acqua, F.; Faccio, A.; Granzhan, A.; Ihmels, H.; Moro, S.;
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Photochem. Photobiol. Sci. 2009, 8, 1574.
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Kawase, T.; Bando, T.; Sugiyama, H. J. Am. Chem. Soc. 2010, 132, 3778.
18. Moorthy, J. N.; Venkatakrishnan, P.; Sengupta, S.; Baidya, M. Org. Lett. 2006, 8, 4891.
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