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Hamna Riaz
Comp #23
Modeling of Protein-Small Molecule Complexes:
Human serum albumin (2vdb), S-naproxen (NPS)
Part I
Intro
In this assignment the structure of a heterocompound complexed within a protein is
investigated in multiple modes. The protein chosen is human serum albumin, the structure for which
was first found using protein databases [1][8]. A 3D model of the protein was downloaded from a
database and opened using the program DS Visualizer. The individual heterocompound chosen from this
protein is (2s)-2-(6-methoxynaphthalen-2-yl) propanoic acid or S-naproxen (het-code: NPS). This
heterocompound was extracted then opened in a new file so that the structure could be analyzed
further [2].
Background: Function of S-naproxen in Albumin
Naproxen itself is used as a non-steroid anti-inflammatory drug (or NSAID), prescribed to arthritis
patients in high doses. It has an over the counter (OTC) form as well which can be used as a fever
reducer and pain reliever [5]. Human serum albumin (HSA) is a plasma protein which is responsible for
the transport of vitamins, minerals, hormones and fatty acids through the blood. Naproxen is
complexed within HSA to assist in determining the location of fatty acid binding sites HSA possesses [7].
Properties of naproxen that allow it to bind to this protein well include its electron affinity and the
delocalized negative charge of its carboxylic acid group which make it acidic in nature [6]. This will be
elaborated on in Part II when the protein-ligand interaction of this heterocompound is explored in more
detail.
Fig 1.The structure above is the original protein, human serum albumin as seen
in DS Visualizer.
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Extraction
Fig 2. This is a depiction of the extracted heterocompound, S-naproxen (C14H14O3),
as seen in DS Visualizer.
The Lewis structure of S-naproxen was then analyzed and created using Chemsketch. Snaproxen consists of two benzene rings, carboxylic acid group and a methoxide group. The formal
charge of the carboxylic acid group is -1 due to deprotonation of the hydrogen on the singly bonded
oxygen atom. The chemical formula of the compound was therefore C14H13O3 instead of C14H14O3 when it
is complexed within human serum albumin. Chemsketch was used to create a Lewis structure Snaproxen so that the deprotonated acidic property of the carboxylic acid group can be shown.
CH3
O
H3C
O
O
Fig 3.This is the Lewis structure for S-naproxen. There are two pairs of
non-bonded electrons on each oxygen atom of the carboxylic acid group
as well as the oxygen of the methoxide group.
The original protein structure for human serum albumin was reopened in DS Visualizer and
converted to a solid ribbon form, save for the heterocompound S-naproxen. S-naproxen was then
converted to CPK form. This rendition of the image gives a clearer view to the relative location of the
heterocompound within the protein structure. This is viewable on the next page. S-naproxen is
displayed in a planar view from the side in the following image rather than from the top as it is in the
ball and stick form on the previous page.
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Comp #23
Fig 4. Human serum albumin protein complex is in the ribbon form and S-naproxen is
represented in the CPK form.
Once the structure for S-naproxen is confirmed to match with the literature stereochemistry,
the steric energy of the compound is determined using Chem 3D. In this step, the most preferable
orientation of S-naproxen must be determined through minimization in Chem 3D. This will then be
compared to the steric energy of the compound as it appears in the so that the heterocompound can be
analyzed further. First, a single-point energy calculation of S-naproxen as it appears in human serum
albumin was performed. This structure and the data generated were saved. Next, the structure was
minimized using an MM2 calculation. The output was then saved in a table for comparison:
Energy Calculations
Table 1: S-naproxen steric energy values
S-naproxen steric energy values
Single Point Energy
Single Point Energy (kcal/mol)
Minimized Energy (kcal/mol)
Stretch
11.3798
0.753
Bend
6.5894
2.9806
Stretch-Bend
-0.0576
0.0843
Torsion
-15.8362
-16.3958
Non-1,4 VDW
1.4882
-1.5773
1,4 VDW
17.2805
11.4368
Dipole/Dipole
0.661
0.6472
Total Energy
21.4641
-2.1212
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Comp #23
Fig 5. The image on the left is the structure of S-naproxen as it exists in human serum albumin. The image on the
left is the minimized structure. This represents the geometric conformation at which the energy of the compound
is the lowest and therefore most preferable. The difference in energy between the two conformations is evident
in the calculations shown in the table.
The Images above serve as comparisons in the structure of S-naproxen after a single point
energy calculation and after energy minimization (MM2). Single point energy is a calculation of the
potential energy surface of a compound at a given conformation. There are specific conformations that
are more energetically preferable depending upon the placement of electron withdrawing groups and
lone pairs. The single point energy calculation only displays the energy of the compound as it exists in
the protein. To determine the angles at which the compound will have the least potential energy
surface and what those exact energy values are a geometry optimization or minimization energy
calculation was conducted using Chem 3D.
A dramatic change in energy can be observed from the data on Table 1. Each individual
component contributed to this major difference. The energy values, or components, generated include:
stretch, bend, stretch-bend, torsion, non-1,4 van der Waals, 1,4 van der Waals, dipole-dipole and the
total energy [4].
Stretch represents the energy generated when the optimal length of bonds within the
compound are distorted. The higher the deviation, the higher the energy becomes. A dramatic
difference can be noted between the stretch of the minimized conformation (only .753kcal/mol) and the
structure as it exists in the protein (~11.38kcal/mol). The stretch energy shows the greatest energy
change meaning that the structure of S-naproxen becomes highly distorted due to attractions from
surrounding protein structures.
Bend is a measurement of the energy released when deforming angles of the compound from
optimal values. The bend of the compound before and after minimization shifts substantially. Bond
angles of S-naproxen are altered due to changes in structure when it bonds with structures within the
protein. This measurement would be expected to decrease as the stretch component did since
stretching of bond lengths can cause stretching of bond angles as well.
Stretch-bend is the energy required to stretch two bonds involved in a bond angle when the
bond angle is compressed. According to the results, more energy is required to stretch the bonds of the
minimized structure than the S-naproxen within albumin. This implies that the angles of the minimized
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Comp #23
structure are more compressed than that of the non-minimized structure which contributes to the
higher energy value.
Torsion represents the energy formed when torsional angles in the molecule are deformed from
the ideal formation. There is only a slight difference in the torsional angles of the compound in both
minimized and non-minimized forms which means that torsional strain does not contribute significantly
to the change in total energy.
Non-1,4 van der Waals is a representation of the energy of the interaction between pairs of
atoms that are separated by multiple atoms (usually about 3). For example the interaction between an
oxygen atom of the carboxylic acid group and the hydrogen of the methyl group of the second carbon.
There is only a slight decrease in non-1,4 van der Waals interaction energy which indicates that there
was a small shift in the positioning of the structures involved when they were minimized. The further
apart the atoms become, the weaker their van der Waals interaction.
1,4 van der Waals is the energy of interaction between atoms separated by two other atoms.
There is a slight decrease in this energy after minimization, indicating that the two atoms involved have
been moved apart further. This could be caused by change in the position of the carboxylic acid
substituent.
The Dipole/Dipole energy is a calculation of the energy of the interaction of bond dipoles. There
is a very slight change in this energy, however, so it does not significantly contribute to the decrease in
total energy during minimization. The formal charge of S-naproxen is 0 for every atom except the
deprotonated singly bonded oxygen of the carboxylic acid substituent. This could be the cause of the
slight change.
Changes in energy can simply be viewed by the table but for a clearer depiction of the changes
of stereochemistry before and after minimization, the two structures must be superimposed.
Fig 6. In this image, the two structures have been superimposed. The minimized
energy structure is the one with the carboxylic acid group pointing towards the back.
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The S-naproxen structure complexed within human serum albumin and the minimized form
were both superimposed onto one another using Chem 3D. By observing the superimposed images it is
notable that the overall fit of both forms of the heterocompound is very good. The only exception is in
the orientation of the carboxylic acid group. The minimized structure points further away towards the
back of the plane whereas the complexed form is stretched towards the front. This gives a clear
description for the decrease in stretch energy between the two forms of the heterocompound.
Slight deviation in the location of the singly bonded oxygen atoms is present but, as mentioned
previously, most of the differences in the conformation of the two structures are present in the 6th to
the 10th carbon. The weak van der Waals interaction between carbon atoms of the carbon chain most
likely contributed to the varying 1,4 van der Waals energy change of the structure before and after it
was minimized. Torsional strain could also be the result of interaction between the carbons closest to
the carboxylic acid group and the carbons further away (slight dipole/dipole differences). This change in
bond length contributed to an increase in bond angle (bend) which in turn decreased the 1,4 van der
Waals interactions within this substituent.
Part II.
In part I, the potential energy surface of the heterocompound was determined in its minimized
state and the conformation the compound has within human serum albumin. Changes in the structure
were shown with deviations in the stretch, bend, stretch-bend, torsion, van der Waals (1,4 and non 1,4)
interactions and dipole-dipole interactions. It was mentioned that interactions with other structures
within the protein caused these changes. In part II, these interactions were investigated further.
Comparison
First the wiring diagram of the protein containing S-naproxen was viewed in the PDSum website
[3]. The wire diagram displays the amino acid sequence within human serum albumin and highlights
areas of interactions with the use of colored markers. For example a red dot indicates areas where the
amino acid residues interact with the heterocompound, or ligand. Red triangles are used to mark amino
acid residues that are present in the catalytic active site of the protein. The LigPlot of S-naproxen was
then viewed. A LigPlot is a visual representation of the heterocompound and the compounds it interacts
with, such as amino acid residues and other ligands.
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Comp #23
Fig 7. This is the wiring diagram
of S-naproxen which was
obtained from the PDSum
database [1]. Notice how the
numbering for the red dots
coincides with the “eyelashes”
on the LigPlot on page 8.
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Comp #23
Fig 8. This is the LigPlot for S-naproxen obtained from
PDSum [9]
Interactions labeled in the LigPlot (the
“eyelashes”) were then searched for in the wiring
diagram to ensure that the two concurred. This
was the case since every amino acid labeled as an
“eyelash” in the LigPlot was marked with a red dot
in the wiring diagram which indicates that the
amino acid interacts with the ligand.
The protein structure was opened in DS
Visualizer and the amino acid groups and
heterocompound that S-naproxen interacts were
made prominent. This was done by hiding the rest
of the amino acids and heterocompounds save the
ones the PDSum LigPlot identified as interacting
with S-naproxen. Every amino acid was found
within the structure just as it is mentioned in the
LigPlot, however the location of a few amino acids
is a slightly off. This could simply be caused by
inconsistencies with a 2D figure to properly
represent the positioning of a 3D image. This
difference can be seen in the 3D version of this
image (generated on DS Visualizer) on the next
page.
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Fig 9. This is simply a depiction of S-naproxen in a ball-and-stick rendition and HSA in the solid ribbon
rendition
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Fig 10. This is the heterocompound in a ball and stick rendition within HSA
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fig 11. This is a 3D version of the LigPlot generated in Chem 3D using. S-naproxen is rendered in the ball-andstick style and the amino acid residues and DKA (decanoic acid, a heterocompound) with which it interacts are
rendered in the stick style, colored pale yellow.
Another inconsistency can be noted in this extracted version of the heterocompound and
ligands that it immediately interacts with: The LigPlot makes no mention of hydrogen bonds since all
interacting amino acids are represented with eyelashes whereas the 3D diagram in DS Visualizer does. It
is a curious matter since some atoms seem as if they would form a hydrogen bond with the
electronegative carboxylic acid of S-naproxen (such as ILE 142 directly on top of S-naproxen, or DKA
1585 directly to the left of S-naproxen) however the diagram and LigPlot suggest otherwise.
Nevertheless, the interactions of these ligands with the heterocompound are discussed in a table on the
next page based on the given results.
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Hamna Riaz
Comp #23
Table 2: Protein-Ligand Interactions between S-naproxen and HSA
Amino Acid Residue
Heterocompound Atoms
Nature of Interaction
Leu154
Side chain,
Isopropyl group of Leu with
Hydrophobic attraction of weak
aliphatic
carboxylic acid of NPS
positively charged Leu with the
carboxylic acid group of NPS
Phe 149, 157
Aromatic side
Methoxide group , benzene
The electronegative oxygen of
chain
groups of Phe.
the methoxide group forms a
hydrophobic attraction with
both phenyl groups.
Lys 190
Side chain,
Methyl group with methoxide of Slightly (+) methyl group of Lys
Aminium ion
NPS.
side chain forms an electrostatic
attraction to (-) charge
Phe 157
side chain,
Phe forms a hydrogen bond with Hydrophobic attraction of π
aromatic
Tyr (Phe being the HBA) which
bonds with NSA
interacts with the π -bonds of
NSA
Gly 189
Side chain,
???
Hydrophobic attraction. Gly is a
aliphatic
HBD to Arg186 which gives Gly a
slightly positive charge.
Therefore there could be
electrostatic attraction between
the (+) Gly and (-) methoxide of
NPS
Ile 142
Aliphatic, side
???
Hydrophobic attraction is
chain
possible, perhaps due to
electrostatic attraction
Tyr 161
Aromatic, side ???
Hydrophobic, attractive π –
chain
interaction possible: Alcohol
group of Tyr could have a weak
interaction with the methoxide
of the NSA side chain
DKA 1585
Aliphatic,
???
DKA is a type of fatty acid which
backbone
usually forms a hydrogen bond
with electronegative S-naproxen
[8] but does not in the diagram,
perhaps there is an electrostatic
attraction between the
backbones of both structures
His 146
Aminium ion,
NH+ of His
Electrostatic attraction:
backbone
Carboxylic acid group of NPS
forms an attraction with the NH+
of His
+
Arg 186
Aminium ion,
(CN3H5) of Arg
Hydrogen bonding, H of Arg is a
backbone of
HBD and NPS is the HBA
NPS
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Comp #23
Bear in mind that some bonding may also occur with ligands contained within HSA that are not
represented in the LigPlot. The next diagram depicts the location of the ligands and heterocompounds
relative to the protein, HSA.
fig 12. This is a bottom view of HSA in solid ribbon form. The heterocompound is in a ball and stick rendition and
the ligands it interacts with are colored yellow, in a stick rendition.
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References:
[1]
A. Yamaguchi, K. Iida, N. Matsui, S. Tomoda, K. Yura, M. Go: Het-PDB Navi. : A database for protein-small
molecule interactions. J. Biochem (Tokyo), 135, pp.79-84 (2004)
[2]
Lejon, S., Cramer, J.F., Nordberg, P.A. (2008) Structural Basis for the Binding of Naproxen to Human
Serum Albumin in the Presence of Fatty Acids and the Ga Module. Acta Crystallogr.,Sect.F 64: 64
DOI 10.2210/pdb2vdb/pdb
[3]
S.Lejon et al. (2008). Structural basis for the binding of naproxen to human serum albumin in the
presence of fatty acids and the GA module.. Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 64-69.
[PubMed id: 18259051] [DOI: 10.1107/S174430910706770X]
(abstract only, see [8])
[4]
Chem 3D Help, “Compute Properties.”
[5]
"Naproxen." AHFS Consumer Medication Information. 2009. American Society of Health-System
Pharmacists. 4 May 2009
<http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=meds&log$=drug_bottom_one∂=a681029>.
[6]
Block Drug Co., Inc., Jersey City, NJ 07302; Hazleton Laboratories America, Inc., Vienna, VA 22180;
Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, St. John's
University, Jamaica, NY 11439 [DOI: 10.1002/jps.2600770314]
[7]
MedInnovation GmbH: function of Human Serum Albumin. Retrieved May 4, 2009, from
http://www.medinnovation.de/background/hsa.htm
[8]
For Full Text Article:
S.Lejon et al. (2008). Structural basis for the binding of naproxen to human serum albumin in the
presence of fatty acids and the GA module.. Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 64-69.
[DOI:10.1016/j.physletb.2003.10.071]
[9]
PDBSum: HSA complexed with S-naproxen structure. Retrieved May 5, 2009, from
http://www.ebi.ac.uk/thornton-srv/databases/cgibin/pdbsum/GetPage.pl?pdbcode=2vdb&template=main.html
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