Background
Helicobacter pylori is a prevalent etiologic agent for chronic gastritis, gastric and duodenal ulcers, and in rare cases, gastric adenocarcinoma [
1]. A global systematic review concluded that approximately 4.4 billion individuals are positive for
H. pylori infection worldwide, and its prevalence varies from 18.9 to 87.7% of the populations [
2]. This infection is also associated with an increased incidence of extra-gastric diseases, such as cardiovascular, respiratory, hepatic, and allergic diseases [
3]. Successful eradication of
H. pylori infection would effectively reduce the prevalence of the mentioned complications, especially gastric cancer, and is therefore considered as one of the controllable factors in the process of gastric carcinogenesis [
4].
Amoxicillin (AMX), as a bacterial cell wall synthesis inhibitor, is a common constituent of first-line and rescue treatment, due to its high efficiency and fewer side effects [
5]. Its use is recommended in a 14-day quadruple treatment regimen and 10-day sequential treatment [
6]. A recent meta-analysis, comprising 66,142 clinical isolates from 178 studies, of 65 countries, declared up to 10 percent primary resistance to AMX in clinical
H. pylori strains [
7].
AMX belongs to the beta-lactam family of antibiotics that binds the penicillin-binding proteins (PBPs) [
8]. Bacterial PBPs are membrane-associated enzymes, whose activities are essential for cell division and are classified into low-molecular-mass (LMM) and high-molecular-mass (HMM) categories [
9,
10]. PBPs are responsible for glycosyltransferase and transpeptidase activities that lead to cross-linking of
d-alanine and
d-aspartic acid in bacterial cell walls [
11]. Crosslinking adjacent peptidoglycan strands, via peptide stems, is essential for bacterial cell wall integrity and cell viability [
11,
12]. HMM-PBPs constitute the main targets of β-lactam antibiotics, including AMX [
13,
14]. Bacterial resistance to AMX is mainly due to the production of β-lactamase or structural alterations in one of the PBPs, involved in cell wall synthesis.
Helicobacter pylori seem to differ in this regard, as it is evidenced that point mutations in the
pbp1a gene are the main reason for its AMX-resistance [
15,
16]. Nine different PBPs have been reported for
H. pylori; 3 HMM, including PBP1 (72 kDa), PBP2 (62 kDa) and PBP3 (54 kDa) [
17,
18], and 6 LMM (PBP4-9) with 50, 44, 35.5, 33, 28 and 21 kDa molecular weights, respectively [
17,
19,
20]. Class A PBPs have both glycosyltransferase and transpeptidase activities, whereas class B PBPs possess only the latter. Furthermore, the combination of these two enzymatic activities of PBP1A is essential for cell wall homeostasis [
21]. AMX has binding affinities for PBP1, PBP2, and PBP3. However, in resistant
H. pylori strains, its affinity for PBP1A is significantly diminished [
18]. Accordingly, mutations in PBP1A are considered the predominant cause of AMX resistance in
H. pylori [
15,
22,
23].
Using homology modeling, the role of previously reported amino acid substitutions of
H. pylori PBP1A, in binding to AMX has been carefully analyzed [
24]. However, no crystal structure information is available on the
H. pylori PBP1A or its PBPs in general. Consequently, the exact locations of the active and antibiotic binding sites remain to be explored. In this study, we carried out covalent docking analysis of PBP1A with AMX, to characterize the interactions between AMX and its binding site, as well as to identify the potential drug access routes. Subsequently, we evaluated any existing mutations of these residues, in our few resistant clinical strains of
H. pylori, in correlation with their drug susceptibility.
Discussion
In recent decades,
Helicobacter pylori resistance to antibiotics has significantly increased, thereby decreasing its eradication rate worldwide [
27]. AMX, a β-lactam antibiotic, has long been a common constituent of first-line multiple drug therapy against
H. pylori infection. The worldwide rate of AMX resistance was reported as an average of 4.55%, in a recent systematic review [
27]. In accordance with the worldwide average rate, a 4 percent rate of resistance was detected in our study.
AMX-resistance causing factors include mutations in PBPs [
28], β-lactamases [
29], efflux pumps [
30], and biofilm formation [
31]. Point mutations in the
pbp1a gene are considered as the leading cause of AMX resistance in
H. pylori [
16]. β-lactamases, although involved in AMX-resistance in other gram-negative bacteria, seem less critical in
H. pylori [
29,
32]. On the other hand, although mutations in
pbp2 and
pbp3 genes may also cause AMX resistance [
28], those corresponding to the C-terminus of PBP1A protein, are considered as the main determinants of stable resistance in
H. pylori [
18]. The potential resistance provided by the PBP2X and PBP2B mosaics is limited by the presence of a “virgin” PBP1A, which still justifies particular effectiveness for β-lactam treatment. Thus, high level of resistance is dependent on an altered PBP1A [
26].
In order to better understand this phenomenon, we used computational tools to analyze the interactions between AMX and PBP1A. In
Staphylococcus aureus, PBPs form a stable covalent bond between their catalytic Ser370 residues and AMX, thereby preventing bacterial cell wall synthesis by inactivating the transpeptidase domain [
33]. It is known that modification of amino acid residues lining the drug access tunnels affects the enzyme’s activity, specificity, enantioselectivity, and stability [
34,
35]. In case of enzymes, such as xylanase, with buried binding sites, transporting substrates between active sites and the surrounding solution, through the access tunnels is a critical step in the catalytic cycle of these enzymes. Therefore, tunnel modification impacts the catalytic properties of enzymes [
36]. It has been suggested that Lys371, Ser433, and Lys555 in
H. pylori PBP1A, can form hydrogen bond interactions, with the putative catalytic Ser368 [
24]. Our study has identified the common presence of Lys371 and Ser 433 amongst the binding site and tunnel-1 residues, and Gly367, Lys371, and Thr558 in hydrogen bond interaction with Ser368. Thr556 is another binding site residue, introduced as an important residue, in or adjacent to the penicillin-binding motifs [
24]. Val469, one of the tunnel-1 amino acid residues, is also identified as one of the key residues in amoxicillin resistance, that is located in a loop enclosing the PBP1A binding site [
24].
Then, to confirm our results, we evaluated mutations in the binding site and tunnel-1 residues, in our clinical
H. pylori strains isolated under gastroscopy, which underwent AMX susceptibility testing. In addition, we performed a literature survey on the subject (Table
2). The our experimental data on our very limited number of resistant strains, identified Ser414Arg, Val469Met, and Thr556Ser substitutions (belonging to tunnel-1 and the binding site residues), in 2 of the 4 AMX-resistant and none of the 10 randomly sequenced sensitive strains. Accordingly, amino acid substitutions of binding site residues, including Ala369Thr (3 out of 4) [
28] and Thr541Ile (1 out of 3) [
18], Asn560Thr (1 out of 4) [
23], and Thr556Ser (7 out of 9) [
16,
18,
23,
29] have been previously reported in AMX-resistant and none of the susceptible
H. pylori strains (Table
2). In our study, a binding site (Thr556Ser) mutation was only seen in 1 of the 4 resistant and none of the sequenced susceptible strains. In agreement with our findings, experimental induction of Thr556Ser mutation decreased the AMX susceptibility of the affected
H. pylori strain, from 0.5 to 2 (mg/L) [
16]. Similarly, the structural data on pneumococcal PBPs reveals that mutations surrounding the binding site impact the protein's total charge and polar character, leading to the encapsulation of the binding cleft [
37]. A molecular dynamics simulation study of
Streptococcus pneumoniae PBP1A showed that the key regions of the binding pocket in mutant strains were more flexible, allowing for the detachment of a third-generation β-lactam (cefotaxime) [
38].
Table 2
Reported mutations in the PBP1A binding site and tunnel-1 residues of AMX-resistant and susceptible strains
Ala369Thr | ✓ | ✓ | 3/4R–0/12S | |
Thr541Ilu | ✓ | – | 1/3R–0/9S | |
Asn560Thr | ✓ | ✓ | 1/4R–0/5S | |
Thr556Ser | ✓ | – | 8/12R–0/19S | This study |
Phe366Leu | – | ✓ | 7/7R | |
Ser414Arg | ✓ | ✓ | 31/104R–1/106S | This study |
Val469Met | – | ✓ | 2/5R–0/11S | This study |
Based on the crystal structure of
S. pneumoniae PBP1A, mutations in the hotspot of the catalytic (binding) site entrance, could considerably change the tunnel entry characteristics by modifying surface polarity, which may, in turn, modify the drug accessibility of the mutated PBP1A binding site [
25]. Accordingly, conformational mutations in tunnel-1 residues are expected to play a role in creating resistance, as they affect the drug’s access to the enzyme's active site. In our study, tunnel-1 (Ser414Arg, Val469Met) mutations were only seen in 2 of the 4 resistant and none of the 10 susceptible strains. In agreement with our findings, mutations in the tunnel-1 residues are also previously reported in AMX-resistant
H. pylori strains (Table
2). These residues, in addition to Ala369Thr and Asn560Thr (stated above), include Phe366Leu (7 out of 7 resistant strains) [
15], Ser414Arg (31 out of 104 resistant and only 1 out of 133 sensitive strains) [
15,
18,
22,
28,
39], and Val469Met (2 out of 5 resistant and none of the 11 sensitive strains) [
24]. The Ser414Arg mutation is the most frequently reported mutation in AMX-resistant
H. pylori strains. Its determining role in AMX resistance is evidenced by increased MIC of the parent strain from 0.125 mg/L to 0.5–1 mg/L, in the experimentally mutated strain [
15]. In agreement with previously published studies [
28,
40], Ser414 is among the six critical sites (Ser414, Thr438, Phe473, Ser543, Thr556, and Asn562) for AMX binding to PBP1A. Three of these substitutions are previously reported in multiple clinical
H. pylori strains (Table
2); Ser414Arg in tunnel-1, Thr556Ser in the binding site, and Asn562Tyr [
24]. Taken together, these our findings on our limited number of clinical strains and those of others (Table
2), support the critical essence of the binding site and tunnel-1 residues, in potentially causing AMX resistance.
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