Hasan et al.

Source Code for Biology and Medicine (2015) 10:7

DOI 10.1186/s13029-015-0037-3

RESEARCH Open Access

Molecular-docking study of malaria drug

target enzyme transketolase in Plasmodium
falciparum 3D7 portends the novel
approach to its treatment
Md. Anayet Hasan1*, Md. Habibul Hasan Mazumder1, Afrin Sultana Chowdhury1, Amit Datta1 and Md. Arif Khan2

Abstract
Background: Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of
any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium
falciparum continues to cause persistent deaths in the tropical and sub-tropical region. As a result, demands for
new targets for more effective anti-malarial drugs are escalating. Transketolase is an enzyme of the pentose
phosphate pathway; a novel pathway which is involved in energy generation and nucleic acid synthesis. Moreover,
significant difference in homology between Plasmodium falciparum transketolase (Pftk) and human (Homo sapiens)
transketolase makes it a suitable candidate for drug therapy. Our present study is aimed to predict the 3D structure of
Plasmodium falciparum transketolase and design an inhibitor against it.
Results: The primary and secondary structural features of the protein is calculated by ProtParam and SOPMA
respectively which revealed the protein is composed of 43.3 % alpha helix and 33.04 % random coils along with
15.62 % extended strands, 8.04 % beta turns. The three dimensional structure of the transketolase is constructed
using homology modeling tool MODELLAR utilizing several available transketolase structures as templates. The
structure is then subjected to deep optimization and validated by structure validation tools PROCHECK, VERIFY
3D, ERRAT, QMEAN. The predicted model scored 0.74 for global model reliability in PROCHECK analysis, which
ensures the quality of the model. According to VERIFY 3D the predicted model scored 0.77 which determines
good environmental profile along with ERRAT score of 78.313 which is below 95 % rejection limit. Protein-protein
and residue–residue interaction networks are generated by STRING and RING server respectively. CASTp server
was used to analyze active sites and His 109, Asn 108 and His 515 are found to be more positive site to dock the
substrate, in addition molecular docking simulation with Autodock vina determined the estimated free energy of
molecular binding was of −6.6 kcal/mol for most favorable binding of 6′-Methyl-Thiamin Diphosphate.
Conclusion: This predicted structure of Pftk will serve first hand in the future development of effective Pftk
inhibitors with potential anti-malarial activity. However, this is a preliminary study of designing an inhibitor
against Plasmodium falciparum 3D7; the results await justification by in vitro and in vivo experimentations.
Keywords: Transketolase, Plasmodium falciparum 3D7, Homology modeling, Drug target, Docking studies

* Correspondence: [email protected]
1
Department of Genetic Engineering and Biotechnology, Faculty of Biological
Sciences, University of Chittagong, Chittagong 4331, Bangladesh
Full list of author information is available at the end of the article

© 2015 Hasan et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
(http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium,
provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://
creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 2 of 14

Background of NADPH. This pathway has an oxidative and a non-

The genus Plasmodium is responsible pathogen for malarial oxidative arm where the non-oxidative arm is operated
infection in human and other mammalian species [1]. This by an enzyme, named transketolase. Transketolase serves
disease exists in most of the tropical and subtropical different roles in malarial parasite including pentose sugar
regions including Asia, America and Sub-Saharan Africa. supply for nucleotide synthesis, helps in replication and
Though there are four species (Plasmodium falciparum, survival of the parasite etc. Moreover, the biochemical
Plasmodium vivax, Plasmodium ovale, and Plasmodium analysis of Plasmodium falciparum transketolase (PfTk)
malariae) have been detected from the Plasmodium genus shows least homology with its human host [15]. All these
for causing the disease, the most responsible and virulent make it a potential target for treating malaria.
among them is Plasmodium falciparum [2–5]. It has a wide The preliminary aim of the non-oxidative arm of the PPP
host range and is responsible for causing the severe form of is to generate ribose-5-phosphate (R5P). But when two
malaria. Malaria is transmitted in humans by the Anopheles carbon groups are transferred from xylulose-5-phosphate
mosquito. The infected Anopheles mosquito acts as a to ribose-5-phosphate it generates glyceraldehyde-3-
vector and harbors the Plasmodium [6]. Infected indi- phosphate (G3P), fructose-3-phosphate (F6P) and
vidual may suffer from fever, neurological symptoms, sedoheptulose-7-phosphate. This transfer reaction is
opisthotonous, seizures and even can progress to coma catalyzed by transketolase and as a co-factor it requires
or death. According to World Health Organization thiamine diphosphate (ThDP). Transketolase is also re-
(WHO) about 1.2 million people were killed in 2010 sponsible for the production of erythrose-4-phosphate
due to malaria and another 219 million cases of this from F6P and G3P in the absence transaldolase which
disease were documented [7]. is another enzyme of the non-oxidative arm [16]. The
Recent rise in the death rate due to malaria is con- R5P is used for the synthesis of nucleotides and nucleic
cerning alarmingly as traditional treatment is becoming acids. Therefore, the non-oxidative part of PPP is dir-
obsolete. High price and problems related with distri- ectly or indirectly responsible for generating more than
bution of drug to malaria affected poor communities 80 % of the parasite nucleic acid [17]. Moreover,
(endemic areas) especially in Sub-Saharan Africa made Erythrose-4-phosphate is required as a key metabolite
the situation worse. Considering the scientific ground in the shikimate pathway. It produces chorismate which
eradication of malaria is supposed to be a complex one. is an aromatic precursor. This can be further metabolized
Cases of anti-malarial drug resistance have been growing into other aromatic compounds such as folate. As shi-
expotentially as well as more cases are being recorded with kimate pathway is present in Plasmodium falciparum
P. falciparum strain’s drug-resistance that is accounted for and is absent in mammals, the enzymes of the pathway
about 60 percent of death [8–11]. Another challenge with can be strongly considered as an effective drug target
malarial extermination is that a single-cell parasite is good against malaria [18–21].
enough for causing it as, it has the ability to escape human In the current study Plasmodium falciparum transketo-
immune system. Even if a patient recovers and contracts lase was subjected to extensive computational study to
from malaria, there is no guarantee that he or she will not determine its chemical and structural properties along
be infected by malaria in future. These complications make with its protein -protein interaction network. The study
it difficult to establish a proven vaccine for malaria. In case also predicted good quality model of Pftk using homology
of other viral disease like measles, vaccine that carries a modeling techniques and subsequent computer aided
weakened strain of the virus has been injected into the active site prediction and docking simulation studies for
blood stream which allows the body to create immunity to the development of an effective drug against Plasmodium
that virus in future infection. With malaria parasite, human falciparum 3D7.
body cannot develop this type of immunity as the malaria
parasite go thorough modifications continuously [12]. Con- Materials and methods
sidering all these reasons, it is crucial to find out a new tool Sequence retrieval
that would allow the scientist community to stay one step The amino acid sequences of transketolase [Accession
ahead of more affordable drugs and practical formulations. XP_966097.1] of P. falciparum 3D7 were retrieved from
With the completion of the genome sequencing of P. the protein database of National Center for Biotechnology
falciparum, it has been revealed that working with spe- Information (NCBI). The protein is 672 amino acids long
cific metabolic pathway of the parasite could pave a way and used for further analysis in the current study.
for new mode of action against it. In P. falciparum one
of the most fundamental metabolic pathways is the pen- Primary structure prediction
tose phosphate pathway (PPP) which has been reported ExPasy’s ProtParam tool [22] was utilized to calculate the
to play active role in P. falciparum infected erythrocytes physico-chemical characteristics of the protein. Theoretical
[13, 14]. It can generate reducing equivalents in the form isoelectric point (pI), molecular weight, total number of
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 3 of 14

positive and negative residues, extinction coefficient [23], Table 1 Different physico-chemical properties of transketolase
instability index [24], aliphatic index [25] and grand average (Plasmodium falciparum 3D7)
hydropathicity (GRAVY) of the protein were calculated Parameter Value
using the default parameters. Molecular weight 75815.2
Extinction coefficients 82460
Secondary structure analysis
Abs 0.1 % (=1 g/l) 1.088, assuming all pairs of Cys
Secondary structure was predicted by using the self- residues form cystines
optimized prediction method with alignment (SOPMA). Ext. coefficient 81710
Protein’s secondary structural properties are including α
Abs 0.1 % (=1 g/l) 1.078, assuming all Cys residues are reduced
helix, 310 helix, Pi helix, Beta Bridge, Extended strand,
Bend region, Beta turns, Random coil, Ambiguous states Theoretical pI 6.50
and other states [26]. Total number of negatively charged residues (Asp + Glu): 76
Total number of positively charged residues (Arg + Lys): 70
Disease causing region prediction Instability index 38
GlobPlot 2.3 was used to find out the disease causing Grand average of hydropathicity (GRAVY) -0.402
regions of the protein. This web service looks for
Aliphatic index 82.89
order/globularity or disorder tendency in the query
protein based on a running sum of the propensity for
an amino acid to be in ordered or disordered state by
searching domain databases and known disorders in structures with 1ITZ_A, 1AY0, 1TKA, 1TRK as template
proteins [27]. structures from which the best one is selected on the basis
of lowest discrete optimized protein energy (DOPE) score
Template selection and highest GA341 score [32].
To find out suitable template for the protein PSI
(Position Specific Iterative) BLAST is performed against Structure refinement
PDB database considering the default parameters except Modrefiner [33] is an algorithm for atomic-level, high-
PSI-BLAST threshold to 0.0001. Total three iterations of resolution protein structure refinement, which can start
PSI-BLAST were considered as the BLAST search re- from C-alpha trace, main-chain model or full-atomic
sults converged after three iterations [28]. The PDB model. Modrefiner refine protein structures from Cα traces
structures of 1ITZ_A, 1AY0, 1TKA, 1TRK were selected based on a two-step atomic-level energy minimization.
as template structure. The main-chain structures are first constructed from
initial Cα traces and the side-chain rotamers are then
Template sequence alignment refined together with the backbone atoms with the
Query sequence and the best template sequence according use of a composite physics and knowledge-based force
to identity parameter were aligned by Clustal Omega, the field.
latest of Clustal family. Clustal omega algorithm takes in-
put of an amino acid sequence then produces a pairwise Verification and validation of the structure
alignment using k-tuple method followed by sequence The accuracy and stereo chemical feature of the predicted
clustering through mBed method and k-means clustering model was calculated with PROCHECK [34] by Rama-
method. Final output of multiple sequence alignment is chandran Plot analysis [35] which was done through
done by HHalign package, which aligns two profile hidden
Markov models [29]. Table 2 Secondary structure analysis through SOPMA of
transketolase (Plasmodium falciparum 3D7)
Homology modeling Secondary Structure Percentage
The model was generated using a comparative modeling Alpha helix (Hh) 43.30 %
program MODELLER9v13 [30] which generates a refined
Extended strand (Ee) : 15.62 %
three dimensional homology model of a protein sequence
based on a given sequence alignment and selected template. Beta turn (Tt) : 8.04 %
Homology modeling is able to produce high quality models Random coil (Cc) : 33.04 %
provided that the query and template molecule are closely 310 Helix 0.00 %
related. But model quality can decrease if sequence identity π helix 0.00 %
of target and template sequence falls below 20 % though it’s Isolated β-bridge 0.00 %
proven that protein structures are more conserved than
Bend 0.00 %
their sequences [31]. The MODELLER generated five
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 4 of 14

Fig. 1 Globplot result shows the disease causing regions of transketolase

Fig. 2 Sequence alignment of the template protein and the query protein sequences
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 5 of 14

Fig. 3 Refined model of Transketolase

“Protein structure and model assessment tools” of number, boundary of mouth openings of every pocket,
SWISS-MODEL workspace. The best model was se- molecular reachable surface and area [44]. Active site
lected based on overall G-factor, number of residues analysis provides a significant insight of the docking
in core, allowed, generously allowed and disallowed simulation study.
regions. Verify3D [36], ERRAT [37] and QMEAN [38]
were used for additional analysis of the selected Docking simulation study
model. Finally, the protein was visualized by Swiss- In silico docking simulation study, was carried out to
PDB Viewer [39]. recognize the inhibiting potential against Transketolase
enzyme. Docking study was performed by Autodock
vina [45]. Before starting the docking stimulation study,
Network interaction
transketolase was modified by adding polar hydrogen.
STRING [40] was used to identify protein-protein
A grid box (Box size: 76 × 76 × 76 Å and box center:
interaction. STRING is a biological database which is
11 × 90.5 × 57.5 for x, y, and z, respectively) was
used to construct Protein-protein interaction network
designed in which nine binding modes were generated
for different known and predicted protein interactions.
for the most favorable bindings. The overall combined
At present, string database covers up to 5,214,234 proteins
from 1133 organisms [41]. RING (Residue Interaction
Table 3 Ramachandran plot of transketolase from Plasmodium
Network Generator) was used to analyze residue-residue
falciparum 3D7
interaction of transketolase and generated network was
Ramachandran plot statistics Transketolase
visualized by Cytoscape 3.1.0 [42].
Residue %
Residues in the most favored regions [A,B,L] 547 92.7
Active site analysis
Residues in the additional allowed regions [a,b,l,p] 40 6.8
After modeling the three dimensional structure of
Residues in the generously allowed regions [a,b,l,p] 3 0.5
transketolase, the probable binding sites of the protein
was searched based on the structural association of Residues in the disallowed regions [xx] 0 0.0
template and the model construct with Computed Atlas Number of non-glycine and non-proline residues 590 100.0
of Surface Topography of proteins (CASTp) [43] server. Number of end residues (excl. Gly and Pro) 2
CASTp was used to recognize and determine the bind- Number of glycine residues 49
ing sites, surface structural pockets, active sites, area, Number of proline residues 31
shape and volume of every pocket and internal cavities
Total number of residues 672
of proteins. It could be also used to calculate the
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 6 of 14

Fig. 4 Ramachandran plot analysis of transketolase. Here, red region indicates favored region, yellow region for allowed and light yellow shows
generously allowed region and white for disallowed region. Phi and Psi angels determine torsion angels

binding with Transketolase and 6′-Methyl-Thiamin Di- and function are correlated for any biological molecule.
phosphate was obtained by using PyMOL (The PyMOL Secondary structural features of the protein are predicted
Molecular Graphics System, Version 1.5.0.4, Schrödinger, by SOPMA algorithm. Both the results of primary and
LLC). secondary structure analysis of the protein are presented
in Table 1 and Table 2 respectively.

Results
Primary and Secondary structure analysis Disease causing region prediction
ProtParam computes several parameters analysing the 12 disorder regions were identified by GlobPlot. The
primary structure of the protein sequence. This parame- result is shown in Fig. 1. The regions are from amino
ters are the deciding functions of the proteins stability acid number 1-10, 29-36, 97-125, 258-262, 341-361,
and function. The primary structure of a protein en- 381-388, 428-435, 469-476, 493-499, 504-514, 552-559
codes motifs that are of functional importance, structure and 614-619.

Fig. 5 Verify 3D graph of transketolase (P. falciparum 3D7)

Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 7 of 14

Fig. 6 ERRAT generated result of transketolase where 95 % indicates rejection limit

Allignment of target sequence Active site prediction

Allignment between the target sequences and selected The active site of transketolase was predicted by using
sequence was determined by clustal omega (Fig. 2). Clustal CASTp server. The calculated result shows that the
omega algorithm aligns sequences faster and more accur- amino acid position 46-515 is predicted to be conserved
ately. A good alignment of template sequences along with with the active site. At this point, it is considered that
closely related template models are necessary for predict- the experimental binding sites of 6′-Methyl-Thiamin Di-
ing a better quality model of the query protein through phosphate include some of the residues as stated above.
homology modelling. Therefore in our study His 109, Asn 108 and His 515
are chosen as the more positive sites to dock the sub-
Model building strate. The number of pockets, their area and volume
MODELLER 9.13 was used to determine the three dimen- are graphically represented (Fig. 10).
sional (3D) model of the targeted protein. 3D protein
structures provide valuable insights into the molecular Docking results analysis
basis of protein function. MODELLER generated result The exploration for the top ways is to fit ligand mole-
shows transketolase contains <90 % residues in favored cules into transketolase structure, using Autodock Vina
region and 0.8 % of amino acids in the disallowed region.

Refinement of the predicted model

MODELLER generated model was considered for further
refinement through Modrefiner to gain a better quality
structure. An increase of about 4 % residue in favored
region is seen and other parameters acquired better
acceptable value. The refined model is depicted in Fig. 3.

Model verification and validation

Ramachandran plot was done by PROCHECK to measure
the accuracy of protein model. The results were narrated
in Table 3 and Fig. 4. The profile score above zero in the
Verify3D graph correspond to the acceptable environment
of the model, in Fig. 5. ERRAT; which verifies protein
structure, generated result depicted in Fig. 6. QMEAN ser-
ver was used for the verification of protein model which is
shown in Fig. 7.
Fig. 7 Graphical presentation of estimation of absolute quality of
Network generation model transketolase (P. falciparum 3D7). Here the dark zone indicates
The protein-protein interacting partners of Transketolase that the model has a score <1. Models considered good are expected
of Plasmodium falciparum 3D7 was determined by to position in the dark zone. The red marker shows a generated target
model, which are considered to be a good model according to their
STRING (Fig. 8). Residue interaction network was
position near or in the dark zone
depicted in Fig. 9.
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 8 of 14

Fig. 8 Protein-Protein Interaction network of transketolase (Plasmodium falciparum 3D7) detected through STRING

Fig. 9 Residue interaction network generated by RING was visualized by Cytoscape. Here, nodes represent amino acids and edges represent interaction
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 9 of 14

Fig. 10 a The table of the area and the volume for different active sites of transketolase. b The Three Dimensional structure of the best active
site. c Active site analysis by CASTp server. Green color illustrates the active site position from 46 to 515 with the beta-sheet in connecting them

resulted in docking files that included complete records of the total intermolecular energy, total internal energy
of docking. The obtained log file is given in Table 4. and torsional free energy minus the energy of the unbound
The resemblance of docked structures was computed system. The top nine ligands conformation were generated
by calculating the root mean square deviation (RMSD) based on the energy value through Autodock Vina.
between the coordinates of the atoms and forming the
clusters of the conformations based on the RMSD Discussion
values. The lowest binding energy conformation in all Plasmodium falciparum transketolase (pftk) is an
cluster were considered as the most favorable docking attractive target site candidate for anti-malarial drug dis-
pose. Binding energies that are reported signify the sum covery. As the crystal structure of Pftk is unavailable, the

Table 4 Binding energies (kcal/mol) of the compounds along with their Root Mean Square Distance value obtained from Autodock
Vina tool
Compound 1 2 3 4 5 6 7 8 9
6′-Methyl-Thiamin Diphosphate -6.6 -6.4 -6.0 -5.4 -5.4 -5.4 -5.1 -5.1 -5.0
dist from best mode rmsd l.b. 0.000 3.252 2.378 3.123 4.875 2.724 5.149 25.545 26.623
dist from best mode rmsd u.b. 0.000 4.402 5.402 6.050 5.978 4.884 7.100 28.035 28.663
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 10 of 14

homology modeling technique stands out as an excellent that majority of the residues fall in the favorable core re-
and powerful alternative to predict a reliable 3-D struc- gion including all non-glycine and non-proline residues, in
ture of the protein. the Ramachandran plot, it ensures good stereo-chemical
A physico-chemical analysis of the protein sequence quality of the model.
was done by the Expasy server’s ProtParam tool. It From the refined structures the best structure has
revealed an instability index of 38.00, which denotes, this been selected using structure validation tools; namely
protein will be stable in-vitro because a value over 40 is PROCHECK, Verify 3D and ERRAT. The highest scoring
considered unstable. The instability index is estimated structure was picked as the final structure. VERIFY 3D uses
from a statistical analysis of 12 unstable and 32 stable the 3D profile of a structure to determine its correctness by
proteins where it was found that occurrence of certain matching it with its own amino acid sequence. A high score
dipeptides are significantly different among stable and match is expected between the three dimensional profile of
unstable proteins. This protein was also predicted to a structure and its own sequence. This compatibility score
have high aliphatic index; it is the total volume occupied of an atomic model (3D) with its sequence (1D) ranges
by aliphatic side chains and higher value is considered a from -1 (bad) to +1 (good), so, score 0.77 in verify 3D de-
positive factor for increased thermo stability. Along termines good environmental profile of the structure [53].
with high extinction coefficient and negative GRAVY, ERRAT, the structure verification algorithm interpreted the
the extents of other parameters imply the stability of overall quality of the model with the resulting score 78.313;
the protein [46]. this score denotes the percentage of the protein that falls
Results generated by secondary structure prediction below the rejection limit of 95 % [37].
tool SOPMA showed the enzyme is dominated by The QMEAN scoring function estimates the geometrical
43.3 % alpha helix and 33.04 % random coils along with aspects of a protein structure by a composite function of
15.62 % extended strands and 8.04 % beta turns. The six different structural descriptors; a torsion angle potential
abundance of coiled region indicates higher conservation over three consecutive amino acids to analyze local
and stability of the model [47, 48]. geometry, long range interactions assessed by a secondary
High degree of flexibility in polypeptide chain and structure-specific distance-dependent pairwise residue-
insufficiency of regular secondary structure is considered level potential, a solvation potential describing the the
as disorder in protein [49]. Disordered regions might burial status of the residues and two agreement term
contain functional sites or linear motifs and many pro- determining the agreement of predicted and calculated
teins are intrinsically found disordered in vivo. In Fig. 1 secondary structure and solvent accessibility [38, 54].
the blue colored sections on the X-axis are disordered The Z-scores of the QMEAN terms of the protein
regions and green colored regions are globular or or- model are -0.37, -0.58, -0.11, -1.90, 1.33, 0.16 for C_β
dered domains. Disordered regions are important be- interaction energy, salvation energy, torsion angle energy,
cause many intrinsically disordered proteins exist as secondary structure, and solvent accessibility respectively.
unstructured and become structured when bound to These scores indicate that the predicted protein model
another molecule [50, 51]. can be considered as a good model. Moreover, to estimate
The 3D model of the Pftk derived from Modeller v.9 the absolute quality of the model the QMEAN server [55]
had 89.8 % of all its residues in the favorable region, relates the query model with a representative set of high
9.0 % and 0.3 % in allowed and generously allowed re- resolution X-ray structures of similar size and the resulting
gion. Only 0.8 % of the residues was in the disallowed QMEAN Z-score is an extent of “degree of nativeness” of
region in the Ramachandran plot analysis where the the given structure [56]. The average z-score of high reso-
amino acid residues of a peptide are plotted in favorable, lution models is ‘0’. The QMEAN z-score for the query
allowed and disallowed regions according to their torsion model is -0.29, which is lower than the standard deviation
angles phi (φ) and psi (ψ). Though homology modeling ‘1’ from the mean value ‘0’ of good models, so, this result
algorithm is one of the most robust modeling tools in bio- shows that the predicted model is of comparable quality
informatics, this often contain significant local distortions, to the high resolution models. In addition the range of
including steric clashes, unphysical phi/psi angles and predicted global model reliability is 0 to 1 according to
irregular H-hydrogen bonding networks, which make the Verify 3D. Hence, Plasmodium falciparum transketolase
structure models less useful for high-resolution functional
analysis. Refining the modeled structures could be a solu-
tion of this problem [52]. Refinement through Modrefiner Table 5 Comparative docking study of the ligand to the target
has depicted 92.7 % of its entire residue in the most Ligand Protein No. of H Interacting residues
favored regions, 6.8 % in the additional allowed regions, bonds
0.5 % in the generously allowed regions and 0.0 % in disal- 6′-Methyl-Thiamin Transketolase 5 His 109, Asn 108,
Diphosphate His 515,
lowed regions. The statistics of the refined model showed
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 11 of 14

Fig. 11 The overall binding between the transketolase and 6′-Methyl-Thiamin Diphosphate. a Biological assembly of transketolase and
6′-Methyl-Thiamin Diphosphate, b Mesh structure of transketolase and 6′-Methyl-Thiamin Diphosphate, c Surface structure of transketolase
and 6′-Methyl-Thiamin Diphosphate, d Cartoon structure of transketolase and 6′-Methyl-Thiamin Diphosphate

with a global model reliability score 0.74 has all the poten- that transketolase interacts with twenty other proteins
tials of a good quality model [57–59]. in a high confidence score among which GAPDH
Protein-protein interaction (PPI) networks generation (Glyceraldehyde 3-phosphate dehydrogenase); an exo-
have become crucial tool of modern biomedical research somal protein that functions in some crucial pathways
for the understanding of intricate molecular mechanisms like glycolysis/gluconeogenesis and amino acid biosynthesis.
and for the recognition of novel modulators of disease D-ribulose-5-phosphate 3-epimerase, is the enzyme that
progressions. To study varieties of human diseases as converts D-ribulose 5-phosphate into D-xylulose 5-
well as their signaling pathways, protein interactions give phosphate in Calvin’s reductive pentose phosphate cycle
an immense effect [60–62]. PPI of Transketolase generated [63]. ENO stands for enolase, also known as 2-phospho-D-
through STRING is presented in (Fig. 8). STRING forecasts glycerate hydro-lyase which is a metalloenzyme responsible
a confidence score, 3D structures of protein and Protein for the catalyting of the conversion of 2-phosphoglycerate
domains. STRING utilizes references from UniProt (2-PG) to phosphoenolpyruvate (PEP).
(Universal Protein) resource and predicts functions of Residue interaction networks (RINs) have been used to
different interacting protein. PPI network demonstrates describe the protein three-dimensional structure as a

Fig. 12 Graphical Representation of docking study between 6′-Methyl-Thiamin Diphosphate and Transketolase (yellow dashed-lines indicate
hydrogen bonds). a Visualization of 6′-Methyl-Thiamin Diphosphate-Transketolase interaction b Hydrogen Bond detection through PyMOL
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 12 of 14

Table 6 Description of Ligand molecule

Name 6′-Methyl-Thiamin Diphosphate Chemical structure
Identifiers [2-[3-[(4-amino-2,6-dimethyl-pyrimidin-
5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-
5-yl]ethoxy-hydroxy-phosphoryl] hydrogen
phosphate
Formula C13 H20 N4 O7 P2 S
Molecular Weight 438.33 g/mol
Type non-polymer

graph where nodes and edges represent residues and predicted the 3D structure of PfTk. Evidences have
physico-chemical interactions respectively. To analyze shown that, PfTk (transketolase) can be considered as a
residue-residue interaction, protein stability and folding, remarkable drug target for its role in the regulation of
allosteric communication, enzyme catalysis or mutation non-oxidative arm of the PPP and for the least homology
effect prediction RING is being used. RING uses standard with its human host. The need of a proper vaccine against
programs to create network interaction that is visualized malaria has never been more serious as malaria increas-
through Cytoscape [64–67]. Cytoscape is an open source ingly claiming life in this 21st century. This study is aimed
software package for visualizing, modeling and analyzing to aid the hunt for the proper target site in the quest for a
molecular and genetic interaction networks. A higher sole solution to defend malaria. The structural information
bonding interaction indicates higher probability of protein of our given model will pave the way for further
functioning site [68–70]. Residue-residue interaction net- laboratory experiments to design potential anti-malarial
work of transketolase indicates the probable active site of drug in near future.
the crucial protein of plasmodium falciparum [71].
The active site of transketolase was predicted by Abbreviations
CASTp server as shown in Fig. 10. In our present study, Pftk: Plasmodium falciparum transketolase; GRAVY: Grand average hydropathicity;
SOPMA: Self-optimized prediction method with alignment; PDB: Protein data
we reported the surpass active site area of the enzyme in bank; STRING: Search tool for the retrieval of interacting genes/proteins;
addition to the number of amino acids occupied in it. RING: Residue interaction network generator; CASTp: Computed atlas of surface
The preeminent active site is found with 1118.8 areas topography of proteins; RMSD: Root mean square deviation; PPI: Protein-protein
interaction.
and a volume of 1696.9 amino acids.
The complete profile of the studies by AutoDock Vina, Competing interests
is represented in Table 5. For the most favorable binding The authors declare that they have no competing interests.
6′-Methyl-Thiamin Diphosphate, estimated free energy
of molecular binding was of −6.6 kcal/mol. The overall Authors’ contributions
binding energies as well as RMSD (Å) of 6′-Methyl- MAH has made substantial contributions to conception and design,
acquisition of data, analysis and interpretation of data. MHHM and ASC
Thiamin Diphosphate based on their rank are tabulated in carried out the molecular genetic studies, participated in the sequence
Table 4. Overall binding of transketolase and 6′-Methyl- alignment and drafted the manuscript. AD worked for computational
Thiamin Diphosphate is represented in Fig. 11. It has been analysis. MAK conceived of the study, and participated in its design and
coordination and helped to draft the manuscript. All authors read and
found that 6′-Methyl-Thiamin Diphosphate formed 5 approved the final manuscript.
Hydrogen bonds with the transketolase (Fig. 12). The
Amino acid residues conscientious for the binding interac- Acknowledgements
tions of the 6′-Methyl-Thiamin Diphosphate (Fig. 11b) We cordially thank Adnan Mannan and Omar Faruk Sikder of the
with the enzyme are His 109, His 515, Asn 108. The de- Department of Genetic Engineering and Biotechnology, University of
Chittagong, for their suggestions and inspiration during our research
scription of 6′-Methyl-Thiamin Diphosphate is given in proceedings.
Table 6. After analyzing the results, in case of our selected
ligand it is clearly concluded that this has a crucial role in Author details
1
Department of Genetic Engineering and Biotechnology, Faculty of Biological
ligand binding affinity. Sciences, University of Chittagong, Chittagong 4331, Bangladesh.
2
Department of Biotechnology and Genetic Engineering, Mawlana Bhashani
Conclusion Science and Technology University, Santosh, Tangail 1902, Bangladesh.
By analyzing different structural and physiological Received: 4 October 2014 Accepted: 8 May 2015
parameters of P. falciparum 3D7, in this study we
Hasan et al. Source Code for Biology and Medicine (2015) 10:7 Page 13 of 14

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