4. Molecular Docking
In this study, molecular docking was conducted to elicit the potential molecular interactions between the specific amino acids at the binding site of human ACE2 and our previously identified whey protein-derived peptide sequences with high ACE inhibitory activities.
The peptide sequences were docked into the binding site of human ACE2 using the X-ray crystallographic structure of the human ACE2 receptor (PDB code 6M0J). As 6M0J does not contain a co-crystallized ligand, to validate our docking approach, we used the co-crystallized MLN-4760 ACE2 receptor complex (PDB code 1R4L), whereby we extracted the co-crystallized ligand MLN-4760 and re-docked it into the prepared protein 1R4L. The root-mean square deviation (RMSD) between the docked conformation (as generated by superimposition in the program PyMol) and the native co-crystallized ligand conformation was 0.3 Å, which is well within the 2 Å grid spacing used in the docking procedure, demonstrating that the docking method used was valid and reliable. Furthermore, the interactions between the docked ligand and the prepared target receptor mimicked those observed in the crystal structure of the same protein (PDB code 1R4L)
[54].
To further validate our method, the ligand Carnosine was docked into the prepared X-ray crystal structure of the human ACE2 receptor (PDB code 6M0J) to be used for subsequent docking runs. As Q9BYF1 is the UniPROT code for both 6M0J and 2AJF structures and given that these are 100% identical ACE2 sequences in both X-ray crystal structures (
Figures S1–S3), according to the EMBOSS needle results (
Figure S4), the interactions between the docked ligand Carnosine and those observed in the crystal structure (PDB code 2AJF) were compared (
Figure 2a and
Figure S5)
[24]. In our docking study, Carnosine interacted with key amino acid residues, namely Glu 375, His 378, Glu 402, and Tyr 515 in the active site of ACE2, in accordance with observations reported in the literature
[24][54][55][56]. In a study providing structural insights for the differences in the inhibition pattern and substrate specificity for ACE and ACE2, amino acid residues His 374, His 378, Glu 375, Tyr 515, Glu 402, and Glu 406 were characterized in the active site of ACE2
[55]. These observations were corroborated in the first reported crystal structure of ACE2 in its native and inhibitor-bound states, where key binding residues His 374, His 378, and Glu 402 were identified
[54]. According to Saadah et al.
[24], Carnosine interacted with amino acid residues His 378, Glu 402, and Tyr 515 at the active site of ACE2, which was also confirmed in our docking approach.
Figure 2. (a) Docking results of the peptide Carnosine in the human angiotensin-converting enzyme 2 (ACE2) active site. The interactions of human ACE2 residues with Carnosine (represented in black) are indicated by arrows of different colors, with purple representing hydrogen bond interactions and blue arrows representing salt bridge interactions. (b) Docking results of the synthetic drug Captopril in the human angiotensin-converting enzyme 2 (ACE2) active site. The interaction of human ACE2 residues with Captopril (represented in black) is indicated by a purple arrow representing hydrogen bond interactions.
The synthetic ACE inhibitory drug Captopril was also docked into 6M0J. According to the docking results, Captopril did not interact with any key binding residues in the active site of ACE2 and formed only one potential hydrogen bond with the backbone of the amino acid residue Ala 348 (
Figure 2b and
Figure S6). These observations are in line with those reported in other studies, wherein ACE inhibitors such as Captopril could not inhibit ACE2
[55][57].
Following validation, the human ACE2 receptor (PDB code 6M0J) was then used as the target molecule for docking the peptide sequences of interest into its active site.
Hydrogen bond interactions play a crucial role in the specificity and stability of protein–ligand interactions. The results of ligand-driven docking into the binding site of ACE2 are summarized in
Figure 3,
Figure 4,
Figure 5 and
Figure 6, and
Figures S7–S10, and
Table 1 and
Table S1. It is known that His 374, His 378, and Glu 402 are important ligand-binding residues in the zinc-binding site of ACE2
[54][55][56][57]. In the current study, IPP showed potential interactions with the key residues His 378 and Glu 402 through hydrogen bond interactions at distances of 2.4 Å and 2.9 Å, respectively. Interestingly, IPP also interacted with these two amino acid residues, namely His 378 and Glu 402, similarly to Carnosine, the best-known drug candidate to match an ACE2 inhibitor structure
[24]. Additionally, IPP formed a salt bridge and a hydrogen bond with amino acid residue Glu 375, another key active amino acid residue in ACE2 (
Table 1,
Figure 3)
[55][56]. IIAE, LIVTQ, and LVYPFP also interacted with residue Glu 402 in common with the potent ACE2 inhibitor Carnosine. This was done via hydrogen bonding and salt bridge interaction at distances of 2.9 Å and 4.3 Å, respectively, for IIAE (
Table 1,
Figure 4); through two hydrogen bonds at distances of 2 Å and 2.6 Å, and through one salt bridge interaction at a distance of 4.3 Å for LIVTQ (
Table 1,
Figure 5); and through hydrogen bonding and salt bridge interactions at distances of 2.9 and 3.8 Å, respectively, for LVYPFP (
Table 1,
Figure 6). Additionally, IIAE formed two hydrogen bonds and one salt bridge interaction with key binding amino acid residue Glu 375 (
Table 1,
Figure 4)
[55][56].
Figure 3. Docking results of the peptide IPP in the active site of the human angiotensin 2-converting enzyme (ACE2). Interactions of human ACE2 residues with the peptide IPP (represented in black) are indicated by arrows of different colors, with purple arrows representing hydrogen bond interactions and blue arrows representing salt bridge interactions.
Figure 4. Docking results of the peptide IIAE in the active site of human ACE2. The interactions of human ACE2 residues with the peptide IIAE (represented in black) are indicated by arrows of different colors, with purple arrows representing hydrogen bond interactions and blue arrows representing salt bridge interactions.
Figure 5. Docking results of the peptide LIVTQ in the human ACE2 active site. The interactions of human ACE2 residues with the peptide LIVTQ (represented in black) are indicated by arrows of different colors, with purple arrows representing hydrogen bond interactions and blue arrows representing salt bridge interactions.
Figure 6. Docking results of the peptide LVYPFP in the human ACE2 active site. The interactions of human ACE2 residues with the peptide (represented in black) are indicated by arrows of different colors, with purple arrows representing hydrogen bond interactions and blue arrows representing salt bridge interactions.
Table 1. Docking results of IPP, IIAE, LIVTQ, and LVYPFP.
Protein 6MOJ |
|
Ligand IPP |
Residue |
Atom Name |
Interaction Type |
Distance (Å) |
NH1 Arg 273 |
O− (Pro2) |
Salt bridge |
3.0 |
OE1 Glu 375 |
NH3+ (Ile) |
Salt bridge |
4.1 |
OE2 Glu 375 |
NH3+ (Ile) |
Hydrogen bond |
2.0 |
NE2 His 378 |
NH3+ (Ile) |
Hydrogen bond |
2.4 |
OE1 Glu 402 |
NH3+ (Ile) |
Hydrogen bond |
2.9 |
OE2 Glu 402 |
NH3+ (Ile) |
Salt bridge |
3.1 |
|
|
Ligand IIAE |
NH2 Arg 273 |
O1 (Glu) |
Salt bridge |
3.0 |
NH2 Arg 273 |
OE1 (Glu) |
Hydrogen bond |
2.9 |
NH1 Arg 273 |
OE2 (Glu) |
Salt bridge |
3.0 |
OE1 Glu 375 |
NH3+ (Ile) |
Salt bridge |
3.0 |
OE2 Glu 375 |
NH3+ (Ile) |
Hydrogen bond |
2.6 |
OE2 Glu 375 |
NH (Ile) |
Hydrogen bond |
2.4 |
OE1 Glu 402 |
NH3+ (Ile) |
Hydrogen bond |
2.9 |
OE2 Glu 402 |
NH (Ala) |
Hydrogen bond |
2.9 |
CG Glu 402 |
NH3+ (Ile) |
Salt bridge |
4.3 |
|
|
Ligand LIVTQ |
ND1 His 374 |
O (Gln) |
Hydrogen bond |
2.8 |
OE1 Glu 375 |
NH3+ (Leu) |
Salt bridge |
3.5 |
OE2 Glu 375 |
NH3+ (Leu) |
Hydrogen bond |
2.9 |
OE2 Glu 375 |
NH (Ile) |
Hydrogen bond |
2.3 |
OE1 Glu 402 |
NH3+ (Leu) |
Hydrogen bond |
2.0 |
OE2 Glu 402 |
NH3+ (Leu) |
Salt bridge |
4.3 |
OE2 Glu 402 |
NH (Val) |
Hydrogen bond |
2.6 |
OE1 Glu 406 |
OH (Thr) |
Hydrogen bond |
2.9 |
OE1 Glu 406 |
NH2 (Gln) |
Hydrogen bond |
2.9 |
OE1 Glu 406 |
NH (Gln) |
Hydrogen bond |
2.9 |
OE2 Glu 406 |
NH (Thr) |
Hydrogen bond |
2.9 |
OE2 Glu 406 |
NH (Val) |
Hydrogen bond |
2.3 |
NE2 Gln 442 |
O (Gln) |
Hydrogen bond |
2.8 |
NH2 Arg 518 |
OH (Thr) |
Hydrogen bond |
2.1 |
|
|
Ligand LVYPFP |
CG2 Thr 276 |
O− (Pro) |
Hydrogen bond |
2.6 |
OE1 Glu 402 |
NH3+ (Leu) |
Salt bridge |
3.8 |
OE2 Glu 402 |
NH3+ (Leu) |
Hydrogen bond |
2.9 |
CO Glu 406 |
NH3+ (Leu) |
Salt bridge |
4.0 |
OE1 Glu 406 |
NH (Val) |
Hydrogen bond |
2.8 |
OE1 Glu 406 |
NH (Tyr) |
Hydrogen bond |
2.4 |
OE2 Glu 406 |
NH3+ (Leu) |
Hydrogen bond |
2.8 |
In another molecular docking study conducted by Upreti et al.
[58], chloroquine phosphate, a commercial ACE2 inhibitor, exhibited well-established hydrogen bonds with amino acid residues Glu 406, Asp 367, Asp 269, and Phe 274. Peptides LIVTQ and LVYPFP also interacted with the amino acid residue Glu 406 through hydrogen bonds and salt bridge interactions (
Table 1;
Figure 5 and
Figure 6). Peptide LIVTQ additionally interacted with key residues His 374 and Glu 375 at distances of 2.8 Å and 3.5 Å, respectively (
Table 1 and
Figure 5). Moreover, Arg 273 is a key amino acid residue for substrate-binding in ACE2 that was found to form a salt-bridge with the C-terminal of the potent and selective human ACE2 inhibitor MLN-4760
[54][56][57]. Both peptides IPP and IIAE formed salt bridge interactions and hydrogen bonds with amino acid residue Arg 273 (
Table 1;
Figure 3 and
Figure 4).
6. Potential Use of ACE Inhibitors in the Treatment of COVID-19
To date, there is no effective drug available to treat COVID-19 patients
[60]. Although COVID-19 vaccines were shown to be closely associated with a significant reduction in symptomatic infections
[61], vaccine hesitancy is widespread worldwide, which could hinder populations from achieving herd immunity
[62]. The rapid global emergence of novel SARS-CoV-2 variants, the unequal international distribution of COVID-19 vaccines, and slow vaccine rollouts, especially in developed countries, could also be significant factors obstructing the achievement of herd immunity and the end of the pandemic. Although antimalarial drugs chloroquine and hydroxychloroquine, and some synthetic drugs such as remdesivir
[60] and ritonavir/lopinavir
[60][63] are currently used to treat COVID-19 patients, currently, there remains no effective and approved drug available against COVID-19
[64]. Various side effects associated with the aforementioned drugs were also observed among treated patients
[60][63], delaying widespread acceptance and administration.
Consequently, identifying safe and effective compounds that can restrain the entry of SARS-CoV-2 into host cells via ACE2 is a priority for the scientific community. In this respect, an active area of research is the impact of milk/whey-derived bioactive peptides and their potential health benefits as ingredients of health-promoting functional foods
[65]. Peptide sequences from whey proteins exhibit different bioactivities, including ACE inhibitory activity. In fact, milk is the main source of antihypertensive ACE-inhibitory peptides reported to date
[48][66].
In the scientific community, controversy has arisen regarding whether the use of ACE inhibitors would be harmful or beneficial in the context of the COVID-19 pandemic
[33][34][35][67][68][69]. Although increased COVID-19 disease severity seems to manifest in people with cardiovascular comorbidities
[21][70], it is suggested that this association could be related to advanced age and obesity
[70]. Moreover, there seems to be growing evidence that the use of ACE inhibitors does not worsen the prognosis of COVID-19
[71]. In fact, in a cohort study including 8.3 million people, ACE inhibitors were not found to be significantly associated with increased risks of COVID-19 disease, nor of requiring ICU care
[42]. In agreement, another meta-analysis study also reported that the use of ACE inhibitors was not associated with requiring intensive care, mechanical ventilation, progression to severe disease, and increased risk of death. However, some researchers have reported a 16% reduction in the risk of COVID-related mortality with the use of ACE inhibitors
[68].
Some studies suggest that ACE inhibitors could even play a protective role in hypertensive patients by averting organ injury
[72]. Indeed, in vivo models support the role of ACE inhibitors in blunting lung injury and exerting health benefits in both human and animal trials
[73][74][75][76]. Data from human studies also revealed that ACE inhibitors can reduce or prevent pneumonia
[77][78]; specifically, the (i) treatment of chronic obstructive pulmonary disease with ACE inhibitors was found to reduce disease complications and (ii) treatment with ACE inhibitors was shown to mitigate the effects of radiation pneumonitis
[79]. In short, there is consistent evidence indicating that ACE inhibitors seem to have beneficial effects in modulating lung damage, including in the context of pulmonary injury caused by viral infection. Due to insufficient evidence of the potentially harmful effects of ACE inhibitors and considering the overwhelming evidence supporting their benefits, multiple scientific societies rejected the recommendation to discontinue ACE inhibitors in the context of the COVID-19 pandemic
[80][81][82]. Interestingly, ACE inhibitors were reported to be associated with significant pulmonary inflammatory response reductions in patients admitted with viral pneumonia
[83] and attenuated inflammatory response in COVID-19-infected patients
[84][85]. This emerging evidence prompted many researchers to advocate for the use of RAS inhibitors in the therapeutic management of COVID-19 infection
[68].
Regarding the role of the RAS pathway in the pathophysiology of COVID-19 and SARS-CoV-2 infection, there are two primary theories. First, data from the literature have shown that Ang II-mediated inflammation is a main mediator of acute lung injury and fibrosis
[30][86][87]. Similar to SARS-CoV, loss of ACE2 activity and expression could lead to an increase in Ang II levels in the lungs and could consequently induce COVID-19 acute lung injury. One study reported significantly higher Ang II levels in COVID-19 patients that correlated with viral load and indicators of lung injury. However, this study had considerable methodological limits: only 12 patients took part in the clinical study and circulating levels of ACE and/or ACE2 were not determined
[1][38][88]. Furthermore, data from the original SARS-CoV epidemic indicated that infection with SARS-CoV-2 may lead to ACE-2 dependent myocardium infection, which results in decreased cardiac ACE2 expression, accelerating acute heart injury
[89]. However, it is important to note that there is no clinical data to confirm this.
Second, there is concern that ACE inhibitors may potentially increase the expression and levels of ACE2 in the lungs, which facilitates SARS-CoV-2 infection such that administering ACE inhibitors may increase the risk of severe and fatal disease
[37][90]. In select animal models, ACE inhibitors were able to increase heart and kidney ACE2 expression
[36][91]. However, there are no data proving that these compounds can increase lung ACE2 expression in both animal models and human trials. In a similar manner, there are no available data demonstrating that the increased expression of ACE2 would necessarily indicate an increased risk of disease severity or infection, or that the use of these agents is correlated with increased virulence or viral infectivity. In fact, there does not appear to be any consistent association between increased ACE2/Ang (1–7)/Mas pathway activity and expression, and the use of ACE inhibitors in the few clinical studies assessing the effect of ACE inhibitors on the ACE2/Ang (1–7) pathway
[92][93][94][95]. Although there is a lack of evidence to demonstrate the effect of ACE inhibitors on ACE2 expression and thus SARS-CoV-2 infectivity, the bulk of the experimental evidence indicates that ACE inhibitors may reduce the action of Ang II and consequently attenuate Ang II-driven acute lung injury
[38][39]. ACE inhibitors therefore offer promise as potential novel therapeutics to treat COVID-19 disease
[31].
Intriguingly, based solely on experimental studies in which RAS inhibitors were administered in vivo
[96][97][98][99][100], Zamai, 2020
[101] highlighted a reasonable hypothesis, in which he stated that using inhibitors which block both ACE2 and ACE pathways in COVID-19 patients could be very beneficial in the treatment of COVID-19. In short, observations from these studies indicate that hypoxia/hypercapnia, a condition that occurs in SARS patients, is highly likely to upregulate the activity of both arms of the RAS. A strong correlation was also observed between the gene expression of ACE2 and that of ACE
[102]. Another observation suggested the possibility of a positive feedback induced by SARS-CoV infection, leading to the surface expression of both ACE and ACE2
[103][104][105]. Altogether, these observations indicate that RAS-mediated positive feedback loops can be induced by SARS-CoV-2 at different organ levels. Consequently, in order to block these feedback loops, Zamai, 2020
[101] suggested that different compounds can be produced to inhibit RAS pathways and subsequently to prevent critical, advanced, and untreatable stages of the COVID-19 disease.
IPP, IIAE, LIVTQ, and LVYPFP, which are bioactive peptides derived from whey proteins, were initially characterized as ACE inhibitors through in vitro and in silico assays in our previous works
[52][53]. Findings from the current study demonstrate additional novel effects for these bioactive whey-derived peptides as potential ACE2 inhibitors. These results strongly support our hypothesis that these whey-derived peptides not only could exhibit ACE inhibitory activity but also could bind to ACE2 and, as such, could have a potential effect of intervening in the interaction between the ACE2 and SARS-CoV-2 S protein. Additionally, compared to synthetic ACE-inhibitory drugs, these peptides are from a natural source and do not exhibit toxic side effects, which might also help to reduce the risks associated with traditional drugs in the treatment of COVID-19 infection.