Journal of Molecular Structure 1076 (2014) 153159

Contents lists available at ScienceDirect

Journal of Molecular Structure

journal homepage: www.elsevier.com/locate/molstruc

Impact of the subtle differences in MMP-12 structure on Glide-based

molecular docking for pose prediction of inhibitors
Huan Zhang a,b, Yajing Wang a,c, Feng Xu a,b,
a

State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300071, Peoples Republic of China
Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300071, Peoples Republic of China
c
College of Biotechnology, Tianjin University of Science & Technology, TEDA (Tianjin Economic-Technological Development Area), Tanggu District, Tianjin 300457, Peoples Republic
of China
b

h i g h l i g h t s
 Glide-based cross-docking can be used to access subtle differences in MMP-12 (Matrix metalloproteinase-12) structures.
 Some MMP-12 PDB IDs obtained through Glide-based cross-docking are more suitable for inhibitor pose prediction.
 Many factors from PDB les provide clues for choosing a suitable PDB ID when docking.

a r t i c l e

i n f o

Article history:
Received 30 March 2014
Received in revised form 29 May 2014
Accepted 2 June 2014
Available online 1 July 2014
Keywords:
MMP-12
PDB ID
Docking

a b s t r a c t
Human MMP-12 is involved in many aspects of disease pathology. Substantial efforts have been made to
develop MMP-12 inhibitors. However, the mechanism of some MMP-12 inhibitors is still unclear.
Recently, the method of molecular modeling was used to explore the mechanism, but selecting the best
candidate among the wealth of MMP-12 structures poses a challenge. In this study, we attempted to
identify several criteria to predict the most appropriate MMP-12 PDB ID for enzymeligand interaction
studies based on cross-docking by Glide. Furthermore, the parameters from PDB les such as R-free,
resolution, B factor, and the molecular volume of the ligand in the complex can provide useful clues
for choosing a suitable approximate initial model for pose prediction for MMP-12 inhibitors. This work
might also provide a useful reference for other drug targets.
2014 Elsevier B.V. All rights reserved.

Introduction
MMP-12 is a member of a subclass of the zinc proteinase family
of metzincins [1], the MMPs (matrix metalloproteinases), which
degrade components of the extracellular matrix in processes like
embryonic development, reproduction, cellular migration and
tissue remodeling [2]. All of the MMPs have a similar catalytic
domain, which makes it difcult to develop therapeutic
compounds that inhibit only a given MMP with high specicity
[3]. Recent studies have shown that the overexpression of MMP12 is related to many human pathologies, such as giant cell arteritis
[4], emphysema [5], atherosclerosis [6], osteoarthritis [7],
aneurisms [8], and chronic obstructive pulmonary disease [9]. In
addition, based on a large clinical study, testing for an association
between both asthma and chronic obstructive pulmonary disease
Corresponding author at: Tianjin Key Laboratory of Molecular Drug Research,
Nankai University, Tianjin 300071, Peoples Republic of China.
E-mail address: xufeng@nankai.edu.cn (F. Xu).
http://dx.doi.org/10.1016/j.molstruc.2014.06.002
0022-2860/ 2014 Elsevier B.V. All rights reserved.

and single-nucleotide polymorphisms in the gene encoding

MMP-12, a detrimental role was attributed to the overexpression
of MMP-12 [10]. In animal models, mice decient in MMP-12 were
shown to be less susceptible to emphysema [11], atherosclerosis
[12], and aneurisms [5].
Because of its obvious functions in pathobiology, MMP-12 is a
hot pharmaceutical target and the need for MMP-12 drugs is large
[5]. Nowadays, based on the native ligand, researchers have developed a large family of MMP-12 inhibitors [13]. The rst generation
of MMP inhibitors have strong zinc-binding groups, such as
hydroxamate functions [14]; the second generation of more selective MMP inhibitors which have a less avid zinc-binding group, like
the phosphoryl group present in phosphinic peptide transition
state analogs [15]; the third generation of MMP inhibitors possess
no zinc-binding group and exploit mainly the depth of the S10 cavity present in most MMPs [16]. However, there are indeed many
MMP-12 inhibitors whose mechanism in targeting MMP-12 is still
unknown.

154

H. Zhang et al. / Journal of Molecular Structure 1076 (2014) 153159

Through molecular docking, the ligandreceptor interaction is

evaluated in real-time based on the principles of Geometric complementarity, energy complementarity and chemical environment
complementarity [17]. Molecular docking has become a standard
tool in computational biology for predicting the binding orientation of small molecule drug candidates with their protein targets
in order to predict the afnity and activity of the small molecule.
However, when there are many similar coordinate les of the same
protein in the RCSB (The Research Collaboratory for Structural Bioinformatics) PDB, it is generally difcult to decide which one is
appropriate for docking.
The PDB le selected from RCSB PDB has considerable inuence
on the accuracy of docking. First of all, atom coordination will
directly determine the movement and exibility of each residue
around the active site, which is fundamental to understanding
the principles of molecular recognition between ligand and receptor. Upon ligand binding, many systems undergo rearrangements,
which range from local motions of side-chains to large domain
movements. It has been shown that even small changes in the
receptor conformation can be important in computing binding
afnities [18]. The importance of receptor exibility and its implications in drug discovery has been highlighted in two reviews in
this eld [19,20], and everything points in the direction that protein mobility will have an increasing role in computer-aided drug
design in the future. In addition, the difference between apo-protein and complex structures, or inactive protein and active protein
structures, particularly in receptor membrane proteins, will have a
considerable impact on docking results [21]. Therefore, nding an
appropriate PDB le of the target protein which is diversied in
protein coordinates and exibility is essential to predict the orientation and interactions of native or new ligands, in the absence of
experimental assay information. Accordingly, in this study, we
attempted to dock the ligands from these deposited co-crystallized
complexes to all MMP-12 PDB structures using cross docking with
Glide [22] in order to explore whether any parameters exist for
PDB selection before docking.
Experimental
Protein
We downloaded the available X-ray structures of MMP-12
proteins from the RCSB PDB, as shown in Table 1.
Software
In this study we aligned proteins with Align Structure and performed molecular docking with Glide. In addition, the pipeline
pilot 8.5 is used to calculate molecular properties.
Align Structure a module in Discovery Studio 3.0, can align
multiple protein sequences and overlay the structures according
to their structural similarities using the 3DMA program. All of
the MMP-12 PDB structures as shown in Table 1 were input and
the RMSD (root-mean-square deviation) Cutoff, Length Cutoff,
Bin Size, and Fuzzy Bins parameters were set as default.
Glide uses a hierarchical series of lters to search for possible
locations of the ligand in the active-site region of the receptor.
The shape and properties of the receptor are represented on a grid
by several different sets of elds that provide progressively more
accurate scoring of the ligand poses. Comparisons to published
data on RMSD show that Glide is nearly twice as accurate as GOLD
and more than twice as accurate as FlexX for ligands having up to
20 rotatable bonds. Glide is also found to be more accurate than
the recently described Surex method [22]. Glide from the
Schrdinger Suite 2010 is one of the programs routinely used in
our laboratory to perform docking.

Table 1
All PDB IDs of MMP-12 X-ray structures. The polymers are not listed.
Entry

Resolution ()

Truncation

1JIZ
1JK3
1RMZ
1UTT
1Y93
2HU6
2OXU
2OXW
2OXZ
3BA0
3EHX
3EHY
3F15
3F16
3F17
3F18
3F19
3F1A
3LIK
3LIL
3LIR
3LJG
3LK8
3LKA
3N2U
3N2V
3NX7
3RTS
3RTT
3TS4
3TSK
4EFS
4GUY

2.60
1.09
1.34
2.20
1.03
1.32
1.24
1.15
1.90
3.00
1.9
1.90
1.70
1.16
1.10
1.13
1.13
1.25
1.80
1.80
1.90
1.31
1.80
1.80
1.81
1.55
1.80
1.81
1.82
1.59
2.00
1.63
2.00

100264
106263
106263
106264
106263
106263
106263
106263
106263
106470
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263
106263

Pipeline pilot 8.5 was used to calculate the molecular volume

with the pipeline pilot protocol as shown in Fig. 1.
Protein preparation
The protein receptor was prepared in Protein Preparation Wizard of Schrodinger Suite 2010, including assigning bond orders,
adding hydrogens, treating metals, creating disulde bonds, converting selenomethionines, deleting distant waters, and assigning
the H-bond network with water sampling. All waters and ligands
were then deleted from the structures before grid generation.
The nal rened structure was used for docking calculations. The
grid covering the target is generated by Receptor Grid Generation
module based on the original active pocket of the target protein.
Ligand preparation
The ligands were prepared using the LigPrep and Epik tools at
pH 7.0 2.0, during which LigPrep automatically generated stereoisomers for ligands without specied chirality. Finally, the ligands
were processed by confgen to generate more conformations.
Docking
All docking parameters were set as default. The residues binding the native inhibitor from the PDB le were used to dene the

Fig. 1. The protocol of calculating molecular volume in pipeline pilot 8.5.

155

H. Zhang et al. / Journal of Molecular Structure 1076 (2014) 153159

active pocket of MMP-12. Ligand docking was performed under

standard precision (SP).

may affect the activity of the protein and the ligand binding ability,
and therefore in theory 1JK3 is not a suitable candidate for docking.

Cross-docking

Impact of different MMP-12 structure on accuracy of pose direction

When more than one crystal structure of a target protein is

available, cross-docking is performed to determine which crystal
structure is most suitable for docking [23]. After 30 structures were
overlaid, each selected structure will be docked to each ligand from
co-crystal complexes using Glide. All ligands were prepared by the
above method. The docking reliability was evaluated by calculating
the RMSD between the position of the co-crystallized ligand, taken
as the reference, and the binding mode predicted by the docking
function. The best docking pose was dened as the one with the
lowest RMSD with respect to the native. If the lowest RMSD is
below 2 [24], we can conrm that the protein PDB can efciently
be used to dock the certain ligand.

In order to investigate the impact on docking results induced by

subtle differences in MMP-12 structures, a cross-docking was performed by Glide and the results are listed in Fig. 4. In general, the
smaller the RMSD value means the greater the possibility that each
ligand can be docked to the MMP-12 PDB in an actual docking
pose, and the smaller GScore value means the energy of the ligand
pose is more stable through Glide. Theoretically, a PDB ID is more
suitable for pose prediction and virtual screening if the RMSD and
GScore values of a PDB ID are both relatively low. From the docking
results, we observe that the RMSD and GScore values of 3LIR, 2OXU
and 3BA0 are both large. Those PDB IDs with a high RMSD value
and low GScore value include 1Y93. The PDB IDs with small RMSD
value and high Gscore value include 3F1A and 3TSK. The RMSD and
GScore values of 1RMZ and 3LIK are both small but not the smallest. Another PDB ID in which both values is relatively small is 1JK3,
which has a mutation at position 219 in the amino acid sequence;
as this is one of the active site residues, this PDB ID is considered
unsuitable for use in molecular docking. The results of our analysis
indicate that, in theory, PDB IDs including 1UTT, 2OXZ, 3EHX,
3EHY, 3F15, 3F16, 3F17, 3F18, 3F19, 3F1A, 3LIL, 3LJG, 3LK8, 3LK8,
3N2U, 3NX7, 3RTS, 3RTT, 3TS4, 4EFS, and 4GUY are suitable for
use in molecular docking. From the cross-docking results, the
RMSD values of the ligand from 1UTT to other PDB proteins are
all large, indicating that its pose cannot be predicted. In addition,
the Gscore values of ligands from 2OXZ, 3BA0, 3F15, 3F16, 3F18,
3LK8, 3RTS, 3RTT and 4GUY are all high, which means their poses
are in unstable, high energy states.

Results and discussion

Analyzing the RMSD among the all MMP-12 PDB structure themselves
There are 30 crystal structures of MMP-12 in PDB Bank, as
shown in Table 1. We therefore attempted to study the difference
in structure that may affect docking results and select the best PDB
to dock. The RMSD among all the MMP-12 structures is shown in
Fig. 2. The heatmap in Fig. 2 shows that several PDB IDs including
3BA0, 1UTT, 1JK3 have a relatively large difference in comparison
to other PDB IDs, and the RMSD values are generally greater than
0.5 ; PDB IDs including 3TS4, 3TSK, 4EFS, 4GUY, 3LIK, 3LIL, 3LIR,
3LIG have relatively smaller differences, with the RMSD values
are generally larger than 0.3 and smaller than 0.5 ; other PDB
IDs have the smallest difference with RMSD values smaller than
0.3 . We conclude that the differences between the main-chain
atoms of these structures is small.

PDB le information may provide clues for choosing a suitable PDB ID

for pose prediction with Glide-based docking

Analyzing the sequence difference of MMP-12

A wealth of structural information can be extracted from the

PDB le, such as R-free, resolution, etc. Through some simple calculations, we can also derive information about the B factors and the
molecular volume of ligand. It would be meaningful to determine if
these factors can provide some clues and guidance for identifying
which PDB ID is the best to predict the pose using Glide-based
docking. Thus, a number of factors including R-free, resolution, B
factor, molecular volume of ligand, and the minimal RMSD of
eutectic ligands pose through Glide docking of 30 PDB les of
MMP-12s are collected and summarized in Table 2.

The primary structure of a protein can affect its spatial structure

and there may be mutations in amino acid sequences from different depositors, so we performed a Blastsearch of the 30 MMP-12
sequences shown in Fig. 3a and b. There are almost no differences,
with the exception of Asp 171 Phe of 1UTT and 1JK3, Glu 219 Ala of
1JK3, Gly 263 Gln of 2OXZ. The amino acid residue in position 219
is in the active region of the protein, but amino acids 171 and 263
are not located in the active site region. Residue Ala 219 of 1JK3

Color code
1JK3
1JK3
1RMZ
1UTT
1Y93
2OXU
2OXW
2OXZ
3BA0
3EHX
3EHY
3F15
3F16
3F17
3F18
3F19
3F1A
3LIK
3LIL
3LIR
3LJG
3LK8
3LKA
3N2U
3N2V
3NX7
3RTS
3RTT
3TS4
3TSK
4EFS
4GUY

1RMZ

1UTT
158

0.668
0.674
0.613
0.593
0.558
0.597
0.988
0.643
0.609
0.584
0.528
0.592
0.536
0.561
0.541
0.629
0.577
0.635
0.547
0.529
0.567
0.547
0.567
0.58
0.549
0.593
0.636
0.639
0.634
0.46

0.61
0.449
0.492
0.446
0.42
0.801
0.483
0.49
0.463
0.491
0.39
0.443
0.453
0.487
0.47
0.534
0.379
0.343
0.449
0.464
0.451
0.405
0.415
0.442
0.468
0.395
0.291
0.367
0.448

1Y93
158
158
0.605
0.648
0.638
0.594
0.834
0.641
0.652
0.55
0.623
0.576
0.578
0.581
0.574
0.578
0.477
0.596
0.548
0.606
0.582
0.564
0.574
0.545
0.603
0.624
0.594
0.583
0.559
0.55

2OXU
158
158
158
0.31
0.286
0.261
0.789
0.328
0.311
0.305
0.284
0.237
0.254
0.297
0.323
0.471
0.519
0.471
0.419
0.252
0.234
0.265
0.26
0.291
0.225
0.257
0.468
0.474
0.435
0.418

2OXW
158
158
158
158
0.204
0.271
0.825
0.195
0.214
0.306
0.293
0.291
0.22
0.259
0.274
0.522
0.52
0.465
0.429
0.251
0.248
0.244
0.261
0.296
0.196
0.272
0.449
0.463
0.437
0.398

2OXZ
158
158
158
158
158
0.241
0.785
0.278
0.287
0.255
0.239
0.22
0.17
0.19
0.239
0.497
0.498
0.471
0.407
0.194
0.19
0.202
0.165
0.259
0.173
0.239
0.436
0.461
0.434
0.365

3BA0
158
158
158
158
158
158
0.761
0.282
0.311
0.288
0.3
0.217
0.238
0.274
0.303
0.499
0.497
0.459
0.427
0.255
0.246
0.256
0.207
0.239
0.223
0.25
0.429
0.438
0.427
0.344

3EHX
158
158
159
158
158
158
158
0.82
0.842
0.771
0.827
0.76
0.795
0.791
0.803
0.891
0.85
0.863
0.834
0.81
0.782
0.794
0.764
0.786
0.802
0.795
0.845
0.822
0.813
0.818

3EHY
158
158
158
158
158
158
158
158
0.156
0.328
0.358
0.303
0.267
0.292
0.312
0.54
0.54
0.466
0.441
0.284
0.295
0.261
0.276
0.289
0.239
0.291
0.445
0.472
0.437
0.414

3F15
158
158
158
158
158
158
158
158
158
0.336
0.336
0.31
0.267
0.299
0.307
0.523
0.539
0.457
0.405
0.261
0.289
0.256
0.296
0.302
0.222
0.291
0.452
0.469
0.428
0.405

3F16
158
158
158
158
158
158
158
158
158
158
0.232
0.231
0.194
0.181
0.159
0.501
0.516
0.495
0.433
0.207
0.21
0.202
0.204
0.19
0.236
0.268
0.474
0.441
0.461
0.376

3F17
158
158
158
158
158
158
158
158
158
158
158
0.244
0.177
0.186
0.229
0.489
0.525
0.491
0.425
0.137
0.204
0.194
0.234
0.243
0.203
0.266
0.487
0.484
0.473
0.384

3F18
158
158
158
158
158
158
158
158
158
158
158
158
0.188
0.214
0.268
0.464
0.501
0.434
0.388
0.197
0.215
0.209
0.154
0.184
0.2
0.244
0.413
0.424
0.404
0.365

3F19
158
158
158
158
158
158
158
158
158
158
158
158
158
0.122
0.161
0.466
0.471
0.453
0.38
0.13
0.151
0.138
0.145
0.178
0.149
0.233
0.434
0.444
0.423
0.331

3F1A
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.195
0.488
0.496
0.48
0.403
0.162
0.178
0.137
0.154
0.174
0.194
0.256
0.455
0.462
0.444
0.357

3LIK
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.499
0.496
0.489
0.418
0.195
0.22
0.212
0.223
0.243
0.224
0.285
0.47
0.437
0.456
0.351

3LIL
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.425
0.322
0.352
0.467
0.481
0.471
0.466
0.482
0.464
0.505
0.419
0.485
0.318
0.503

3LIR
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
159
0.482
0.44
0.502
0.492
0.481
0.477
0.495
0.49
0.53
0.577
0.535
0.467
0.449

3LJG
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
159
159
0.301
0.455
0.479
0.463
0.449
0.457
0.442
0.49
0.388
0.383
0.199
0.487

3LK8
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
159
159
159
0.379
0.393
0.379
0.386
0.406
0.368
0.426
0.401
0.364
0.292
0.383

3LKA
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.162
0.133
0.172
0.196
0.136
0.211
0.437
0.452
0.433
0.334

3N2U
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.159
0.177
0.218
0.153
0.199
0.462
0.468
0.438
0.358

3N2V
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.167
0.176
0.146
0.218
0.441
0.458
0.434
0.333

3NX7
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.181
0.183
0.229
0.409
0.432
0.412
0.332

3RTS
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.225
0.263
0.435
0.444
0.432
0.342

3RTT
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.175
0.424
0.441
0.413
0.339

3TS4
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
0.465
0.479
0.457
0.381

3TSK
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
159
159
159
159
158
158
158
158
158
158
158
0.425
0.338
0.45

4EFS
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
159
159
159
159
158
158
158
158
158
158
158
159
0.359
0.462

4GUY
158
159
158
158
158
158
158
158
158
158
158
158
158
158
158
158
159
159
159
159
158
158
158
158
158
158
158
159
159

158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158
158

0.472

Fig. 2. It shows Main-chain RMSD (angstrom) between each two structures below the diagonal and Number of Overlapping Residues above the diagonal of 30 MMP-12
structures.

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H. Zhang et al. / Journal of Molecular Structure 1076 (2014) 153159

Fig. 3. Structural alignment of all MMP-12 PDB structures. (a) Sequence alignment of the amino acid sequences of 30 MMP-12 PDB structures. The number is amino acid ID.
Residues with red background are strictly conserved and those with white background indicate an amino acid substitution. As 3BA0 is a full-length crystal structure of MMP12 and others represent only a part of MMP-12, a more reliable alignment result was generated using just residues 106263 for analysis. (b) Structural superimposition of
1JK3 (red), 1UTT (green) and 2OXZ (blue). Inserts show details of superimposition around the mutated positions in MMP-12, and the residues in green stick represent the
mutated residues.

H. Zhang et al. / Journal of Molecular Structure 1076 (2014) 153159

RMSD color code

157

Gscore color code

Fig. 4. 28 ligands (excluding the ligand from 2OXU and 1Y93, as there is no native ligand in 2OXZ and the native ligand from 1Y93 could not be docked) were each docked to
30 MMP-12 proteins downloaded from the PDB. The above heatmap displays the smallest RMSD of each ligand docked to each PDB ID protein, and the lower heatmap shows
the Gscore of each ligand which has smallest RMSD docking to each PDB ID protein.

Resolution is one measure of the quality of the data that has

been collected on the crystal. In theory, if all of the proteins in
the crystal are aligned in an identical way to form a very perfect
crystal, then all of the proteins will scatter X-rays in an identical
manner and the diffraction pattern will show the ne details of
crystal. On the other hand, if the proteins in the crystal are all
slightly different because of local exibility or motion, the diffraction pattern will lose some of that ne information. Resolution can
provide more structure details: for instance, water molecules will
be dened while the resolution of a structure is higher than 2.8
but those structures with resolution lower than 3 cannot. Essentially, resolution is a measure of the level of detail present in the
diffraction pattern and the level of detail that will be seen when
the electron density map is calculated. High-resolution structures,
with resolution values of 1 or so, are highly ordered and every
atom in the electron density map. Lower resolution structures,
show only the basic contours of the protein chain, and the atomic
structure must be inferred. Only in the higher resolution structures, can the interaction between atoms can be identied.
R-free is the measure of the quality of the atomic model
obtained from the crystallographic data. The R-free value measures
how well the simulated diffraction pattern matches the experimentally-observed diffraction pattern. Structures with lower Rfree values can closely match the real structure and be used in
molecular docking.
The B factor reects the diffusion of density of electrons in an
atom in the crystal, which in fact reects the conformation of
protein molecules in the crystal state. The higher the B factor,

the greater the diffusion is and the corresponding parts of the conformation become more unstable. As crystallography data in the
PDB les is based on atomic units, the B factor given is relative
to each atom. In statistical terms, the B factor of each atom should
be in the conversion of each residue, namely getting the average B
factor of all atoms of each residue. For the residues on the surface
of protein to residues buried inside, the B factor is relatively high,
so this part residues should be removed in the statistics [25]. The
specic method involves removing 10% of the high B factors of
the residues in the data and calculating the average of the remaining residues through the ba2r program (http://dxli75.blog.163.com/blog/static/106768289200911962735786/).
The volume of eutectic ligands can, to a certain extent, be
responsible for the size of the protein active pocket, especially
for the exible active pocket. The volume is calculated through
the component of surface area and volume, one of whose properties is molecular volume calculation, in the pipeline pilot.
The minimal RMSD of eutectic ligand poses through Glide docking is summarized in Fig. 4. As shown in Table 2, ve factors for
each PDB ID are highlighted in color order. We propose that if
the shading of each value of 5 factors are all not in red, then the
PDB is suitable for molecular docking. According to this principle,
1JK3, 3EHX, 3F15, 3F16, 3F17, 3F18, 3LIR, 3N2U, 3N2V, 3NX7,
and 3RTS were selected and could be used for pose prediction
based on the molecular docking method. This is consistent with
the results by cross-docking, which means we can easily select
PDB IDs for pose prediction by analyzing the information contained
within the PDB le.

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H. Zhang et al. / Journal of Molecular Structure 1076 (2014) 153159

Table 2
Information for 30 MMP-12 PDB les. The PDB IDs shown in bold represent the better PDB IDs which can be used for pose prediction of MMP-12 inhibitors.

Conclusions
When a compound can interact with a protein, which means
that clear experimental data show the compound has certain activity to the protein, then the molecular mechanism between them is
a need to clarify. At this stage the complex structure between a
protein and a compound can be obtained by X-ray crystallography,
nuclear magnetic resonance (NMR) and electron microscopy (EM).
From the three-dimensional structure, the interaction can be clear
at a glance. In the past few decades, a large number of structures
have been resolved and deposited in the Protein Data Bank
(PDB), thus making structure-based drug design possible. However, it is usually very difcult to obtain a three-dimensional structure, especially for Guanosine-binding Protein Coupled Receptors
(GPCR), which require a high cost in terms of manpower and material resources. Fortunately, in theory, the ligand pose in a protein
complex can also be obtained by means of molecular simulation
in cases where few or no experimental structures of proteinligand
complexes are available. Once the three-dimensional structure is
attained, it can be used to predict the ligand pose. However, when
more than one crystal structure is available, choosing a suitable
protein PDB ID will be very important for the results because of

the protein exibility, which seriously affects the protein

conformation.
Choosing a suitable PDB requires the consideration of two factors. The rst is the protein itself, such as side-chain exibility,
and bond rearrangement. The second are the external parameters:
the structure-determination method (X-ray, NMR, EM, model) and
the quality of the crystallization and structure determination,
including R-free, B-factor, and resolution. In low quality structures,
potential binders can be lost in the molecular docking for the following reasons: (i) they are mis-docked because of clashes with
the receptor or because the ligandprotein contacts are not strong
enough to hold the ligand in a correct position (for example, if the
quality of the crystal structure is bad or residues within the pocket
have high B-factors); (ii) they are docked correctly, but they do not
score properly because the ligandreceptor contacts are not optimal; (iii) they are mis-docked because water molecules or ions
are not included in the receptor model; and (iv) uncertainty in
the ionization state of the ligand or the receptor, due to receptorinduced (ligand-induced) pKa changes in the ligand (receptor).
MMP-12 is a validated drug target that is associated with many
diseases. So far, many related inhibitors have been identied.
However, because of the marked sequence similarities between

H. Zhang et al. / Journal of Molecular Structure 1076 (2014) 153159

the catalytic domains of MMPs, a well conserved enzyme active

site topology (backbone RMSD between the MMP catalytic domain
is 0.70.8 ), and the mobility of residues in the so-called S10 specicity loop [26,27], researchers are still searching for new specic
and selective inhibitors. Among these inhibitors, some can interact
with MMP-12 but their mechanism of action is still unclear. This
paper attempts to answer the question encountered when the
Glide-based molecular docking is used to predict the pose of
MMP-12 inhibitors: which PDB is more suitable as an input target
protein in the docking calculation? On the one hand, the accuracy
of each PDB to each eutectic ligand, dened by the RMSD, was analyzed through the cross-docking method based on Glide, with the
results showing that 1UTT, 2OXZ, 3EHX, 3EHY, 3F15, 3F16, 3F17,
3F18, 3F19, 3LIK, 3LIL, 3LJG, 3LK8, 3LK8, 3N2U, 3NX7, 3RTS,
3RTT, 3TS4, 4EFS, 4GUY are suitable for pose prediction of MMP12 inhibitors based on molecular docking. In general, we suggest
the apo-protein structure should not be used for docking as the
RMSD of all ligands to PDB 2OXU is high. Our results indicate the
apo-structure is not a good choice, unless no complex crystal structure is available. Additionally, structures containing mutations are
generally not useful as targets for molecular docking. However,
1JK3 has a single amino acid mutation in the active region but its
RMSD values are all small, which suggests that some structures
containing mutations can be used in molecular docking for pose
prediction where no other structures are available. On the other
hand, data contained within MMP-12 PDB les such as the B factor,
R-free, resolution, and ligand volume are related to the choice of
PDB ID, which is very interesting. This provides some useful hints
for choosing a better and more appropriate PDB ID to predict the
ligand pose of other targets when using Glide-based docking: we
can select a suitable PDB ID through the analysis of these readily-obtained factors.
In summary, this paper expounds the inuence of subtle differences in MMP structure on molecular docking and attempts to provide a useful method for choosing a suitable PDB ID. As the use of
different PDB IDs can have a serious effect on the results, so there is
a need to consider some important factors: three-dimensional
structure of the target protein, active pocket size, the resolution,
R-free, B factor, and the size of the eutectic ligand of a PDB le. This
paper has focused only on the use of Glide to perform the molecular simulation. Next, we intend to use other common simulation
tools such as Surex and Autodock for more general analysis and
evaluation.
Acknowledgements
Funds were provided by NSFC (National natural Science Foundation of China) (21302102) and Tianjin Municipal Science and
Technology Commission (12ZCZDSY14500, 13JCYBJC20900).

159

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