Helicobacter pylori causes gastric pathologies to human after attachment to gastric epithelial layer via BabA protein, which is considered as one of the most important virulence factors. The study aimed to find inhibitors to this protein using structure-based drug design (SBDD) approach on the protein 3D structure (pdb ID 4zh0) . Large number of molecules / ligands were obtained as the protein gets many binding pockets. Checking and filtering the compounds depending on different parameters such as types of toxicity , ADME (absorption, distribution, metabolism, and excretion ) characters and others , only 6 molecules were obtained , these were redocked with the protein , they gave reasonable binding affinity at root-mean-square deviation (RMSD) of zero which represented by mode 1 of results performed by AutoDock vina.

1. Inhibitors for Attachment Protein BabA of Helicobacter pylori
Inhibitors for Attachment Protein BabA of Helicobacter pylori
Zahra M. Al-Khafaji*1, Aaisha B. Mahmood2, Marium B. Mahmood3
1Institute of Genetic Engineering and Biotechnology for Postgraduate Studies, University of Baghdad, Iraq.
2Ministry of Agriculture, Veterinary Directorate, Baghdad Veterinary Hospital, Al-Dora Hospital, Iraq.
3Financial Affairs Department, Computer Science, University of Baghdad
Helicobacter pylori causes gastric pathologies to human after attachment to gastric epithelial
layer via BabA protein, which is considered as one of the most important virulence factors. The
study aimed to find inhibitors to this protein using structure-based drug design (SBDD) approach
on the protein 3D structure (pdb ID 4zh0) . Large number of molecules / ligands were obtained as
the protein gets many binding pockets. Checking and filtering the compounds depending on
different parameters such as types of toxicity , ADME (absorption, distribution, metabolism, and
excretion ) characters and others , only 6 molecules were obtained , these were redocked with the
protein , they gave reasonable binding affinity at root-mean-square deviation (RMSD) of zero
which represented by mode 1 of results performed by AutoDock vina.
Keywords: Helicobacter pylori, BabA, Antiadhesive compounds, SBDD, Iraq
INTRODUCTION
Helicobacter pylori (H. pylori) specifically colonizes human
stomach, can lead to different gastric pathologies. The
bacterium equipped with an extraordinary large number of
outer membrane proteins , and among the main features
of the bacterium is the high genome plasticity , which is
resulted from an elevated mutation rate and extensive
exchange of genetic materials leading to free
recombination of H. pylori genes ( Wang et al.( 2019);
Suerbaum et al.( 1998) Wang et al. 1999). The bacterium
has been classified as class I carcinogen (IARC,1994;
Ansari and Yamaoka, 2017). It is prevalent in developing
countries, where up to 80% of the mid-aged adults may be
infected De Falco et al. (2015). Many virulence factors
are used by the bacterium such as outer membrane
proteins (adhesins), which attach the bacterial cells to host
surfaces, these adhesins play a vital role in pathogenesis,
they can recognize the structures of glycans expressed in
the gastric mucosa Huang et al. (2016). Among these
adhesins is the blood group -binding antigen (BabA),
which is one of the Hop family (known as HopS or
OMP28), this protein can identify (MUC5AC) the
difucosylated ABO/Lewis b (LeB) antigen found on red
blood cells and gastrointestinal mucosa epithelial cells
(Huang et al. 2016; Kusters et al. 2006 ; Odenbreit et al.
2009) . BabA receptors also found on oral cavity and
stomach (Ansari and Yamaoka, 2017), it is nearly 78kDa
encoded by babA gene Kao et al.(2016). BabA and other
adhesins are important to the bacterium, since any H.
pylori cell that does not adhere to the epithelial cell/ layer
would be quickly removed from the epithelial layer and the
mucus gel (Huang et al. 2016). In addition the BabA-LeB
interaction which is resulted in adherence and initial
colonization to the stomach surface , it also helps in
anchoring and insertion of bacterial factors in host cell
cytosol such as CagA and VacA (Kusters et al. 2006 ;
Waskito et al. 2018; Sweeney and Guillemin, 2016).This
leads to signaling process , since the injected type IV
secretion system (TFSS) will result in induction of
transcription of genes that enhance many associated
activities related to pathogeny Ishijima et al.( 2011).
On the other hand, due to tremendous advances in 3D
structure estimation of proteins, and the rapid growing field
in the in-silico drug discovery, these approaches can be
exploited to find out inhibitors/drugs for many virulence
factors. In this aspect Structure-Based Drug Design
(SBDD) which is an in-silico method can be used during
the early stages of drug discovery or design Garyfallia et
al. (2018).
*Corresponding Author: Zahra M. Al-Khafaji,
Department of Institute of Genetic Engineering and
Biotechnology for Postgraduate Studies, University of
Baghdad, Iraq. E-mail: zahranasserk@gmail.com
Research Article
Vol. 5(1), pp. 146-154, May, 2020. © www.premierpublishers.org. ISSN: 0379-9160
World Journal of Microbiology

2. Inhibitors for Attachment Protein BabA of Helicobacter pylori
Al-Khafaji et al. 147
Choosing the target is quite essential for SBDD, the target
should be essential and is a part of life cycle of the cell,
targeting bacterial adherence can form of an effective
nonantibiotic treatment(Cusumano et al. 2011; Spaulding
et al. 2017), BabA represents a good and promising target
as it is found at the out borders of cells and is unique for
H. pylori . The aim of this work was to find chemical
inhibitors to BabA of H. pylori for future development of
anti-Helicobacter agents.
MATERIALS AND METHODS
Different databases and software were used, for different
purposes:
DATABASES
NCBI: https://www.ncbi.nlm.nih.gov/
Used for retrieve sequences and BLASTing
pdb database: https://www.rcsb.org/
Used to find out the pdb structure of BabA (4zh0) protein .
Uniprot database: https://www.uniprot.org/
To find out some information about the target (BabA).
Zinc database: http://zinc.docking.org/
Used to download different chemical formats, and
information about compounds.
SOFTWARE
MarvinSketch : https://chemaxon.com/products/marvin
Used for chemical format manipulation, and finding some
molecule descriptors.
Online SMILES Translator and Structure File
Generator https://cactus.nci.nih.gov/translate/
Used to get SMILES format of some molecules.
Swiss ADME: http://www.swissadme.ch/
Used for finding pharmacokinetic characters of molecules.
T.E.S.T. software: https://www.epa.gov/
Toxicity-Estimation-Software tool-Test , to find out the
safety of molecules.
PyRx software v.8: https://pyrx.sourceforge.io/
Used for molecular docking.
PyMOL software https://pymol.org/2/.
Used for docking vitalization.
Discovery Studio Visualizer
Used for docking vitalization .
RESULTS AND DISCUSSION
BabA is important for initial colonization of H. pylori
(Waskito et al. 2018;Moonens et al. 2016 ;Prinz et al.,
2001;Ilver , 1998), its binding affinities (Ka~107-1012 M-1),
which means that it is greater than most carbohydrate
binding proteins (Aspholm-Hurtig et al. 2004 ;Imberty et
al. 2005). Adherence of the bacteria to cell receptors offers
several advantages to the bacteria , such as protection
from washing out during mucus shedding, getting nutrients
from damaged host epithelial cells, promotes delivery of
bacterial toxins and effector molecules such as CagA
oncoprotein , VacA and others helping in development of
pathogenicity and persistence infections (Kable et al.
2017; Odenbreit , 2005; Rhen et al. 2003 ;Aspholm et al.
2006) . And since the transmission thought to take place
through the oral route , then the possible initial attachment
could be occurred with salivary proteins as it has been
found that BabA mediates the attachment by binding with
difucosylated glycans found on LeB antigens of salivary
mucin MUC58 serving as a receptor of BabA (Walz et al.
2009 ;Prakobphol et al. 2005).
The drug target should be characterized with some criteria
such as to be essential to the pathogen , in addition ,it
should be unique , this was explained by BLASTing the
BabA sequence (pdb ID 4zh0) using BLAST algorithm and
non-redundant database , the results showed that this
protein is restricted to H. pylori . The retrieved crystal
structure of BabA (pdb ID 4zh0) Hage et al. (2015 )was
found to be acceptable for drug design purposes .The
recommended and acceptable resolution of crystal
structure of protein is 2.5 Aᴼ , the resolution of 4zh0 is 1.91
Aᴼ, other criteria required are Rfactor which should be below
25% , this value for 4zh0 is 0.145, in addition , the Rfree
recommended values is below 28% and ideally below 25%
, for the protein 4zh0 this value is 0.14 , the other criteria
concerning coordinate errors are low and satisfy the
crystal structure to be drug target , finally 97.5% of the
protein residues fall in favored region of Ramachandran
plot (Anderson , 2003).
The target protein should be druggable with binding
pockets, this was demonstrated using DoGsiteScorer
(Volkamer et al. 2012) , the results shown in Figure 1.
The protein shows different binding pockets with drug
score extended from (0.24-0.8), this means that the protein
can bind different ligands that complementary to its
pockets which might lead to total modulation of its activity
and death of the pathogen (Anderson , 2003; Volkamer et
al. 2012; Yuan et al. 2013).
In this study SBDD was used which comprises several
steps, the initial virtual screening was carried out using
MTiOpenScreen server, this allows performing docking of
ligands in suitable pocket using blind docketing via
AutoDock 4.2 and automated virtual screening with
AutoDock vina (Labb´ et al. 2015; Lagarde et al. 2019)

3. Inhibitors for Attachment Protein BabA of Helicobacter pylori
World J. Microbiol. 148
Figure 1: Pockets of BabA protein (pdb ID 4zh0) and druggability
and providing starting collections, the web site has
different databases to be screened. Such servers give the
ligands with the best score concerning affinity and
specificity, the resulted ligands then subjected for
optimization for different aspects (Dhanik and Kavraki,
2012).
In this study the top 100 molecules of diverse-library were
used, these were checked and filtered for different criteria,
since the molecules with high score could fail in different
assays or with other characters. BabA is related to
stomach site, so it would be preferred to evaluate for orally
bioavailability using Lipinski rule of five (Lipinski et al.
1997) , in addition to check the ADME characters (Wanga
et al. 2018), and different types of toxicity, synthetic
accessibility of resulted ligands . The primary study
checked mutagenicity and teratogenicity using T.E.S.T.
software and LAZAR software, hREG was also estimated,
only 6 molecules satisfied most criteria, shown in Table 1.

4. Inhibitors for Attachment Protein BabA of Helicobacter pylori
Al-Khafaji et al. 149
Table 1: Some characters of selected ligands
Synthetic
Accessibility
bioavailabilityPgpBBBGI
absorption
hERGTeratogenicityMutagenicityCompound
#
2.810.55--+24827103
3.130.55NoNohigh---3712259
2.310.55NoNohigh---24833135
3.570.55NoNohigh---26535128
2.260.55NoNohigh-+51087930
2.280.55NoNohigh--85149061
Other physico-chemical characters of the selected molecules are shown in Table 2
Table 2: Physico-chemical properties of selected ligands
TPSALogPHBDHBALeadLikenRotMW
Compound
#
96.262.1515Yes3271.294524827103
80.712.3106Yes4265.652551087930
103.340.5616Yes4291.32563712259
94.531.8324Yes6253.317424833135
99.24-1.5637Yes6240.25985149061
73.561.4215Yes8240.298826535128
Docking Studies
Molecular docking is a decisive step of SBDD, which helps
in visualizing the interaction pattern and binding energy of
receptor-ligand complexes, this could be carried out atom-
by-atom or fragment-by-fragment (Wanga et al. 2018;
Verlinde and Hol 1994). Therefore, it is considered as a
key of success of placing/docking the ligand in the binding
pocket of the target. Docking studies of this work used
AutoDock vina implemented in PyRx package using
Force-field based scoring function and the binding affinity
(kcal/mol) is calculating through the sum of non-bound
interactions such as electrostatics and van der Waals in
addition to hydrogen bonds , solvents and entropy
contributions with each conformational states of ligands
(Wanga et al. 2018; Huang and Zou, 2010; Kapetanovic
,2008; Carlson and Jorgensen , 1995 ) . The binding
affinity of selected ligands with BabA (pdb ID 4zh0) are
shown in Table 3.
Table 3: Binding affinity of docked ligands, RMSD of zero
Binding Affinity (kcal/mol)Molecules
-5.53712259
-6.524827103
-5.424833135
-4.426535128
-5.851087930
-4.985149061
These values were for best mode at RMSD ( Root-Mean
Squared Deviation ) values of zero , as in terms of docking
accuracy , a threshold of 1.0-3.0 Aᴼ RMSD between the
docked and X-ray pose has been generally considered to
be a "successfully" docked structure (Halperin et al. 2002;
Muegge and Rarey, 2001; Abagyan and Totrov , 2001;
Taylor et al. 2002), the visualization of docked ligands are
shown in Figure 2.

5. Inhibitors for Attachment Protein BabA of Helicobacter pylori
World J. Microbiol. 150

6. Inhibitors for Attachment Protein BabA of Helicobacter pylori
Al-Khafaji et al. 151
Figure 2: Docking results of studied ligands with BabA protein (pdb ID 4zh0)
It is known that binding site can be active site as in
enzymes or may be any other site such as communication
site necessary in the metabolism , with concave surface
on the protein that can accommodate drug molecules , this
can induce conformational changes upon binding to a
protein ( Erickson et al.2004 ; Anderson, 2003). So the
potential drug target are not necessarily disease causing
but must by definition be disease modifying as with BabA
protein.
Generally, SBDD has emerged as promising tool for drug
industry following by ligands optimization. On the other
hand , suggesting anti-adhesive molecules cannot cure
the acute infection , but might be used after eradication
treatment to inhibit recurrence by preventing
recolonization of the stomach, as they interact with surface
protein of H. pylori and would work by clearing the
bacterium out of the stomach through dislodging the
bacterium off the stomach wall as in using BabA inhibitors.
Such strategies are necessary to help in H. pylori
eradication since BabA is unique in this bacterium, and the
inhibitors will not affect normal flora Messing et al. (2014).

7. Inhibitors for Attachment Protein BabA of Helicobacter pylori
World J. Microbiol. 152
The suggested molecules are:
IUPAC Recommended Name
24827103: N‐[4‐(pyridin‐2‐yl)‐1,3‐thiazol‐2‐yl]furan‐2
Carboxamide
protein (pdb ID 4zh0)
51087930: {1‐[2‐(4‐chlorophenyl)‐2‐oxoethyl]‐1H‐
imidazol‐4 yl}dihydroxyaminyl
3712259: 2‐[(1‐hydroxy‐1,4‐dihydropyridin‐2‐yl)sulfanyl]‐N
(1‐methyl‐1H‐pyrrole‐2‐carbonyl)acetamide
24833135 : ((2R)‐4‐(methylsulfanyl)‐2‐
(phenylformamido)butanoic acid
85149061: 2‐(4‐amino‐2‐oxo‐1,2‐dihydropyrimidin‐1‐yl)‐
N‐(3 -methoxypropyl)acetamide
26535128: propyl 2‐(aminomethyl)‐3‐{[(2R)‐2
hydroxybutyl](methyl)amino}prop‐2‐enoate
The chemical synthesis seems to be possible (see Table
2), the enhancement of molecule action could be improved
through scaffold hopping when required. Most of the
molecules are with limitation of Lipinski rule of five Wanga
et al.(2018 ), which is necessary for oral drugs as in the
case of H. pylori which resident in the stomach , except the
molecule (# 26535128) with high rotatable bonds (8
rotatable bonds) , this makes the molecule highly flexible
and might bind to off-target , in addition this high number
of bonds was found to decrease the docking accuracy
(Verlinde and Hol 1994; Erickson et al. 2004).
Finally, inhibition of BabA might be possible and promising
for future pharmaceutical and clinical treatment of H.
pylori.
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Accepted 16 May 2020
Citation: Al-Khafaji ZM, Mahmood AB, Mahmood MB
(2020). Inhibitors for Attachment Protein BabA of
Helicobacter pylori. World Journal of Microbiology, 5(1):
146-154.
Copyright: © 2020 Al-Khafaji et al. This is an open-access
article distributed under the terms of the Creative
Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium,
provided the original author and source are cited.