Final Report

Molecular Modelling Portfolio 2009

Information on ligand

CHEMICAL NAME

6-BENZO[1,3]DIOXOL-5-YL-2-METHYL-2,3,6,7,12,12A-HEXAHYDRO-PYRAZINO[1',2':1,6]PYRIDO[3,4-B]INDOLE-1,4-DIONE

COMMON NAME TADALAFIL, CIALIS

MOLECULAR FORMULA C22 H19 N3 O4

SMILES STRINGCN1CC(=O)N2[CH](Cc3c([nH]c4ccccc34)[CH]2c5ccc6OCOc6c5)C1=O

2D structure of ligand :

Fig 1: Tadalafil (2D structure)

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3D structure of ligand :

Fig 2: Tadalafil (3D structure)

Ligand optimization by MOPAC

Information as in Table 2 is obtained by ligand poptimization, after running mopac process in VEGA. The structure of the ligand after energy minimization changes to as in Fig 3.

Parameters Values

HEAT OF FORMATION -17.929575 KCAL

ELECTRONIC ENERGY -39795.618392 EV

CORE-CORE REPULSION 34817.754630 EV

GRADIENT NORM 20.380683

DIPOLE 1.53840 DEBYE

NO. OF FILLED LEVELS 73

IONIZATION POTENTIAL 8.477715 EV

MOLECULAR WEIGHT 389.410

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SCF CALCULATIONS 116

COMPUTATION TIME 14.984 SECONDS

Table 2

Fig 3: ligand structure after energy minimization

Chiral Centres: On detecting stereo chemistry of ligand in Chem Bio3D software, Two chiral carbon atoms were found to be

present at C11(S) and C13(R).

Molecular Propertis: Following details were obtained by computing properties of ligand Chem Bio 3D software. Various properties of

ligand is given in Table 1.

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Molecular Properties Values

LogP 1.128

Mol Refractivity 10.610

Mol Weight 389.40396

Partition Coefficient 2.583999

Polar Surface Area 71.11Angstrom Squared

Number of Rotatable Bonds 1bond

Henry's Law Constant 20.972


Table- 1

Information on Protein

The PDB code given to me was 1UDU. I inserted that code in PDB site and reached to my protein, which was Human Phosphodiesterase 5 enzyme. IT is form the phosphopdiesterase class of proteins. This enzyme can be found mainly in corpus cavernosum and retina, but it is also present in some of the other tissues such as platelets, smooth muscles and skeletal muscles in lower concentrations. PDE5 is target for many diseases such as heart failure, depression, asthma, inflammation and erectile dysfunctions. PDE5 has ability to degrade intracellular second messenger cAMP and cGMP. In corpus cavernosum tissue PDE5 hydrolyses the cGMP, hence it is a suitable drug target for sidenafil and tadalafil(Viagra) like drugs. Sidenafil and tadalafil bind to the PDE5 catalytic site with high affinity and specificity. These drugs are used to treat erectile dysfunction.

Sequence for Phosphodiesterase chain A

1 TRELQSLAAA VVPSAQTLKI TDFSFSDFEL SDLETALCTI RMFTDLNLVQ TTHHHHHSS TTTTTT T TT STTS HHHHHHHHH HHHHTTTHHH

51 NFQMKHEVLC RWILSVKKNY RKNVAYHNWR HAFNTAQCMF AALKAGKIQN HTT HHHHH HHHHHHHHTS TTSSSSSHH HHHHHHHHHH HHHTTTT GG

101 KLTDLEILAL LIAALSHDLD HRGVNNSYIQ RSEHPLAQLY CHSIMEHHHF GS SHHHHHH HHHHTSTTTT S SHHHHHHH

151 DQCLMILNSP GNQILSGLSI EEYKTTLKII KQAILATDLA LYIKRRGEFF HHHHHHHHST T TTTTS H HHHHHHHHHH HHHHTT HH HHHSSTTTTT

201 ELIRKNQFNL EDPHQKELFL AMLMTACDLS AITKPWPIQQ RIAELVATEF TTTTT S SSHHHHHHHH HHHHHHHHGG GGGS HHHHH HHHHHHHHHH

251 FDQGDRERKE LNIEPTDLMN REKKNKIPSM QVGFIDAICL

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QLYEALTHVS HHHHHHTTTS S STTS SS TTSHHHH HHHHHHHTHH HHHHHHHHH

301 EDCFPLLDGC RKNRQKWQAL AEQQ GGGHHHHHHH HHHTTTHHHH HTT

Table2

Cavities without Ligand:

Q-site finder is a software, which can predict the possible binding sites of ligand in protein molecule. Fig 3 obtained from this software shows almost 10 possible binding sites for tadalafil ligand molecule in protein structure. These binding sites are in different colours as shown in Fig 3.

Fig 3: ligand binding sites

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Missing Residues:

PDB file can be open in chimera by clicking on Fetch by PDB ID.

Moreover it can be saved in PDB in format in chimera. by doing so, that saved file can

also be opened in notepad, which gives complete details about protein structure such as

name if residues, in what chain they are present, sequence number of residues, name of

the ligand present in it, class of the protein and also missing residues. From the obtained

details I have selected information about missing residues of protein which is presented in

Table 3

Residue Name Chain Sequence Number

ILE A 665

GLN A 666

ARG A 667

SER A 668

GLU A 669

HIS A 670

PRO A 671

LEU A 672

ALA A 673

GLN A 674

LEU A 675

ILE B 665

GLN B 666

ARG B 667

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SER B 668

GLU B 669

HIS B 670

PRO B 671

LEU B 672

ALA B 673

GLN B 674

LEU B 675

Table 3

Is it a part of bigger protein?

In chimera software, “higher-order structure” is available in tool bar. By clicking on it, we can reach to the ‘make unit cell option’. That option shows all other supporting molecules of the protein. However, all other protein molecules are exactly same in all manners as shown in Fig 4. From this information it is understood that the given phosphodiesterase enzyme molecule is actually a part of bigger protein.

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Fig 4: Complete protein molecule (unit cell)

Secondary Structure Composition

Chimera is useful tool in determining secondary structure composition of protein. Secondary structure of the given protein was found to be as in Fig 5 for my protein.

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Fig 5 Secondary Structure

LIGPLOT

Fig 6 Ligplot

INTERACATIONS

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Atom 1 Atom 2 Distance Type

A:1003:CIA:C2 A:612:TYR:CE1 3.60 Hydrophobic

A:1003:CIA:C2 A:612:TYR:CZ 3.41 Hydrophobic

A:1003:CIA:C1 A:782:VAL:CG2 3.59 Hydrophobic

A:1003:CIA:C7 A:820:PHE:CE2 3.80 Hydrophobic

A:1003:CIA:C8 A:820:PHE:CD2 3.67 Hydrophobic


A:1003:CIA:N9 A:817:GLN:OE1 2.55 Hydrogen Bond

A:1003:CIA:C13 A:820:PHE:CG 3.83 Hydrophobic


A:1003:CIA:C17 A:804:LEU:CD1 3.69 Hydrophobic

A:1003:CIA:O20 A:816:MET:O 2.85 Hydrogen Bond




A:1003:CIA:C11 A:820:PHE:CZ 3.63 Hydrophobic

A:1003:CIA:C10 A:786:PHE:CZ 3.83 Hydrophobic

A:1003:CIA:C18 A:663:SER:CA 3.10 Hydrophobic

A:1003:CIA:C18 A:663:SER:C 3.48 Hydrophobic



A:1003:CIA:C27 A:816:MET:C 3.40 Hydrophobic

A:1003:CIA:C27 A:816:MET:CB 3.57 Hydrophobic

A:1003:CIA:C27 A:817:GLN:CA 3.84 Hydrophobic

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A:1003:CIA:C27 A:817:GLN:CG 3.80 Hydrophobic

A:1003:CIA:C27 A:817:GLN:CD 3.82 Hydrophobic


A:1003:CIA:C26 A:816:MET:CB 3.29 Hydrophobic


A:1003:CIA:C29 A:783:ALA:CA 3.31 Hydrophobic

A:1003:CIA:C29 A:783:ALA:CB 3.52 Hydrophobic




A:1003:CIA:C23 A:782:VAL:CG1 3.78 Hydrophobic




Table 4

From the ligplot Fig 5 and Table 4 about interactions of ligand with the receptor, it is very well clear that ligand binds with the receptor with high affinity and specificity. Most of the ligand-protein interactions are hydrophobic in nature; however two hydrogen bonds are also present, hydrogen of pyrole nitrogen atom and oxygen of carbonyl group of 817 amino acid forms a hydrogen bond. Whereas, another hydrogen bond is formed between oxygen atom of carbonyl group of 816 amino acid and hydrogen atom dioxolane ring. Length of these two hydrogen bonds are 2.55A N and 2.85A N respectively.

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Protein-ligand complex

Two molecules of ligand (tadalafil) bind in protein at two different positions. Ligand binding in the structure can be illustrated in three different ways as in Fig 7a, 7b and 7c. According to me Fig 7a represents the ligand binding with protein in most proper way.

Fig 7a

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Fig 7b

Fig 7c

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Final Report

Documents

ligand structure

protein structure

d structure of ligand

molecular modelling

ligand present

tadalafil ligand molecule

ligand poptimization

ligand binding sites