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Human Papilloma Virus Proteins Biology

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3.1.1 Human villoma virus proteins and their manner of action

Human papillomavirus ( HPV ) is a omnipresent sexually transmitted DNA virus. A subset of mucosal HPVs are termed “ bad ” ( for illustration, types 16, 18 and 31 ) because of an increased association with cervical malignant neoplastic disease ( Zur Hausen. , 1996 ) . Among this group, HPV16 is the most common type, being found in approximately 50 per centum of invasive malignant neoplastic diseases worldwide ( Clifford et al. , 2003 ) . Two HPV16 oncoproteins, E6 and E7, are actively expressed in cervical malignant neoplastic disease cells and are responsible for host cell transmutation and malignant neoplastic disease patterned advance ( Griep et al.

, 1993, Yutsudo et al. , 1998 ) . From old surveies, the E6 ( I ) transcript has been found to be the most abundant one detected in HPV16 transformed cells, transgenic animate beings, cervical malignant neoplastic disease cell lines and clinical samples ( Griep et al.,1993, Smotkin et al.

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, 1989, Cornelissen et al. , 1990 ) . While E7 is predicted to interpret from spliced merchandises every bit good as full-length transcripts, E6 protein can merely be encoded from full-length transcripts ( Smotkin et al. , 1989, Schneider et al. , 1988 ) . The splice has been proposed to advance E7 interlingual rendition by supplying infinite for ribosome induction to happen ( Smotkin et al. , 1989, Smotkin et al. , 1986 ) . However, it has been revealed that the interlingual rendition of E7 from the full-length transcript is every bit efficient as those from spliced transcripts and that splicing is non required for E7 synthesis ( Stacey et al. , 1995 ) .

3.1.2 Human villoma virus -16 E6 and E7 proteins construction

The mark for unwritten and cervical malignant neoplastic disease as HPV 16 E6 and E7 has been taken for this survey. The proteins taken for this survey retrieved from the PDB ( Protein Data Bank ) . The X-ray crystallography construction ( 3D construction ) taken for the HPV 16 E6 ( PDB ID: 2FFK4 ) and HPV E7 ( PDB ID: 2B9D ) protein taken for this survey. The of sequence informations for both the protein in fig 3.1.2.1 and 3.1.2.2.

& gt ; 2FK4: A |PDBID|CHAIN|SEQUENCE

GAMSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSRTRRETQL

& gt ; SPR|P03126|VE6_HPV16 ( 158 AA ) E6 protein [ Human papillomavirus type 16 ]

MHQKRTAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYCYSLYGTTLEQQYNKPLCDLLIRCINCQKPLCPEEKQRHLDKKQRFHNIRGRWTGRCMSCCRSSRTRRETQL

Fig. 3.1.2.1 Fasta Sequence of HPV16 E7 Protein In PDB ( PDB ID: 2FK4 )

& gt ; 2B9D: A|PDBID|CHAIN|SEQUENCE

MKQPYAVVASCAYCEKLVRLTVLADHSAIRQLEEMLLRSLNIVCPLCTLQRQ

Fig. 3.1.2.2 Fasta Sequence of HPV E7 Protein

3.1.3 Structural composing of mark proteins

This has been good known that Papillomaviruses ( PV ) infect mammals, birds and reptilians universe broad. The virus is little round two-base hit stranded DNA ( 8 kilobit ) more than 170 PV ( & gt ; 100 HPV ) strains. These viruses infect cutaneal or mucosal epithelial cells. Papilloma viruses were classified as High hazard and Low hazard on the footing of infection. Low hazard HPVs generate benign lesions ( warts ) while High hazard HPVs may bring forth tumors. The per centum of virus in cervical malignant neoplastic diseases is linked to HPV infection are 99 per centum. Link between HPV and malignant neoplastic disease was being recognised by Nobel Prize victor H. zur Hausen in 2008. The chief oncoproteins of HPV are called E6 and E7. E6 and E7 cooperate to prime cell proliferation for the interest of viral replication.E6 ( venereal bad HPVs ) . E6 participates to proliferation of septic cells in host cells and besides participates to care of viral episomes. This is good reported that E6 and E7 cistrons ever integrated in cervical malignant neoplastic disease cells. E6 has immortalizing and transforming effects.E6 modulates programmed cell death, aging and cell adhesion processes excessively in malignant neoplastic disease pathogenesis.

The construction of shows that HPV 16 E6 contains 150 residues, 2 Zn sites. The cellular localisation of HPV 16 E6 is preferentially atomic and it binds and frequently degrades more than 50 cellular mark proteins. The protein recruits the cellular ubiquitin ligase E6AP and helps promotes debasement of tumour suppresser p53 ( E6/E6AP/p53 composite ) . The protein promotes debasement of several PDZ sphere proteins and promotes look of the RT fractional monetary unit of telomerase is a DNA-binding protein acknowledging four-way Holliday junctions and it strongly binds to RNA Fig.3.1.3.1 ( A ) . The two spheres of dwelling of mated CXXC motive that are each related to the E7 carboxyl end point ( Cole et al, 1987 ) .

A

Fig.3.1.3.1 ( A ) .Schematic representation of the HPV-16 E6 oncoprotein. The sequence contains two metal adhering motives that are related to the E7 carboxyl end point ( bluish ) . The E6 carboxyl end point contains a PDZ protein-binding motive ( xanthous ) that is similar to the carboxyl-terminal PDZ adhering motive of Ad9 E4 ORF1. Many HPV-16 E6 binding proteins, including E6-AP, paxillin, E6-BP, and IRF-3, incorporate a conserved I±-helical sphere and presumptively interact with similar E6 sequences. The isoleucine residue at place 128 significantly contributes to interaction with I±-helix spheres incorporating E6 binding proteins. Identical and chemically similar amino acid residues are highlighted by ruddy and bluish boxes, severally.

Bacillus

Fig.3.1.3.1 ( B ) Schematic representation of the HPV-16 E7 oncoprotein. The amino-terminal 37 amino acid residues have sequence similarity to a part of CR1 ( green ) and to CR2 ( ruddy ) of Ad E1A. Identical and chemically similar amino acid residues between HPV-16 E7 and Ad5 E1A are highlighted by ruddy and bluish boxes, severally. CR1 sequences are necessary for cellular transmutation and pRB debasement but do non straight contribute to pRB binding. Sequences in CR2 include the nucleus pRB adhering site ( LXCXE ) , which is necessary for cellular transmutation, every bit good as a casein kinase II consensus phosphorylation site ( CKII ) . The E7 carboxyl end point ( bluish ) contains a metal adhering motive and mediates association with multiple host cellular proteins, including histone-modifying enzymes, which may besides lend to cellular transmutation.

The ability of bad HPV E6 proteins to tie in with PDZ host proteins is relevant to cellular transmutation. This relevancy has been best illustrated in a transgenic mouse theoretical account in which the ability of HPV-16 E6 to bring on skin hyperplasias ( Lambert et Al, 1993 ) is dependent on the unity of the carboxyl-terminal PDZ binding sphere. A considerable figure of extra cellular proteins have been reported to tie in with E6. These include the EF-hand calcium-binding protein E6-BP ( reticulocalbin 2 ) ( Chen et al. , 1995 ) the interferon regulative factor IRF-3 ( Ronco et al. , 1998 ) and the focal adhesion protein paxillin ( Tong et al. , 1997, Vande et al. , 1998. ) . Hyperactivity of focal adhesion kinase ( FAK ) has been detected in cervical malignant neoplastic disease and HPV immortalized epithelial cell lines, but the mechanism is ill-defined ( McCormack et al. , 1997 ) . Because these and other possible E6 cellular mark proteins portion a conserved I±-helical interaction site for E6 association ( Elston et al. , 1998 ) ( Fig.3.1.3.1 ( A ) ) , it has been difi¬?cult to find the relevancy of these single interactions to the biological activities of bad HPV E6 proteins.

Bad HPV-derived E7 proteins interact with pRB more efi¬?ciently than E7 proteins encoded by low-risk mucosal HPVs ( Gage et al. , 1990, Munger et al. , 1989 ) , and mutants in the LXCXE sphere that affect pocket protein association are transmutation faulty in different assay systems. Bad HPV E7 proteins have the alone ability to destabilise the pocket proteins through a proteasome-dependent mechanism ( Berezutskaya et al. , 1997, Boyer et al. , 1996 ) . In add-on to the LXCXE sphere, sequences within the amino-terminal CR1 homology sphere of bad HPV E7 are necessary for the ability to destabilise pocket proteins. Bad HPV E7 proteins with mutants in the CR1 homology sphere are besides transformation dei¬?cient Hence, the ability of bad E7 proteins to destabilise pocket proteins is critical for cellular transmutation ( Fig.3.1.3.1 ( A ) ) . In add-on to pRB binding and debasement, E7 has other cellular marks that are relevant to cellular transformation.HPV E7 can overrule the growth-inhibitory activities of cyclin dependent kinase inhibitors, including p21CIP1 ( Funk et al. , 1997 ) and p27KIP1 ( Zerfass et al.,1996 ) . Since these proteins are critical regulators of cell rhythm apprehension during keratinocyte distinction, their suppression by E7 may besides lend to the care of a replication-competent cellular surroundings in differentiated host epithelial cells. Similar to the instance for the amino-terminal pRB adhering site, the unity of the carboxyl terminal E7 sequences that have been implicated in histone deacetylase binding are necessary for the viral life rhythm ( 88 ) . Hence, these interactions may lend to transforming activities of bad HPV E7 proteins ( Fig.3.1.3.1 ( B ) ) .

3.2 Materials and Methods

3.2.1 Docking and their types

The procedure by which a new drug is brought to market phase is referred to by a figure of names most normally as the development concatenation or “ grapevine ” , and consists of a figure of distinguishable phases

Phases in drug find and development:

1. Discovery/Basic Research

Synthesis and Extraction- the procedure of placing new molecules with the possible to bring forth a coveted alteration in a biological system

Biological Screening and Pharmacological Testing- surveies to research the pharmacological activity and curative potency of compounds

2. Preclinical Testing

Toxicology and Safety Testing- trials to find the possible hazard a compound poses to worlds and the environment, involve usage of animate beings, tissue civilizations or other trial systems

Pharmaceutical Dosage Formulation and Stability – the procedure of turning an active compound into a signifier and strength suited for human usage

3. Regulative Reappraisal: IND

Application to regulative authorization to utilize compound in human proving. In

the US the compound is so called an Investigational New Drug ( IND )

4. Phase I Clinical Tests

Testing of a new compound in 20-80 healthy human voluntaries to find tolerance, pharmacological effects, and soaking up, distribution, metamorphosis and elimination ( ADME ) forms

5. Phase II Clinical Tests

Tests in 100-300 patients with the targeted status to find effectivity in handling disease or medical status and short term hazards

6. Phase III Clinical Tests

Tests on 1000-5000 patients to find clinical benefit and incidence of inauspicious reactions

7. Procedure Development for Manufacturing and Quality Control

Engineering and fabricating design activities to set up capacity to bring forth in big volumes and to guarantee stableness, uniformity and overall quality

8. Bioavailability Studies

Use of healthy voluntaries to demo that preparation used in tests is tantamount to merchandise to be marketed

9. Regulative Reappraisal: NDA

Application for blessing to market a new drug. In the US this is called a New Drug Application ( NDA )

10. Phase IV

Post selling tests to place undetected inauspicious effects and long term

morbidity and mortality profile

Molecular acknowledgment plays a cardinal function in advancing cardinal biomolecular events such as enzyme-substrate, drug-protein and drug-nucleic acid interactions. Detailed apprehension of the general rules that govern the nature of the interactions ( van der Waals, H bonding, electrostatic ) between the ligands and their protein or nucleic acerb marks may supply a conceptual model for planing the coveted authority and specificity of possible drug leads for a given curative mark. Practical application of this cognition requires structural informations for the mark of involvement and a process for measuring campaigner ligands. There are assorted computational moorage methods are available ( Kuntzet et al. , 1982, DesJarlais et al. , 1988, Rarey et al. , 1996, Jones et al. , 1997. Abagyan et al.,1994 ) . These provide one attack to the ranking of possible ligands with regard to their ability to interact with a given mark.

Computational moorage of a little molecule to a biological mark involves efficient sampling of possible airss of the former in the specified binding pocket of the latter in order to place the optimum binding geometry, as measured by a user-defined fittingness or mark map. X-ray crystallography and NMR spectroscopy continue to be the primary beginning of three-dimensional structural informations for protein and nucleic acerb marks. In favourable instances where proteins of unknown construction have high sequence homology to cognize constructions, homology mold can supply a feasible option by bring forthing a suited starting point for ‘in silico ‘ find of high affinity ligands. Over the last few old ages a huge sum of attempt has been directed toward developing efficient docking methods and hiting maps as tools for the designation of lead compounds.

The complexness of computational moorage additions in the undermentioned order: ( a ) stiff organic structure moorage, where both the receptor and little molecule are treated as stiff. ( B ) flexible ligand moorage, where the receptor is held stiff, but the ligand is treated as flexible ; and ( degree Celsius ) flexible moorage, where both receptor and ligand flexibleness is considered. Therefore far, the most normally used docking algorithms use the stiff receptor/flexible ligand theoretical account. The chief moorage methods that are used extensively employ hunt algorithms based on Monte Carlo, familial algorithm, fragment-based and molecular kineticss. Some plans that are well-suited for high throughput moorage of a big database of molecules include: DOCK ( Kuntzet et al. , 1982, DesJarlais et al. , 1988 ) , FlexX ( Rarey et al. , 1996 ) , GOLD ( Jones et al. , 1997 ) , and ICM ( Abagyan et al. , 1994 ) .

3.2.2 Softwares procurance for active site designation

The In silico interaction survey for the active site designation was carried out by the undermentioned packages.

1. Ligsite: online package for active site anticipation ( hypertext transfer protocol: //gopubmed2.biotec.tudresden.de/cgibin/index.php )

2. Deep position /swiss -pdb Viewer3.7: for the visual image of proteins

3-D construction and active site designation in marks.

3.2.3 Softwares procurance for docking survey

Python -2.4.4: As back uping tool for the moorage procedure

Autodock Tools-1.5.1: for the moorage advancement

Cygwin: As back uping tool for the moorage procedure

3.2.4 Softwares procurance for visual image of mark ligand interactions

Chimera-1.2470 ( win 32 ) : for the visual image of proteins and ligands interaction in the signifier of H-Bonds.

The NMR construction of oncoprotein HPV 16 E6 was downloaded from the Brookhaven Protein Data Bank ( PDB ) with PDB entry of 2FK4. Three Pockets were identified in 2fk4 by the LIGSITE. The grid infinite taken for 3 pockets was 1.0 Angstrom and the investigation radius for possible binding site was 5.0 Angstrom. All 3 pockets were being visualized by Swiss-Pdb spectator ( hypertext transfer protocol: //www.expasy.org/spdbv/ ) . Finding of 3 nearest residues to these pockets was besides determined within the scope of 5 AA° .

It was found that GLY 8, ARG 25 and GLN 46 are the closest residues to PKT 1, PKT 2 and PKT 14 in HPV 16 E6 ( PDB CODE: 2FK4 ) severally ( Fig.3.3.1 ) . GLN44, LYS 57 and LEU77 of HPV E7 ( PDB CODE: 2B9D ) of chain-B were the closest residue ( Fig. 3.3.2 ) .

Fig. 3.3.1 Three pockets of ( PDB ID: 2FK4 ) demoing closest residue GLY 8, ARG 25 and GLN 46 in scope of 5 AA° .

Fig. 3.3.2 Three pockets of ( PDB ID: 2B9D ) demoing closest residue GLN44, LYS 57 and LEU77 in scope of 5 AA° .

Curcuminoids and its parallels ( Table: 2.6.1 ) were generated in PDB file format and were docked individually on three pockets of both proteins by Autodock 4.0. Crystal constructions of known mark protein of HPV 16 E6 ( PDB Idaho: 2FK4 ) and HPV E7 ( PDB CODE: 2B9D ) were retrieved from PDB ( Protein Data Bank ) .

The moorage survey parametric quantities by Autodock 4 includes grid infinite 60A-60A-60 AA° . Genetic algorithms method was used as seeking method to foretell best adhering verification. In GA method entire 10 tallies with population size 150 and 2500000 rating were used in docking procedure by Autodock4 to foretell the best interactions ( Fig. 3.3.3 ) . All ligands were docked on the all three residues of HPV 16 E6 and E7 proteins.

Fig. 3.3.3: Search parametric quantities through Genetic algorithms in docking analysis by Autodock 4.0 for Ligands

3.3 Consequences

3.3.1 Docking parametric quantities

HPV 16 E6 and E7 proteins in silico moorage survey were done by the following parametric quantities by Autodock 4.0 programm.

Run ( Out of 10 Run in which the lower limit energy was calculated )

Minimum Binding energy

Inter molecular H-Bond

Intra molecular H-Bond

3.3.2 Docking consequences of HPV 16 E6 and E7 protein with ligands by Autodock 4.0

There were 10 tallies for each docking places and the minimal binding energy tally was taken for best docking on HPV 16 E6 ( PDB ID: 2FK4 ) . The ligands were visualized by Chimera for the figure of inter and intra H-Bonds ( Table-3.3.1 ) . The three active site were docked by Autodock 4.0 programm in which shows Curcumin exhibits maximal figure i.e. 10 of intra molecular H-bonding on 1st active site with residue GLY 8 which is an indicant of highest authority while Cholorogenic acid and cyclocurcumin indicated -7.13 and -4.41 Kcal/mol adhering energy on GLY 8 residue severally. Piperic acids show 9 intra molecular H Bonds after curcumin on GLY 8 mark residue.

The 2nd residue ARG 25 shows best adhering energy for Cholorogenic acids, cyclocurcumin and demethoxycurcumin which were -7.28, -6.88 and-6.30 Kcal/mol severally. Maximal H-Bond interaction bisdemethoxy curcumin and demethoxy curcumin exhibits 9, 8, 8 severally.

The 3rd residue GLN 8 shows best adhering for bisdemethoxy curcumin, cholorogenic acid, caffeic acid and cyclocurcumin shows +24.69, -6.38, -5.49, and -5.44 Kcal/mol severally ( Table-3.3.1 ) .

The moorage survey on HPV E7 ( PDB ID: 2B9D ) shows that on first residue GLN 44 cholorogenic acid, quercetin, cyclocurcumin, bisdemethoxy curcumin -7.66, -5.83, -5.47 and -5.17 Kcal/mol adhering energy severally. The Highest intra molecular H-Bonds found in capsaicin, eugenol, Bis demethoxy curcumin, curcumin dipiperoyl ester i.e, 43, 19, 16 and 16 severally.

Second residue LYS 57 shows maximal binding for the cholorogenic acid, quercetin, ferulic acid, cyclocurcumin -5.80, -5.49, -5.07 and -5.36 Kcal/Mol severally. The intra-molecular H Bond in instance of quercetin, cholorogenic acid, ferulic acid, 45, 41, and 35 severally. Third residue of HPV E7 shows maximal adhering for cyclocurcumin, cholorogenic acid, and dibenzoyl methane shows -6.03, – 5.63 and -5.58 k cal/mol severally. Intra-molecular H Bonds maximally shows in 44, 43, 42 for piperic acid, Yakuchinone B and Dehydro Zingerone severally ( Table -3.3.2 ) .

Ligands

No of H bond on 1st active site

( Residue 8: GLY )

No of H bond on 2st active site

( Residue 25: ARG )

No of H bond on 3st active site

( Residue 46: GLN )

Run

Minimum Binding energy

Inter

molecular

H-Bond

Intra molecular

H-Bond

Run

Minimum Binding energy

Inter

molecular

H-Bond

Intra molecular

H-Bond

Run

Minimum Binding energy

Inter

molecular

H-Bond

Intra molecular

H-Bond

Curcumin

5

63.44

4

10

3

-5.62

8

3

4

-4.66

3

1

Bisdemethoxy Curcumin

6

-4.09

5

1

6

-5.90

9

3

3

+24.69

4

6

Caffeic acid

2

-4.01

5

4

3

-5.06

4

0

2

-5.49

3

0

Capsaicin

6

19.05

0

7

4

-3.99

2

1

8

-3.53

1

7

Cassumunins A

7

-0.17

3

4

10

-3.73

3

3

1

-2.37

4

6

Cassumunins B

6

-2.72

0

7

9

-3.41

2

1

7

-3.71

1

2

Cholorogenic

Acid

6

-7.13

4

2

2

-7.28

5

4

8

-6.38

3

2

Curcumin dipiperoyl ester

1

-2.20

3

7

7

-3.58

5

4

1

-2.64

3

0

Cyclocurcumin

5

-4.41

4

4

5

-6.88

3

2

3

-5.44

2

1

Dehydro

Zingerone

10

-3.99

3

1

1

-4.17

3

0

3

-3.99

3

3

Demethoxy

Curcumin

2

-3.81

3

3

8

-6.30

8

3

9

-4.93

3

1

Diaryl

Pentanoids

9

-4.27

3

4

4

-6.55

2

3

3

-4.48

4

6

Diaryl

Pentanoids II

6

-2.45

2

3

7

-3.51

2

4

10

-3.88

1

6

Dibenzoyl

Methane

9

-4.20

0

2

4

-5.40

0

0

4

-5.39

1

3

Dihydro guarietic acid

10

-3.99

1

3

1

-4.17

3

1

3

-3.99

2

7

Eugenol

10

-3.99

2

1

3

-4.30

2

0

2

-3.36

2

2

Ferulic acid

7

-4.86

2

1

1

-5.70

5

0

2

-5.81

3

3

Iso Eugenol

8

-3.98

2

1

7

-4.36

2

1

1

-3.32

2

1

Piperic acid

2

-3.08

3

9

2

-4.20

5

1

9

-3.68

3

3

Quercetin

( Flavnoids )

10

-4.05

3

3

7

-5.30

6

1

4

-5.23

5

0

Yakuchinone A

7

-0.17

0

2

10

-3.73

4

3

1

-2.37

0

1

Yakuchinone B

6

-2.72

2

1

9

-3.41

2

1

7

-3.71

2

6

Zingerone

2

-3.67

1

1

8

-4.27

3

0

10

-3.94

4

3

Table 3.3.1: Consequences of Docking survey on ligand HPV16 E6 protein ( PDB ID: 2FK4 )

No of H bond on 1st active site

( Residue 44: GLN )

No of H bond on 2st active site

( Residue 57: LYS )

No of H bond on 3st active site

( Residue 77: Leu )

Run

Minimum Binding energy

Inter

molecular

H-Bond

Intra molecular

H-Bond

Run

Minimum Binding energy

Inter

molecular

H-Bond

Intra molecular

H-Bond

Run

Minimum Binding energy

Inter

molecular

H-Bond

Intra molecular

H-Bond

Curcumin

6

-4.89

5

9

9

-4.08

5

7

10

-4.74

9

33

Bisdemethoxy Curcumin

2

-5.17

3

16

4

-4.25

4

9

6

-4.69

5

14

Caffeic acid

7

-4.68

6

6

3

-4.59

5

4

7

-4.23

7

37

Capsaicin

2

-3.71

6

43

6

-2.94

3

11

6

-3.90

2

6

CassumuninsA

2

-4.35

4

8

2

-3.37

5

23

7

-4.54

0

16

CassumuninsB

7

-4.32

3

7

2

-2.35

1

20

7

-5.09

4

11

Cholorogenic Acid

2

-7.66

9

9

8

-5.80

13

41

2

-5.63

7

41

Curcumin dipiperoyl ester

2

-5.02

3

16

4

-3.46

6

20

7

-4.15

4

36

Cyclocurcumin

10

-5.47

5

10

4

-5.36

3

11

1

-6.03

1

6

Dehydro Zingerone

7

-3.83

5

7

3

-3.40

3

9

3

-3.96

6

42

Demethoxy Curcumin

10

-5.15

7

11

5

-3.92

3

7

3

-4.36

6

11

Diaryl Pentanoids

5

-5.83

2

14

6

-5.38

11

2

2

-5.47

2

11

DiarylPentanoids II

1

-4.46

2

12

7

-4.00

5

40

4

-4.45

2

16

Dibenzoyl methane

5

+0.23

0

0

4

-4.72

7

7

4

-5.58

0

6

Dihydro guarietic acid

2

-4.68

4

8

3

-4.48

2

7

2

-4.94

2

7

Eugenol

2

-3.54

5

19

8

-3.82

2

7

7

-3.82

4

39

Ferulic acid

5

-5.37

7

7

4

-5.07

6

35

6

-5.10

6

35

Flavnoids

2

-4.47

0

6

3

-3.80

2

15

6

-4.44

2

37

Iso Eugenol

9

-3.73

5

16

4

-3.36

0

34

4

-3.82

3

34

Piperic acid

8

-4.0

6

10

9

-4.12

5

30

2

-4.17

6

44

Quercetin ( Flavnoids )

9

-5.83

8

11

9

-5.49

9

45

4

-5.48

6

40

Yakuchinone A

6

-4.65

5

9

5

-3.28

4

27

3

-4.24

2

9

Yakuchinone B

1

-4.56

4

15

6

-3.88

1

10

6

-4.91

5

43

Zingerone

4

-3.99

2

11

9

-3.29

4

9

10

-4.01

6

31

Table 3.3.1: Consequences of Docking survey on ligand HPV E7 protein ( PDB ID: 2B9D )

3.2.3 Docking analysis of HPV 16 E6 and E7 protein with ligands by Scigress 7.7.0.47

The Automatic moorage ( Blind docking ) analysis was performed by Scigress 7.7.0.47. The docking analysis includes the readying of ligands, cleansing of targeted proteins HPV 16 E6 and E7and optimisation of ligands. The consequences were predicted on the footing of PMF mark – dock flexible ligand in stiff active site ( kcal/mol ) for both the proteins.

No.

Name of Ligands

PMF mark for E6 Protein

( PDB ID: 2FK4 )

PMF mark for E6 Protein

( PDB ID: 2B9D )

1.

Bis Demethoxy Curcumin

-51.503

-54.278

2.

Caffeic acid

-62.267

-42.377

3.

Capsaicin

-50.654

-25.771

4

Cholorogenic Acid

-99.782*

-68.327*

5.

Cassumunins A

-44.556

-25.806

6.

Cassumunins B

-55.462

-23.38

7.

Curcumin

-85.699*

-64.03*

8.

Curcumin dipiperoyl ester

-74.859

-34.066

9.

Cyclocurcmin

-54.515

-44.148

10.

Demethoxy Curcumin

-78.974*

-64.011*

11.

Dehydro Zingerone

-41.759

-32.664

12.

Diaryl Pentanoids

-61.251

-22.691

13.

Diaryl Pentanoids II

-54.224

-22.753

14.

Dihydro guarietic acid

-65.578

-45.978

15.

Eugenol

-37.275

-26.938

16.

Ferulic acid

-46.627

-43.631

17.

Piperic acid

-60.454

-42.662

18.

Quercetin

-67.679

-56.059

19.

Yakuchinone A

-45.20

-47.719

20.

Yakuchinone B

-53.811

-50.084

21.

Zingerone

-40.826

-33.878

*Ligands shows the best binding consequence on marks by PMF

Table: 3.2.1 Automated Docking analysis consequences by Scigress 7.7.0.47. on HPV 16 E6 and E7 Protein

The docking survey of protein and ligands were performed by converted from.pdb to.csf format utilizing standard functionality from the Workspace faculty of Scigress Explorer 7.7.0.47. The both marks ( PBD ID: 2FK4 and 2B9D ) was docked with ligands ( Table: 3.2.1 ) and was scored on the footing of automatic dock, which scores a ligand in an active site from the workspace application utilizing a potency of average force ( PMF ) with a familial moorage algorithm.

The moorage consequences shows highest adhering in footings of PMF mark for Cholorogenic acid -99.782 and -68.327, curcumin -85.699 and -64.03, demethoxy curcumin -78.97 and -64.011 on 2FK4 and 2B9D severally.

Cite this Human Papilloma Virus Proteins Biology

Human Papilloma Virus Proteins Biology. (2016, Dec 06). Retrieved from https://graduateway.com/human-papilloma-virus-proteins-biology-essay/

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