36
In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4 Page -141- 4.1 Introduction 4.1.1 Environmental Chemical Causing Cancer People are continuously exposed exogenously to varying amounts of chemicals that have been shown to have carcinogenic or mutagenic properties in experimental systems. Exposure can occur exogenously when these agents are present in food, air or water, and also endogenously when they are products of metabolism or pathophysiologic states such as inflammation. It has been estimated that exposure to environmental chemical carcinogens may contribute significantly to the causation of a sizable fraction, perhaps a majority, of human cancers, when exposures are related to "life-style" factors such as diet, tobacco use, etc. A causative relationship between exposure to aflatoxin, a strongly carcinogenic mold-produced contaminant of dietary staples in Asia and Africa, and elevated risk for primary liver cancer has been demonstrated through the application of well-validated biomarkers in molecular epidemiology. These studies have also identified a striking synergistic interaction between aflatoxin and hepatitis B virus infection in elevating liver cancer risk. Use of tobacco products provides a clear example of cancer causation by a life-style factor involving carcinogen exposure. Tobacco carcinogens and their DNA adducts are central to cancer induction by tobacco products, and the contribution of specific tobacco carcinogens (e.g. PAH and NNK) to tobacco-induced lung cancer, can be evaluated by a weight of evidence approach. Factors considered include presence in tobacco products, carcinogenicity in laboratory animals, human uptake, and metabolism and adduct formation, possible role in causing molecular changes in oncogenes or suppressor genes, and other relevant data. This approach can be applied to evaluation of other environmental carcinogens, and the evaluations would be markedly facilitated by prospective epidemiologic studies incorporating phenotypic carcinogen-specific

In silico designing and synthesis of nanoparticles ...shodhganga.inflibnet.ac.in/bitstream/10603/36851/7/chapter-4.pdf · properties and surface chemistry of nanoparticles are the

  • Upload
    lamcong

  • View
    237

  • Download
    1

Embed Size (px)

Citation preview

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -141-

4.1 Introduction

4.1.1 Environmental Chemical Causing Cancer

People are continuously exposed exogenously to varying amounts of chemicals that

have been shown to have carcinogenic or mutagenic properties in experimental

systems. Exposure can occur exogenously when these agents are present in food, air

or water, and also endogenously when they are products of metabolism or

pathophysiologic states such as inflammation. It has been estimated that exposure

to environmental chemical carcinogens may contribute significantly to the causation

of a sizable fraction, perhaps a majority, of human cancers, when exposures are

related to "life-style" factors such as diet, tobacco use, etc. A causative relationship

between exposure to aflatoxin, a strongly carcinogenic mold-produced contaminant

of dietary staples in Asia and Africa, and elevated risk for primary liver cancer has

been demonstrated through the application of well-validated biomarkers in

molecular epidemiology. These studies have also identified a striking synergistic

interaction between aflatoxin and hepatitis B virus infection in elevating

liver cancer risk. Use of tobacco products provides a clear example

of cancer causation by a life-style factor involving carcinogen exposure. Tobacco

carcinogens and their DNA adducts are central to cancer induction by tobacco

products, and the contribution of specific tobacco carcinogens (e.g. PAH and NNK)

to tobacco-induced lung cancer, can be evaluated by a weight of evidence approach.

Factors considered include presence in tobacco products, carcinogenicity in

laboratory animals, human uptake, and metabolism and adduct formation, possible

role in causing molecular changes in oncogenes or suppressor genes, and other

relevant data. This approach can be applied to evaluation of

other environmental carcinogens, and the evaluations would be markedly facilitated

by prospective epidemiologic studies incorporating phenotypic carcinogen-specific

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -142-

biomarkers. Heterocyclic amines represent an important class of carcinogens in

foods. They are mutagens and carcinogens at numerous organ sites in experimental

animals, are produced when meats are heated above 180 degrees oC for long

periods. Four of these compounds can consistently be identified in well-done meat

products from the North American diet, and although a causal linkage has not been

established, a majority of epidemiology studies have linked consumption of well-

done meat products to cancer of the colon, breast and stomach. Studies employing

molecular biomarkers suggest that individuals may differ in their susceptibility to

these carcinogens, and genetic polymorphisms may contribute to this variability.

Heterocyclic amines, like most other chemical carcinogens, are not carcinogenic per

se but must be metabolized by a family of cytochrome P450 enzymes to chemically

reactive electrophiles prior to reacting with DNA to initiate a carcinogenic response.

These same cytochrome P450 enzymes--as well as enzymes that act on the metabolic

products of the cytochromes P450 (e.g. glucuronyl transferase, glutathione S-

transferase and others)--also metabolize chemicals by inactivation pathways, and the

relative amounts of activation and detoxification will determine whether a chemical

is carcinogenic. Because both genetic and environmental factors influence the levels

of enzymes that metabolically activate and detoxify chemicals, they can also

influence carcinogenic risk. Many of the phenotypes of cancer cells can be the result

of mutations, i.e., changes in the nucleotide sequence of DNA that accumulate as

tumors progress.

These can arise as a result of DNA damage or by the incorporation of non-

complementary nucleotides during DNA synthetic processes. Based upon the

disparity between the infrequency of spontaneous mutations and the large

numbers of mutations reported in human tumors, it has been postulated that

cancers must exhibit a mutator phenotype, which would represent an early

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -143-

event in cancer progression. A mutator phenotype could be generated by

mutations in genes that normally function to guarantee genetic stability. These

mutations presumably arise via DNA damage by environmental or endogenous

agents, but it remains to be determined whether the acquisition of a mutator

phenotype is a necessary event during tumor progression ( Wogan GN et

al.,2004 ).

4.1.2 Prevention of Carcinogenesis by using Nanoparticles as a Scavenger

Nanotechnology, actually means the exploitation of the substances at their nano-

meter size, is expected to enhance the quality of life and economic development on

the global basis. Understanding of biological processes on the nanoscale level is a

strong driving force behind development of nanotechnology. Out of surplus of size-

dependant physical properties of nanomaterials like optical and magnetic effects

have been exploited for a number of biological/medical applications, eg: their use as

fluorescent biological labels, for the drug and gene delivery, for the detection of

pathogens, detection of proteins, Probing of DNA structure, in tissue engineering, for

the treatment of cancer by tumor destruction via heating (hyperthermia), for the

separation and purification of biological molecules and cells, in the contrast

enhancement of MRI, and phagokinetic studies etc. The list of applications of

nanomaterials to biology or medicine is ever escalating. Recently some of the

nanoparticles have been employed in scavenging the high molecular weight PAHs

from the contaminated soils (Karnchanasest and Santisukkasaem, 2007). Amphiphilic

polymer nanoparticles have been used as nano-absorbent for pollutants in aqueous

phase (Jin- Kie S him et al.,2007).

The scavenging capacities of the nanoparticles for PAH and other toxicants could

probably be attributed to their higher affinity towards the xenobiotics. The structural

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -144-

properties and surface chemistry of nanoparticles are the players, further, extremely

high surface area to volume ratio results in multiple enhancements of such

properties.

4.1.3 Nanoparticles (TiO2) have capacity to efficiently reduces the harmful

compounds -

TiO2 is biological Inert but in ultrafine form and in high conc. TiO2 causes the fibrosis

in tissues which may lead the cancer . In 2006, the International Agency for Research on

Cancer (IARC) reviewed the carcinogenic risk of TiO2 concluding that it is “possibly

carcinogenic to humans” (Group 2B) based primarily on studies in rats indicating lung

tumors. However, the results from four large human epidemiology studies involving more

than 40,000 workers in the titanium dioxide industry at manufacturing locations in North

America and Europe indicate neither association with an increased risk of lung cancer nor

with any other adverse lung effects.

Inhalation exposures to TiO2 in rats can result in lung effects and lung tumors. It is

generally recognized that the rat is uniquely sensitive to the effects of “lung overload”,

with the production of chronic lung inflammation and subsequent lung fibrosis and

tumor formation; a process not observed in other species including humans. The IARC

conclusion was based on studies that involved rat “lung overload” effects. But in low

and definite conc., UltraFine TiO2 significantly reduced the harmful compounds from

the cigarette smoke (Qixin Deng et al., 2011).

The scavenging capacities of the nanoparticles for PAH and other toxicants could

probably be attributed to their higher affinity towards the xenobiotics. The structural

properties and surface chemistry of nanoparticles are the players, further, extremely

high surface area to volume ratio results in multiple enhancements of such properties.

Cigarette smoke (CS) is a complex aerosol containing more than 2000 chemical

constituents, which are present in both particulate and vapour phase. The former is

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -145-

composed primarily of tar, nicotine and water. Tar contains various toxic or

carcinogenic chemicals such as polycyclic aromatic hydrocarbons (PAHs) and

tobacco-specific nitrosamines (TSNAs), even a trace amount of PAHs or TSNAs are

able to cause serious health risk.

Titanate nanosheets (TNS) and Titanate Nano Tubes (TNT) have also been

synthesized and then used as additives for removing harmful compounds in CS for

the first time (add Reference). After TNS and TNT were introduced into cigarette

filter, a great range of harmful compounds including nicotine, tar, ammonia,

hydrogen cyanide, selected carbonyls and phenolic compounds can be reduced

efficiently. Interestingly, TNT exhibits highly efficient reduction capability for the

most of the harmful compounds. This might be related to the intrinsic properties of

TNT (Qixin Deng et al., 2011).

Hence, we have followed a methodology to compare the binding efficiency of

nanoparticles and cigarette smoke carcinogens. The molecular interactions have been

accomplished using PatchDock server and interestingly got desirable results for our

hypothesis.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -146-

4.2 Materials & Methods

Minimum system Requirement for the project is:

1) Supported Operating Systems

Discovery Studio Visualizer is supported on the following operating systems:

Microsoft® Windows XP Professional, SP2 and SP3

Microsoft Windows Vista, Business and Enterprise Editions, SP1

Red Hat® Enterprise Linux® 4.0, Updates 4-7

Red Hat Enterprise Linux 5, Retail, Updates 1-2

SUSE® Linux Enterprise 10 (SP2)

2) Processor and RAM Requirements

Processor: An Intel-compatible ≥2 GHz is required.

RAM: A minimum of 2 GB of memory for the visualizer.

3) Disk Space Requirements

A standard installation of Discovery Studio Visualizer requires 272 MB of disk space on

Windows and 454 MB on Linux.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -147-

4) Software:

Accelrys discovery studio visualizer 2.5 (Designing of crystal structure, visualizing

and manipulating protein and crystal 3D structures)

PatchDock (Docking server)

Open Babel (File converter)

An Internet Browser and valid internet connection.

After studying the anatase crystal structure, we found that Accelrys Discovery studio

would be the most suitable software for the designing of TiO2 anatase crystal structure.

4.2.1 Method for Designing Crystal Structure

From the start menu,goto the all programs option and select the Accelrys

Discovery Studio 2.5 program.

Now goto file menu >> New >> Molecule Window.

A black sub window / tab will open up. Goto the Structure menu >> Crystal cell

>> Create cell.

A Crystal cell outline will appear in the black window in select mode (yellow

colour).

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -148-

Figure 4.1 Crystal Cell Outline

Now again goto Structure menu >> Crystal cell >> Edit Parameters…. A small

dialog box of Crystal Builder with 4 tabs will pop up.In the first tab, i.e. of Cell

parameters, edit the crystal lengths(A, B and C) and angles(alpha, beta and

gamma) according to the anatase lattice parameters,i.e.,

A = B = 3.785.

C = 9.514.

Alpha = beta = gamma = 90.

Now under the space group tab select the “I41/amd” space group and origin as

“origin-1 choice: 1”, and calculate the lattice positions of Ti atoms by the help of

the formulae given under positions in the space group tab.

The calculated positions are:-

1) 0, 0, 0

2) 0.5, 0.5, 0.5

3) 1, 0.5, 0.25

4) 0.5, 1, 0.75

5) 0.5, 0, 0.25

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -149-

6) 0, 0.5, 0.75

7) 0.5, 0.5, 0.5

8) 1, 1, 1

9) 1, 0.5, 0.75

10) 0.5, 0, 0.25

11) 0, 1, 1

12) 0.5, 0.5, 0.5

13) 0.5, 0.5, 0.5

14) 1, 0, 0

15) 0.5, 1, 0.75

16) 0, 0.5, 0.25

17) 0.5, 0.5, 0.5

18) 0, 0, 1

19) 0.5, 1, 0.75

20) 1, 0.5, 1.25

21) 0, 0.5, -0.25

22) 0.5, 0, 0.25

23) 1, 1, 0

24) 0.5, 0.5, 0.5

25) 0.5, 0, 0.25

26) 1, 0.5, -0.25

27) 0.5, 0.5, 0.5

28) 0, 1, 0

29) 1, 0, 1

30) 0.5, 0.5, 0.5

31) 0, 0.5, 1.25

32) 0.5, 1, 0.75

These are the 32 Wyckoff positions of the I41/amd space group. These are pre defined

positions,which were calculated using the general formulae for different wycoff

positions,

1. x, y, z

2. -x+1/2, -y+1/2, z+1/2

3. -y, x+1/2, z+1/4

4. y+1/2, -x, z+3/4

5. -x+1/2, y, -z+3/4

6. x, -y+1/2, -z+1/4

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -150-

7. y+1/2, x+1/2, -z+1/2

8. -y, -x, -z

9. -x, -y+1/2, -z+1/4

10. x+1/2, y, -z+3/4

11. y, -x, -z

12. -y+1/2, x+1/2, -z+1/2

13. x+1/2 , -y+1/2, z+1/2

14. -x, y, z

15. -y+1/2, -x, z+3/4

16. y, x+1/2, z+1/4

17. x+1/2, y+1/2, z+1/2

18. -x+1, -y+1, z+1

19. -y+1/2, x+1, z+3/4

20. y+1, -x+1/2, z+1.250000

21. -x+1, y+1/2, -z+1.250000

22. x+1/2, -y+1, -z+3/4

23. y+1, x+1, -z+1

24. -y+1/2, -x+1/2, -z+1/2

25. -x+1/2, -y+1, -z+3/4

26. x+1, y+1/2, -z+1.250000

27. y+1/2, -x+1/2, -z+1/2

28. -y+1, x+1, -z+1

29. x+1, -y+1, z+1

30. -x+1/2, y+1/2, z+1/2

31. -y+1, -x+1/2, z+1.250000

32. y+1/2, x+1, z+3/4

Considering x, y, z to be complementary with -x, -y, -z, i.e., here considering x = y = z = 0

and -x = -y = -z = 1.here the minus sign indicates the complementary function.

Note: fractional co ordinate = Actual length along an axis

Total length of a unit cell along that axis

These are the positions (fractional co ordinates) of Titanium. Now according to

the bond angle and bond length the corresponding Oxygen co ordinates are

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -151-

calculated. For faster calculation write a program in C to calculate the co

ordinates of Oxygen. The program which I have written is:

/*A program for calculation of the fractional co-ordinates of oxygen in anatase*/

/*Author QMSJ date:17/03/2012*/

#include<stdio.h>

#include<conio.h>

#include<math.h>

void main()

{

float xa,xb,xc,ya,yb,yc,za,zb,zc,x,y,z=0;

clrscr();

printf("Enter the values of the fractional co-ordinates(x,y,z):");

scanf("%f %f %f",&x,&y,&z);

if(x<1)

{

xa=x + (1.937*cos(12.308))/3.785;

xc=z + (1.937*sin(12.308))/9.514;

xb=0;

}

if(y<1)

{

ya=0;

yb=y + (1.937*cos(12.308))/3.785;

yc=z - (1.937*sin(12.308))/9.514;

}

if(z<1)

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -152-

{

za=0;

zb=0;

zc=z + (1.966/9.514);

}

printf("The fractional co-ordinates for Oxygen atoms

are:\n%f\t%f\t%f\n%f\t%f\t%f\n%f\t%f\t%f",xa,xb,xc,ya,yb,yc,za,zb,zc);

getch();

}

Now go back to accelrys Discovery studio and then goto Structure >> Crystal cell

>> create atom… a dialog box will appear. In it, click on the table button, the

periodic table will open up.Then choose Ti from it and click the “ok” button.

Now give the X, Y, Z fractional co ordinates (Wyckoff positions) of the Ti atoms

as calculated above.

Note: Care should be taken that no two co ordinates are same, i.e., avoid duplicity. Also

delete the Ti atoms lying outside the unit cell.

Figure 4.2 Duplicacy of Co ordinates

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -153-

Repeat the above step for oxygen atoms, the co ordinates of which are obtained

from the self designed program.(avoid duplicacy of co ordinates here too.)

Now select a Ti atom and then select adjacent O atom while pressing the

“SHIFT” key, so that both Ti and O are selected. Then go to Chemistry >> Bond

>> Single. A bond will be created between the two atoms now proceed further

keeping the picture of anatase unit cell in mind, obtained from literature.

Thus finally a unit cell of anatase is formed.

Figure 4.3 unit cell of anatase

Now to create a surface we have to extend this unit cell in the desired directions

(axis). Lets make a [1,0,1] surface comprising of 5 unit cells in X direction and 2

unit cells in the Z direction, this will give us a surface of dimensions 18.925 ×

3.785 × 19.028 Å3.

To implement this go to Structure >> Crystal cell >> Edit Parameters… the

Crystal Builder dialog box will open up. In it choose the Preference tab. In this,

select Symmetry Style as Positions from the drop down menu, set Special

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -154-

position tolerance to 0.05, uncheck the Proximity Binding check box, in view

range set A : 5 , B : 1 , C : 2. Then click on the “apply” button and then the “ok”

button. The surface gets generated!!

Figure 4.4 3D structure of Anatase Figure 4.5 3D structure of Anatase

Now save this as “.sd” file. Goto File >> Save As , write “Ligand.sd”, select a

preferred location to save the file and then click Save button.

Next step is to convert this file format to “*.pdb” format, for this go to Start menu

>> All Programs >> Open Babel 2.2.3 >> OpenBabelGUI. The program will open

up. In this select the input file format as “.sd”, then click browse, open the

location of the input file “Ligand.sd” and open it. Then choose the output format

as “.pdb”. Now enter the address of the output file, i.e., where it has to be saved,

give the file name as “Ligand.pdb”. Finally press convert button.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -155-

Figure 4.6 OpenBabel

Open the “model.pdb” in Accelrys Discovery Studio. Goto Chemistry >>

Hydrogens >> Add, and then click save. Now our Protein is also ready.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -156-

Figure 4.7 Visualization of 3D enzymes structure

Docking studies using PatchDock Server

Now we’ll goto PatchDock server(http://bioinfo3d.cs.tau.ac.il/PatchDock/ ).

Figure 4.8 Home Page of PatchDock

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -157-

In the receptor molecule option click “choose file” button,and select the protein

file “model.pdb”, from the location where it has been saved. Then in the Ligand

molecule option “choose file”, and select the ligand file “Ligand.pdb” ,from the

location where it has been saved.

Give your e-mail address in the space provided where the results would be sent.

Keeps the default clustering RMSD value, i.e., 4.0.

Select complex type from the drop down menu as Protein-Small Ligand.

Press “submit form” button. Results would be sent to the provided e-mail

address after sometime.

4.3 Results and Discussion

We have performed molecular docking method using Patchdock server to find out the

interaction between NNK Vs Nanoparticles and NNK Vs proteins involved in DNA

repair Pathways. The implemented hypothesis suggest that if NNK/NNAL and

nanoparticles would be present in the cellular system than nanoparticles could interact

with carcinogens like NNK and NNAL firstly on the basis of obtained binding energy

using PatchDock tool.

The Pathdock algorithm divides the molecular surface into shape-based patches. This

division addresses both the efficiency and at the same time, distinguishes between

residue types (polar/non-polar) in the patches. Further, we make use of residue hot

spots in the patches. Second, the method utilizes distance transform to improve the

shape complementarily function. Third, it implements faster scoring, based on multi-

resolution surface data structure. Our improved shape complementarily function

further contributes to the quality of the results. While here the docking is rigid, the

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -158-

utilization of the last three components enables us to permit more liberal intermolecular

penetration. Patchdock results showed nanoparticles could be able to trap cigarette

smoke carcinogens efficiently in the cellular system. The highest obtained binding

efficiency between NNK vs SWcNT is 2632 score in contrast with NNK Vs 3K05 shows

2454 score,which means NNK could interact with SWcNT more efficiently than 3K05.

Other part of the study shows that the highest binding efficiency NNAL vs SWcNT

=2746 score and NNAL vs TiO2 Rutile= 2110 score in contract with NNAL vs 2RBA

shows 1696 score. It is also signify that NNAL interact with SWcNT and TiO2 rutile

more efficiently than 2RBA.

Table 4.1 Comparison of Patch dock scores obtain from docked NNK vs Proteins and

NNK Vs Nanoparticles conformations

S.No. Protein’s

Name

Protein Vs

NNK

SWNT Vs

NNK

TiO2

Anatase Vs

NNK

TiO2

Rutile Vs

NNK

Fullerene

Vs

NNK

1. 1CKJ 2790 2632 2068 1360 910

2. 2O8B 2720 2632 2068 1360 910

3. 3K05 2454 2632 2068 1360 910

4. 3GQC 3054 2632 2068 1360 910

Table 4.2 Comparison of Patch dock scores obtain from docked NNAL Vs Proteins

and NNAL Vs Nanoparticles conformations

S.No. Protein’s

Name

Protein Vs

NNAL

SWNT Vs

NNAL

TiO2

Anatase

TiO2

Rutile

Fullerene

1. 1CKJ 3688 2746 2110 1360 954

2. 1Q2Z 3374 2746 2110 1360 954

3. 1T38 3240 2746 2110 1360 954

4. 2RBA 1696 2746 2110 1360 954

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -159-

Figure: 4.9 TiO2 Docked with 1CKJ Figure: 4.10 TiO2 docked with 1Q2Z

Figure 4.11 TiO2 Docked with 2O8B Figure 4.12 TiO2 docked with 1T38

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -160-

Figure 4.13 TiO2 Docked with 3GQC Figure 4.14 TiO2 Docked with 3K05

Figure 4.15 TiO2 Docked with 2RBA

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -161-

Figure 4.16 Fullerene docked with 1CKJ Figure: 4.17 Fullerene Docked with 1Q2Z

Figure 4.18 Fullerene Docked with 1T38 Figure 4.19 Fullerene Docked with 2O8B

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -162-

Figure: 4.20 Fullerene Docked with 3GQC Figure: 4.21 Fullerene Docked with 3K05

Figure: 4.22 Fullerene Docked with 2RBA

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -163-

Figure: 4.23 SWNT docked with 1CKJ Figure: 4.24 SWNT Docked with 1Q2Z

Figure:4.25 SWNT Docked with 1T38 Figure: 4.26 SWNT Docked with 2O8B

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -164-

Figure: 4.27 SWNT Docked with 3GQC Figure: 4.28 SWNT Docked with 3K05

Figure: 4.29 SWNT Doked with 2RBA

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -165-

Figure 4.30 visualization of SWcNT and NNAL interaction

Figure 4.31 visualization of SWcNT and NNK interaction

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -166-

4.4 Conclusion

As mentioned earlier, the fact that technical TiO2 is very often of the (metastable)

anatase form; most TiO2 nanomaterials are of anatase form, and in many cases anatase

is photocatalytically more active than rutile. This has motivated theoretical

investigations of anatase, but there are hardly any experiments on well-characterized

surfaces that would enable verification of these theoretical predictions. This lack of

experimental data is mostly due to the limited availability of anatase crystals of

sufficiently large size.

This study of anatase [1,0,1] surface may prove to be very valuable for biotechnologists

as this aspect of biotechnology has yet not been explored. The [1,0,1] surface is also the

surface mostly available for interactions, this surface is also found over TiO2 nanotubes,

which are presently the subject of interest of the research community of electronics and

nanotechnology innovators.In low and definite conc., TiO2 significantly reduced the

harmful compounds from the cigarette smoke (Qixin Deng et.al, 2011).

The scavenging capacities of the nanoparticles for PAH and other toxicants could

probably be attributed to their higher affinity towards the xenobiotics. The structural

properties and surface chemistry of nanoparticles are the players, further, extremely

high surface area to volume ratio results in multiple enhancements of such properties.

Our study is conformity of study of Qixin Deng et al.,2011, who reported the use of

titanate nanosheets and nanotubes are significantly reduces the harmful compounds in

tobacco smoke .Our study confirmed this action in Biological system that by using of

Bioinformatics tools we have done the comparative docking study between

Nanoparticles-biomolecules and NNK/NNAL-Nanoparticles, we concluded that

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -167-

SWcNT,TiO2-Biomolecules binding shown lower scores and NNK/NNAL-

Nanoparticles binding shown higher scores. Hence, Results clearly signifying that

SWcNT/TiO2 are binding with NNK/NNAL more efficiently than biomolecules.

4.4.1 Future Scope:

There is a lot to be done in this research work. We are just at the beginning; much have

yet to be studied. Further studies can be done by applying force fields like crystal-

CHARMm, CFF or SIBFA (these are the few force fields which deals with metals and

crystal structures) and then going for various interaction studies and energy

calculations. The major Hurdle in this work is that most of the softwares currently

available do not recognize, i.e., they do not contain information regarding

crystallographic bonding (or arrangements) and metallic atoms, their physical, chemical

and quantum mechanical properties for molecular dynamic simulations of the same.

There is an urgent requirement for a complete software package which can be used to

design and manipulate inorganic or organic crystals as well as the biomolecules. In this

chapter itself we have written a code in the C language to calculate the co ordinates of

oxygen atom with respect to the titanium atoms. This can be considered as part of a

larger software program.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -168-

4.5 References

1. 25th anniversary of the Buckyball celebrated by interactive Google Doodle,

Telegraph.co.uk 4 September 2010.

2. Arndt, M.; et al. (1999). "Wave-particle duality of C60".Nature 401 (6754):

6802. Bibcode 1999 Natur.401.680A.doi:10.1038/44348. PMID 18494170.

3. Atkinson, Nancy (2010-10-27). "Buckyballs Could Be Plentiful in the

Universe". Universe Today. Retrieved 2010-10-28.

4. Baati, Tarek; Bourasset F, Gharbi N, Njim L, Abderrabba M, Kerkeni A, Szwarc

H, Moussa F (June 2012). "The prolongation of the lifespan of rats by repeated

oral administration of [60 fullerene"]. Biomaterials 33 (19): 4936

4946. doi:10.1016/j.biomaterials.2012.03.036.PMID 22498298.

5. Beavers, C.M.; et al. (2006). "Tb3N@C84: An improbable, egg-shaped

endohedral fullerene that violates the isolated pentagon rule". Journal of the

AmericanChemical Society128 (35):11352–3. doi:10.1021/ja063636k.PMID 16939248.

6. Beck, Mihály T.; Mándi, Géza (1997). "Solubility of C60".Fullerenes, Nanotubes

and Carbon Nanostructures 5 (2): 291. doi:10.1080/15363839708011993.

7. Bezmel'nitsyn, V.N.; Eletskii, A.V.; Okun', M.V. (1998). "Fullerenes in

solutions". PhysicsUspekhi 41 (11):1091.Bibcode 1998PhyU...41.1091B.doi:10.107

0/PU1998v041n11ABEH000502.

8. Blank, V. (1998). "Ultrahard and superhard phases of fullerite C60: Comparison

with diamond on hardness and wear". Diamond and Related Materials 7 (2–5):

427.Bibcode 1998DRM.....7..427B. doi:10.1016/S0925-9635(97)00232-X.

9. Bochvar, D.A.; Galpern, E.G. (1973). Dokl. Acad. Nauk SSSR 209: 610.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -169-

10. Brown, S.B. (2004). "The present and future role of photodynamic therapy in

cancer treatment". Lancet Oncology5 (8): 497–508. doi:10.1016/S1470-

2045(04)01529-3.

11. Buseck, P.R.; Tsipursky, S.J.; Hettich, R. (1992). "Fullerenes from the Geological

Environment". Science 257(5067):2157. Bibcode 1992Sci...257..215B.doi:10.1126/sc

ience.257.5067.215. PMID 17794751.

12. C.H. Lin and H. Bai, (2003) Appl. Catal. B 42 279.

13. C.Morterra, J. (1988) Chem. Soc. Faraday Trans. 1 84 1617.

14. Cami, J; Bernard-Salas, J.; Peeters, E.; Malek, S. E. (2010-09-02). "Detection of C60

and C70 in a Young Planetary Nebula". Science 329 (5996): 1180–

2. Bibcode2010Sci...329.1180C. doi:10.1126/science.1192035.PMID 20651118.

15. D. Sprinceana, M. Caldararu, N.I. Ionescu, A. Auroux, (1999) J. Therm. Anal.

Calorim. 56 109.

16. Diebold, U. (2002), Appl. Phys. A., 76, 186.

17. Diebold, U. (2003) The Surface Science of Titanium Dioxide. Surface Science

Reports, 48, 53–229.

18. Diebold, U., Ruzycki, N., Herman, G. S. & Selloni, A. (2003) One step towards

bridging the materials gap: Surface studies of TiO2 anatase. Catal. Today, 85,

93.

19. Duhovny D, Nussinov R, Wolfson HJ. (2002) Efficient Unbound Docking of

Rigid Molecules. In Gusfield et al., Ed. Proceedings of the 2'nd Workshop on

Algorithms in Bioinformatics(WABI) Rome, Italy, Lecture Notes in Computer

Science 2452, pp. 185-200, Springer Verlag.

20. G. Busca, L. Lietti, G. Ramis, F. Berti, (1998) Appl. Catal. B 18 1.

21. G. Munuera, F. Moreno, F. Gonzales, (1972) A model for anatase TiO2 surfaces:

interpretation of some interface processes. reactivity of solids, in: Proceedings

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -170-

of the 7th International Symposium Reaction Solids, Chapman & Hall, London,

p. 681.

22. G. Ramis, L. Yi, G. Busca, (1996) Catal. Today 28 373.

23. G. Ramis, L. Yi, G. Busca, M. Turco, E. Kotur, R.J. Willey, (1995) J. Catal. 157 523.

24. Ganapathy, Vadivel (2009). "Nutrient transporters in cancer: Relevance to

Warburg hypothesis and beyond".Pharmacology & Therapeutics 121 (1): 29–

40.doi:10.1016/j.pharmthera.2008.09.005.

25. Gharbi, N.; et al. (2005). "[60] fullerene is a powerful antioxidant in vivo with

no acute or sub acute toxicity". NanoLetters 5 (12):

257885. Bibcode 2005NanoL...5.2578G.doi:10.1021/nl051866b. PMID 16351219.

26. Gonzalez Szwacki, N.; Sadrzadeh, A.; Yakobson, B. (2007). "B80 Fullerene: An

Ab Initio Prediction of Geometry, Stability, and Electronic

Structure". PhysicalReviewLetters 98 (16):166804. Bibcode 2007PhRvL..98p6804

G.doi:10.1103/PhysRevLett.98.166804. PMID 17501448.

27. Google celebrates 25 years of the 'buckyball'Guardian.co.uk, 4 September 2010.

28. Gopakumar, G.; Nguyen, M.T.; Ceulemans, A. (2008). "The boron buckyball has

an unexpected Thsymmetry". Chemical Physics Letters 450 (4–6):

175.arXiv:0708.2331. Bibcode 2008CPL..450..175G.doi:10.1016/j.cplett.2007.11.030.

29. Guo, T.; Smalley, R.E.; Scuseria, G.E. (1993). "Ab initio theoretical predictions of

C28, C28H4, C28F4, (Ti at C28)H4, and M at C28 (M = Mg, Al, Si, S, Ca, Sc, Ti,

Ge, Zr, and Sn)".Journal of Chemical Physics 99 (1):

352. Bibcode1993JChPh..99..352G. doi:10.1063/1.465758.

30. Halford, B. (2006). "The World According to Rick". Chemical & Engineering

News 84 (41): 13.

31. Henson, R.W.. "The History of Carbon 60 or Buckminsterfullerene". Retrieved

2010-07-04.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -171-

32. Hiorns, R.C.; et al. (2010). "Synthesis of Donor-Acceptor Multiblock

Copolymers Incorporating Fullerene Backbone Repeat

Units". Macromolecules.14 43:60336044. Bibcode2010MaMol..43.6033H. doi:10.10

21/ma100694y.

33. http://www.nanodic.com/Carbon/Carbon_nanobud.htm

34. Hu, Zhen (2012). "Photodynamic anticancer activities of water-soluble

C60 derivatives and their biolgoical consequences in a HeLa cell

line.". Chemico-biological interactions 195 (1):8694. doi:10.1016/j.cbi.2011.11.003.

35. Iijima, S (1980). "Direct observation of the tetrahedral bonding in graphitized

carbon black by high resolution electron microscopy". Journal of Crystal

Growth 50 (3): 675.Bibcode 1980JCrGr.50..675I. doi:10.1016/0022-0248(80)90013-5.

36. Isik Onal, Sezen Soyer and Selim Senkan (2006) Adsorption of water and

ammonia on TiO2-anatase cluster models. Surf. Sci. 600 2457.

37. Jin- Kie S him, In-Sook Park, and Ju-Young Kim (2007) Use of Amphiphilic

Polymer Nanoparticles as a Nano-Absorbent for Enhancing Efficiency of

Micelle-enhanced Ultrafiltration Process, J. Ind. Eng. Chem., Vol. 13, No. 6, 917-

925.

38. Johansson, M.P.; Jusélius, J.; Sundholm, D. (2005). "Sphere Currents of

Buckminsterfullerene". Angewandte Chemie International Edition 44 (12):

1843–6.doi:10.1002/anie.200462348. PMID 15706578.

39. Jones, D. (1966). New Scientist 32: 245.

40. Kolosnjaj, J.; Szwarc, H.; Moussa, F. (2007). "Toxicity studies of carbon

nanotubes". Advances in Experimental Medicine and Biology. Advances in

Experimental Medicine and Biology 620: 181–204. doi:10.1007/978-0-387-76713-

0_14. ISBN 978-0-387-76712-3. PMID 18217344.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -172-

41. Kolosnjaj, J.; et al. (2007). "Toxicity studies of fullerenes and derivatives". In

Chan, W.C.. Bioapplications of Nanoparticles. Landes Bioscience. pp. 168–180.

42. Kroto, H.W.; et al. (1985). "C60: Buckminsterfullerene".Nature 318 (6042): 162–

163. Bibcode1985 Natur.318..162K. doi:10.1038/318162a0.

43. Li, Y.; et al. (2001). "Structures and stabilities of C60-rings". Chemical Physics

Letters 335 (56):524. Bibcode2001CPL.335.524L. doi:10.1016/S00092614(01)00064-

1.

44. Locke, W. (13 October 1996). "Buckminsterfullerene: Molecule of the

Month". Imperial College. Retrieved 2010-07-04.

45. Luann, B.; et al. (2007). "Impact Event at the Permian-Triassic Boundary:

Evidence from Extraterrestrial Noble Gases in Fullerenes". Science 291 (5508):

1530–3. Bibcode2001Sci...291.1530B. doi:10.1126/science.1057243.PMID 11222855.

46. M. Calatayud, P. Mori-Sa´nchez, A. Beltra´n, A. Martı´n Penda´s, E. Francisco, J.

Andre´s and J. M. Recio( 2001) Quantum-mechanical analysis of the equation of

state of anatase TiO2. J. Phys. Rev. B., 64,184113-1.

47. M. Primet, P. Pichat, M-V. Mathieu, (1971) J. Phys. Chem. 75 1216.

48. Markovic, Zoran (2008). "Biomedical potential of the reactive oxygen species

generation and quenching by fullerenes". Biomaterials 29 (26): 3561–

3573.doi:10.1016/j.biomaterials.2008.05.005.

49. Meija, J. (2006). "Goldberg Variations Challenge".Analytical and Bioanalytical

Chemistry 385: 6–7.doi:10.1007/s00216-006-0358-9.

50. Miessler, G.L.; Tarr, D.A. (2004). Inorganic Chemistry (3rd ed.). Pearson

Education. ISBN 0-13-120198-0.

51. Mitchel, D.R.; et al. (2001). "The Synthesis of Megatubes: New Dimensions in

Carbon Materials". Inorganic Chemistry40 (12): 2751–

5. doi:10.1021/ic000551q.PMID 11375691.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -173-

52. Mori, T.; et al. (2006). "Preclinical studies on safety of fullerene upon acute oral

administration and evaluation for no mutagenesis". Toxicology 225 (1): 48–

54.doi:10.1016/j.tox.2006.05.001. PMID 16782258.

53. Moussa, F.; et al. (1996). "Early effects of C60Administration in Swiss Mice: A

Preliminary Account forIn VivoC60Toxicity". Fullerene Science and

Technology 4: 21. doi:10.1080/10641229608001534.

54. Moussa, F.; et al. (1997). Proceedings of the Electrochemical Society 5: 332.

55. Mroz, Pawel (2007). "Functionalized fullerenes mediate photodynamic killing

of cancer cells: type I versus typee II photochemical mechanism". Free Radical

Biology & Medicine (43): 711–719.doi:10.1016/j.freeradbiomed.2007.05.005.

56. N. Sivaraman; R. Dhamodaran; I. Kaliappan et. al., "SOLUBILITY OF C-70 IN

ORGANIC-SOLVENTS", Fullerene Science and Technology, 1994, 2, 233.

57. N.A. Kachurovskaya, E.P. Mikheeva, G.M. Zhidomirov, (2000) J. Mol. Catal. 178

191.

58. N-Y. Topsøe, H. Topsøe, J.A. Dumesic, (1995) J Catal. 151, 226.

59. N-Y. Topsøe, H. Topsøe, J.A. Dumesic, (1995) J Catal. 151 ,241.

60. Osawa, E. (1970). Kagaku 25: 854.

61. P.C. Redfern, P. Zapol, L.A. Curtiss, T. Rajh, M.C. Thurnauer, (2003) J. Phys.

Chem. B 107,11419.

62. P.W. Fowler and D. E. Manolopoulos, "An atlas of fullerenes",

andhttp://www.nanotube.msu.edu/fullerene/fullerene-isomers.html

63. Poland, C.A.; et al. (2008). "Carbon nanotubes introduced into the abdominal

cavity of mice show asbestos-like pathogenicity in a pilot study". Nature

Nanotechnology 3 (7): 423–8. doi:10.1038/nnano.2008.111. PMID 18654567.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -174-

64. Postgraduate Research with Sussex Fullerene

Grouphttp://www.chm.bris.ac.uk/motm/buckyball/c60a.htm

65. Prasad, D.; Jemmis, E. (2008). "Stuffing Improves the Stability of Fullerenelike

Boron Clusters". Physical Review Letters 100 (16):

165504. Bibcode2008PhRvL.100p5504P.doi:10.1103/PhysRevLett.100.165504. PMI

D 18518216.

66. Pushparaj, V.L.; et al. (2007). "Flexible energy storage devices based on

nanocomposite paper". Proceedings of the National Academy of

Sciences 104 (34):135747.Bibcode 2007PNAS..10413574P.doi:10.1073/pnas.070650

8104. PMC 195942.PMID 17699622.

67. Qiao, Rui; Roberts, Aaron P.; Mount, Andrew S.; Klaine, Stephen J.; Ke, Pu

Chun. (2010)"Translocation of C60 and Its Derivatives Across a Lipid

Bilayer". Nano Letters. Retrieved 4 September.

68. Qixin Deng,ab Chaozhang Huang,a Wei Xie,a Jianping Zhang,a Yiqiang

Zhao,aZhensheng Hong,b Aiying Pangb and Mingdeng Wei*, (2011) Significant

reduction of harmful compounds in tobacco smoke by the use of titanate

nanosheets and nanotubes, Chem. Commun., 47, 6153–6155.

69. R. Hengerer, B. Bolliger, M. Erbudak, M. Grätzel, (2000) Surf. Sci. 460 162.

70. Ruoff, R.S.; et al. (1993). "Solubility of fullerene (C60) in a variety of

solvents". Journal of Physical Chemistry 97 (13): 3379. doi:10.1021/j100115a049.

71. Sano, N.; et al. (2001). "Synthesis of carbon 'onions' in water". Nature 414 (6863):

506–7. Bibcode2001Natur.414..506S. doi:10.1038/35107141.PMID 11734841.

72. Sayes, C.M.; et al. (2007). "Comparative Pulmonary Toxicity Assessments of

C60Water Suspensions in Rats: Few Differences in Fullerene Toxicity in Vivo

in Contrast to in Vitro Profiles". Nano Letters 7 (8): 2399–

406. Bibcode2007NanoL...7.2399S. doi:10.1021/nl0710710.PMID 17630811.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -175-

73. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ. (2005) PatchDock

and SymmDock: servers for rigid and symmetric docking. Nucl. Acids. Res. 33:

W363-367.

74. Schultz, H.P. (1965). "Topological Organic Chemistry. Polyhedranes and

Prismanes". Journal of Organic Chemistry 30 (5): 1361. doi:10.1021/jo01016a005.

75. Shvartsburg, A.A.; et al. (1999). "Ball-and-Chain Dimers from a Hot Fullerene

Plasma". Journal of Physical Chemistry A 103: 5275. doi:10.1021/jp9906379.

76. Stars reveal carbon 'spaceballs' July 22, 2010

77. Sutassana Na-Phattalung, M. F. Smith, Kwiseon Kim, Mao-Hua Du, Su-Huai

Wei, S. B. Zhang and Sukit Limpijumnong (2006) First-principles study of native

defects in anatase TiO2 J. Phys. Rev. B., 73, 125205-1.

78. T. Bredow and K. Jug, (1995) Surf. Sci. 327 398.

79. T. Bredzona, G. Puchkovska, V. Shymanovska, J. Baran, H. Ratajczak, (2004) J.

Mol. Struct. 700 175.

80. T.Z. Srnak, J.A. Dumesic, B.S. Clausen, E. Tornqvist, N.Y. Topsoe, (1992) J.

Catal. 135 2246.

81. Talyzin, A.V. (1997). "Phase Transition C60−C60*4C6H6in Liquid

Benzene". Journal of Physical Chemistry B 101 (47): 9679. doi:10.1021/jp9720303.

82. Talyzin, A.V.; Engström, I. (1998). "C70 in Benzene, Hexane, and Toluene

Solutions". Journal of Physical Chemistry B 102 (34):

6477. doi:10.1021/jp9815255.

83. Tegos, G.; et al. (2005). "Cationic Fullerenes Are Effective and Selective

Antimicrobial Photosensitizers". Chemistry & Biology 12 (10): 1127–

1135.doi:10.1016/j.chembiol.2005.08.014. PMC 3071678.PMID 16242655.

84. The allotropes of carbon". Interactive Nano-Visualization in Science &

Engineering Education. Retrieved 2010-08-29.

In silico designing and synthesis of nanoparticles……………………..biomolecules Chapter 4

Page -176-

85. Thrower, P.A. (1999). "Editorial". Carbon 37 (11): 1677.doi:10.1016/S0008-

6223(99)00191-8.

86. Yanagisawa, K.; Overstone, J. (1999) Crystallization of Anatase from

Amorphous Titania Using the Hydrothermal Technique: Effects of Starting

Material and Temperature. J. Phys. Chem. B, 103, 7781.