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

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HELICENES AND THEIR IMPORTANCE AS APPLIED TO BIOLOGICAL ACTIVITY

Jarugu Narasimha Moorthy

Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016

moorthy@iitk.ac.in

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

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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.

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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

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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

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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

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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

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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.

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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

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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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V. References:

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Soc. 2010, 132, 4536.

2. Graule, S.; Rudolph, M.; Vanthuyne, N.; Autschbach, J.; Roussel, C.; Crassous, J.; Reau,

R. J. Am. Chem. Soc. 2009, 131, 3183.

3. Wigglesworth, T. J.; Sud, D.; Norsten, T. B.; Lekhi, V. S. ; Branda, N. R. J. Am. Chem.

Soc. 2005, 127, 7272.

4. Li, M.; Lu, H. Y.; Liu, R. L.; Chen, J. D. ; Chen, C. F. J. Org. Chem. 2012, 77, 3670.

5. Fuchter, M. J.; Schaefer, J.; Judge, D. K.; Wardzinski, B.; Weimar, M. ; Krossing, I.

Dalton Trans. 2012, 41, 8238.

6. Shi, L.; Liu, Z.; Dong, G.; Duan, L.; Qiu, Y.; Jia, J.; Guo, W.; Zhao, D.; Cui, D.; Tao, X.

Chem. –Eur. J. 2012, 18, 8092.

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.

10. Waring, M. J. In Sequence-specific DNA binding agents; RSC Publishing, Cambridge,

U.K., 2006.

11. Hannon, M. J. Chem. Soc. Rev. 2007, 36, 280.

12. Misra, B.; Amin, S. J. Org. Chem. 1990, 55, 4478.

13. Honzawa, S.; Okubo, H.; Anzai, S.; Yamaguchi, M.; Tsumoto, K.; Kumagai, I. Bioorg. &

Med. Chem. 2002, 10, 3213.

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15. Basili, S.; Bergen, A.; Dall’Acqua, F.; Faccio, A.; Granzhan, A.; Ihmels, H.; Moro, S.;

Viola, G. Biochemistry 2007, 46, 12721.

16. Passeri, R.; Aloisi, G. G.; Elisei, F.; Latterini, L.; Caronna, T.; Fontana, F.; Sora, I. N.

Photochem. Photobiol. Sci. 2009, 8, 1574.

17. Shinohara, K.; Sannohe, Y.; Kaieda, S.; Tanaka, K.; Osuga, H.; Tahara, H.; Xu, Y.;

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.

19. Jørgensen, K. B. Molecules 2010, 15, 4334.

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