The potential peptides against angiotensin-I converting enzyme through a virtual tripeptide-constructing library

A novel heat-stable angiotensin-converting enzyme zinc-binding motif inhibitory peptide identified from corn silk

ETHNOPHARMACOLOGICAL RELEVANCE

Hypertension is the most common and chronic severe health problem globally. Corn silk (CS), the silky fibers of corn (Zea mays L.), has a long history of traditional usage as a remedy for edema and hypertension.

AIM OF THE STUDY

The aim of the study was to explore the underlying mechanism by which CS exerts its anti-hypertensive effects and investigate the presence of bioactive molecules in CS aqueous extract.

MATERIALS AND METHODS

We analyzed the effects of boiling water extract of CS on angiotensin-converting enzyme (ACE) activities, the critical enzyme involved in the regulation of blood pressure. ACE inhibitory peptides from CS extract were identified using proteomics and bioinformatics tools. The binding interfaces between these peptides and ACE were defined by hydrogen-deuterium exchange mass spectrometry (HDX-MS). Subsequently, the anti-hypertensive effects of peptides were further investigated in spontaneously hypertensive rats (SHR).

RESULTS

Our data showed that CS extract exhibited dose-dependent inhibition of ACE activity. Liquid chromatography-tandem mass spectrometry identified a heat-stable peptide bank with 1313 distinct peptide fragments within the CS boiling water extract. Among these, CS-1 (LVPGWTKPICIGR) was selected through PeptideRanker and BIOPEP-UWM analyses. In vitro ACE inhibitory assays confirmed that CS-1 exhibited dose-dependent ACE inhibition, with IC50 values of 10.32 ± 0.41 μmol/L (using HHL as the substrate) and 13.74 ± 1.87 μmol/L (using ZFHL as the substrate). Oral administration of CS-1 led to a significant dose-dependent reduction in blood pressure, with the maximal decrease (42.33 ± 13.08 mmHg) occurring 0.5 h after ingestion. HDX-MS analysis revealed that CS-1 interacted with the zinc-binding motif of ACE, and hydrogen bond interactions were predicted between CS-1 and specific residues, including His361 in the N-domain, as well as His382, Gly386, and His387 in the C-domain of ACE. These findings suggested that the interaction of CS-1 with the residues in the zinc-binding motif of ACE led to ACE activity inhibition and a subsequent decrease in blood pressure in rats.

CONCLUSIONS

A novel heat-stable ACE inhibitory peptide, which interacted with the zinc-binding motif of ACE and reduced blood pressure in SHR, was identified in the CS extract. The presence of ACE inhibitory peptides in the CS extract supports its traditional use in ethnopharmacology for hypertension.

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).

Redocking the PDB

Molecular docking is a standard technique in structure-based drug design (SBDD). It aims to predict the 3D structure of a small molecule in the binding site of a receptor (often a protein). Despite being a common technique, it often necessitates multiple tools and involves manual steps. Here, we present the JAMDA preprocessing and docking workflow that is easy to use and allows fully automated docking. We evaluate the JAMDA docking workflow on binding sites extracted from the complete PDB and derive key factors determining JAMDA's docking performance. With that, we try to remove most of the bias due to manual intervention and provide a realistic estimate of the redocking performance of our JAMDA preprocessing and docking workflow for any PDB structure. On this large PDBScan22 data set, our JAMDA workflow finds a pose with an RMSD of at most 2 Å to the crystal ligand on the top rank for 30.1% of the structures. When applying objective structure quality filters to the PDBScan22 data set, the success rate increases to 61.8%. Given the prepared structures from the JAMDA preprocessing pipeline, both JAMDA and the widely used AutoDock Vina perform comparably on this filtered data set (the PDBScan22-HQ data set).

Angiotensin I-Converting Enzyme Inhibitory Activity of Two Peptides Derived from In Vitro Digestion Products of Pork Sausage with Partial Substitution of NaCl by KCl

This study aimed to identify angiotensin I-converting enzyme (ACE) from in vitro digestion products of pork sausage with partial substitution of NaCl by KCl (PSRK). Peptides from in vitro digestion products of PSRK were identified through liquid chromatography with tandem mass spectrometry analysis coupled with de novo sequencing. Subsequently, the ACE inhibitory peptides LIVGFPAYGH and IVGFPAYGH were screened based on PeptideRanker, in silico absorption, molecular docking, and the determination of ACE inhibitory activity. In addition, the ACE inhibitory peptides LIVGFPAYGH and IVGFPAYGH were mixed-type inhibitors; these peptides' ACE inhibitory activities were expressed as the 50% inhibitory concentration (IC₅₀) values in vitro, which were 196.16 and 150.88 μM, respectively. After 2 h of incubation, LIVGFPAYGH and IVGFPAYGH could be transported through Caco-2 cell monolayers with paracellular passive diffusion. Furthermore, LIVGFPAYGH and IVGFPAYGH significantly increased the levels of ACE2 and nitric oxide while decreasing the levels of ACE, angiotensin II, and endothelin-1 in Ang I-treated human umbilical vein endothelial cells, indicating the ACE inhibitory effect of LIVGFPAYGH and IVGFPAYGH. In summary, LIVGFPAYGH and IVGFPAYGH from PSRK can be used as functional foods with antihypertensive activity.

Dock-able linear and homodetic di, tri, tetra and pentapeptide library from canonical amino acids: SARS-CoV-2 Mpro as a case study

Peptide-based therapeutics are increasingly pushing to the forefront of biomedicine with their promise of high specificity and low toxicity. Although noncanonical residues can always be used, employing only the natural 20 residues restricts the chemical space to a finite dimension allowing for comprehensive in silico screening. Towards this goal, the dataset comprising all possible di-, tri-, and tetra-peptide combinations of the canonical residues has been previously reported. However, with increasing computational power, the comprehensive set of pentapeptides is now also feasible for screening as the comprehensive set of cyclic peptides comprising four or five residues. Here, we provide both the complete and prefiltered libraries of all di-, tri-, tetra-, and penta-peptide sequences from 20 canonical amino acids and their homodetic (N-to-C-terminal) cyclic homologues. The FASTA, simplified molecular-input line-entry system (SMILES), and structure-data file (SDF)-three dimension (3D) libraries can be readily used for screening against protein targets. We also provide a simple method and tool for conducting identity-based filtering. Access to this dataset will accelerate small peptide screening workflows and encourage their use in drug discovery campaigns. As a case study, the developed library was screened against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease to identify potential small peptide inhibitors.

Revealing the Sequence Characteristics and Molecular Mechanisms of ACE Inhibitory Peptides by Comprehensive Characterization of 160,000 Tetrapeptides

Chronic diseases, such as hypertension, cause great harm to human health. Conventional drugs have promising therapeutic effects, but also cause significant side effects. Food-sourced angiotensin-converting enzyme (ACE) inhibitory peptides are an excellent therapeutic alternative to pharmaceuticals, as they have fewer side effects. However, there is no systematic and effective screening method for ACE inhibitory peptides, and the lack of understanding of the sequence characteristics and molecular mechanism of these inhibitory peptides poses a major obstacle to the development of ACE inhibitory peptides. Through systematically calculating the binding effects of 160,000 tetrapeptides with ACE by molecular docking, we found that peptides with Tyr, Phe, His, Arg, and especially Trp were the characteristic amino acids of ACE inhibitory peptides. The tetrapeptides of WWNW, WRQF, WFRV, YYWK, WWDW, and WWTY rank in the top 10 peptides exhibiting significantly high ACE inhibiting behaviors, with IC₅₀ values between 19.98 ± 8.19 μM and 36.76 ± 1.32 μM. Salt bridges, π-π stacking, π-cations, and hydrogen bonds contributed to the high binding characteristics of the inhibitors and ACE. Introducing eight Trp into rabbit skeletal muscle protein (no Trp in wide sequence) endowed the protein with a more than 90% ACE inhibition rate, further suggesting that meat with a high content of Trp could have potential utility in hypertension regulation. This study provides a clear direction for the development and screening of ACE inhibitory peptides.

On-Farm and Processing Factors Affecting Rabbit Carcass and Meat Quality Attributes

Rabbit meat has high nutritional and dietetic characteristics, but its consumption rate is comparatively lower than other meat types. The nutritional profile of rabbit meat, by comparison with beef, pork, and poultry, is attributed to relatively higher proportions of n-3 fatty acids and low amounts of intramuscular fat, cholesterol, and sodium, indicating its consumption may provide health benefits to consumers. But, the quality attributes of rabbit meat can be originated from different factors such as genetics, environment, diet, rearing system, pre-, peri-, and post-slaughter conditions, and others. Different rabbit breeds and the anatomical location of muscles may also affect the nutritional profile and physicochemical properties of rabbit meat. However, adequate information about the effect of those two factors on rabbit meat is limited. Therefore, cumulative information on nutritional composition and carcass and meat quality attributes of rabbit meat in terms of different breeds and muscle types and associated factors is more important for the production and processing of rabbits. Moreover, some studies reported that rabbit meat proteins exhibited angiotensin-converting enzyme inhibitory characteristics and antioxidant properties. The aim of this review is to elucidate the determinants of rabbit meat quality of different breeds and its influencing factors. In addition, the proven biological activities of rabbit meat are introduced to ensure consumer satisfaction.

A novel strategy for screening angiotensin-converting enzyme inhibitors from natural products based on enzyme-immobilized ligand fishing combined with active-site blocking and directional enrichment

Some natural products are important sources of treatments for hypertension based on their potential inhibitory effects on angiotensin-converting enzyme (ACE); however, it is difficult to identify natural ACE inhibitors (ACEIs) due to the complex secondary metabolite environment of natural products. Enzyme immobilization is an important method for screening active constituents in natural products, but this method can sometimes return false-positive and false-negative results. To improve the accuracy and reliability of ligand-fishing methods, we established a novel strategy based on enzyme-immobilized ligand fishing combined with active-site blocking and directional enrichment technologies. We first synthesized ACE-immobilized mesoporous magnetic beads and then verified the screened compounds by molecular docking and in vitro activity detection. We then used active-site blocking to exclude non-specific binding constituents and applied directional enrichment to enrich the low-content constituents for ligand fishing. The screening identified six potential ACEIs from Scutellariae Radix and eight potential ACEIs from Lonicerae japonicae flos, and their inhibitory activity was confirmed by molecular docking simulations and in vitro activity detection. This process screened six additional compounds and excluded two false-positive results as compared with results exclusively using enzyme immobilization. This strategy provides a feasible method for screening active compounds in natural products.

A novel angiotensin-converting enzyme inhibitory peptide from rabbit meat protein hydrolysate: identification, molecular mechanism, and antihypertensive effect in vivo

Bioactive peptides exhibiting angiotensin-converting enzyme (ACE) inhibitory effects and extracted from natural foods have potential as healthy and safe therapeutics for high blood pressure. The aim of this study was to isolate and purify ACE inhibitory peptides from rabbit meat protein hydrolysate, to explore the underlying mechanisms by molecular docking, and to evaluate the antihypertensive effects in vivo. A novel ACE inhibitory tetrapeptide Trp-Gly-Ala-Pro (WGAP) was identified and purified from a bromelain hydrolysate. WGAP acted against ACE in a non-competitive manner with an IC₅₀ of 140.70 ± 4.51 μM. It was resistant to enzymatic degradation by pepsin and trypsin in vitro. Molecular docking analysis indicated that WGAP formed stable hydrogen bonds with ACE residues His353, Ala354 and ALA356. In vivo, 100 mg kg^-1 WGAP significantly reduced systolic and diastolic blood pressure in hypertensive rats by up to 42.66 ± 2.87 and 28.56 ± 2.71 mmHg, respectively, 4 h after oral administration. ACE inhibitory peptides derived from rabbit meat have potential antihypertensive effects and provide a new route for the exploration of novel hypertension inhibitors and the utilization of rabbit meat.

Screening and mechanisms of novel angiotensin-I-converting enzyme inhibitory peptides from rabbit meat proteins: A combined in silico and in vitro study

Bioactive peptides derived from food proteins have various physiological roles and have attracted increasing attention in recent years. In this study, two novel ACE inhibitory peptides (EACF and CDF), screened from rabbit meat proteins using in silico methods, exhibited strong inhibitory effects in vitro. EACF and CDF were competitive and non-competitive inhibitors with half-maximal inhibitory concentrations of 41.06 ± 0.82 µM and 192.17 ± 2.46 µM, respectively. Molecular docking experiments revealed that EACF established eight H-bond interactions in the S1 and S2 pockets, and a metal-acceptor interaction with Zn 701. CDF shared four H-bond interactions in the S1 pocket of ACE. The results suggested that rabbit meat proteins could be a suitable material for the preparation of ACE inhibitory peptides, and that virtual screening is an effective, accurate and promising method for the discovery of novel active peptides.

Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation

Food-derived angiotensin I-converting enzyme (ACE) inhibitory peptides represent a potential source of new antihypertensive. However, their characteristics and binding mechanisms were not well understood. In this study, novel energy calculation and experimentation were combined to elucidate the characteristics and mechanisms of ACE inhibitory tripeptides. ACE inhibitory activity of all 8,000 tripeptides was investigated by in silico experiments. IC50 values of the five top-rated tripeptides ranged from 5.86 to 21.84 μM. Five hundred top-ranked tripeptides were chosen for detailed structure-activity analysis, and a significant preference for aromatic amino acids at both C- and N-terminus was found. By binding free energy analysis of nine representative tripeptides via MM/GBSA, electrostatic energy was found to be the leading energy that contributed to the binding of ACE with its high affinity tripeptides. Besides, S355, V380, and V518, three residues positioned around the classical binding pockets of ACE, also played a key role in ACE's binding. Therefore, for tripeptides, their binding pockets in ACE were redefined. In conclusion, the characteristics of ACE inhibitory peptides were more deeply illustrated by the thorough analysis of all tripeptides. The energy analysis allows a better understanding of the binding mechanisms of ACE inhibitory peptides, which could be used to redesign the ACE inhibitors for stronger inhibitory activity.

Targeting Tumors Using Peptides

To penetrate solid tumors, low molecular weight (Mw < 10 KDa) compounds have an edge over antibodies: their higher penetration because of their small size. Because of the dense stroma and high interstitial fluid pressure of solid tumors, the penetration of higher Mw compounds is unfavored and being small thus becomes an advantage. This review covers a wide range of peptidic ligands—linear, cyclic, macrocyclic and cyclotidic peptides—to target tumors: We describe the main tools to identify peptides experimentally, such as phage display, and the possible chemical modifications to enhance the properties of the identified peptides. We also review in silico identification of peptides and the most salient non-peptidic ligands in clinical stages. We later focus the attention on the current validated ligands available to target different tumor compartments: blood vessels, extracelullar matrix, and tumor associated macrophages. The clinical advances and failures of these ligands and their therapeutic conjugates will be discussed. We aim to present the reader with the state-of-the-art in targeting tumors, by using low Mw molecules, and the tools to identify new ligands.

Improving Health-Promoting Effects of Food-Derived Bioactive Peptides through Rational Design and Oral Delivery Strategies

Over the last few decades, scientific interest in food-derived bioactive peptides has grown as an alternative to pharmacological treatments in the control of lifestyle-associated diseases, which represent a serious health problem worldwide. Interest has been directed towards the control of hypertension, the management of type 2 diabetes and oxidative stress. Many food-derived antihypertensive peptides act primarily by inhibiting angiotensin I-converting enzyme (ACE), and to a lesser extent, renin enzyme activities. Antidiabetic peptides mainly inhibit dipeptidyl peptidase-IV (DPP-IV) activity, whereas antioxidant peptides act through inactivation of reactive oxygen species, free radicals scavenging, chelation of pro-oxidative transition metals and promoting the activities of intracellular antioxidant enzymes. However, food-derived bioactive peptides have intrinsic weaknesses, including poor chemical and physical stability and a short circulating plasma half-life that must be addressed for their application as nutraceuticals or in functional foods. This review summarizes the application of common pharmaceutical approaches such as rational design and oral delivery strategies to improve the health-promoting effects of food-derived bioactive peptides. We review the structural requirements of antihypertensive, antidiabetic and antioxidant peptides established by integrated computational methods and provide relevant examples of effective oral delivery systems to enhance solubility, stability and permeability of bioactive peptides.

FeptideDB: A web application for new bioactive peptides from food protein

BACKGROUND

Bioactive peptides derived from food are important sources for alternative medicine and possess therapeutic activity. Several biochemical methods have been achieved to isolate bioactive peptides from food, which are tedious and time consuming. In silico methods are an alternative process to reduce cost and time with respect to bioactive peptide production. In this paper, FeptideDB was used to collect bioactive peptide (BP) data from both published research articles and available bioactive peptide databases. FeptideDB was developed to assist in forecasting bioactive peptides from food by combining peptide cleavage tools and database matching. Furthermore, this application was able to predict the potential of cleaved peptides from 'enzyme digestion module' to identify new ACE (angiotensin converting enzyme) inhibitors using an automatic molecular docking approach.

RESULTS

The FeptideDB web application contains tools for generating all possible peptides cleaved from input protein by various available enzymes. This database was also used for analysis and visualization to assist in bioactive peptide discovery. One module of FeptideDB has the ability to create 3-dimensional peptide structures to further predict inhibitors for the target protein, ACE (angiotensin converting enzyme).

CONCLUSIONS

FeptideDB is freely available to researchers who are interested in exploring bioactive peptides. The FeptideDB interface is easy to use, allowing users to rapidly retrieve data based on desired search criteria. FeptideDB is freely available at http://www4g.biotec.or.th/FeptideDB/. Ultimately, FeptideDB is a computational aid for assessing peptide bioactivities.

Preparation and Identification of Novel Antihypertensive Peptides from the In Vitro Gastrointestinal Digestion of Marine Cobia Skin Hydrolysates

This research focuses on cobia skin hydrolysates and their antihypertensive effects via the inhibitory activities of angiotensin I-converting enzyme (ACE). Marine fish Cobia (Rachycentron canadum) skin was hydrolysed for 5 h using Protamex and Protease N to obtain the cobia skin protein hydrolysates PX-5 and PN-5, respectively. The soluble protein and peptide contents of the PX-5 were 612 and 270 mg/g, respectively, and for the PN-5, 531 and 400 mg/g, respectively. The IC₅₀ of PX-5 and PN-5 on ACE was 0.221 and 0.291 mg/mL, respectively. Increasing the IC₅₀ from 0.221 to 0.044 mg/mL by simulated gastrointestinal digestion (PX-5G) reduced the ACE-inhibitory capacity of PX-5. Using gel filtration chromatography, the PX-5G was fractioned into eight fractions. The molecular weight of the fifth fraction from PX-5G was between 630 and 450 Da, and the highest inhibitory efficiency ratio on ACE was 1552.4%/mg/mL. We identified four peptide sequences: Trp-Ala-Ala, Ala-Trp-Trp, Ile-Trp-Trp, and Trp-Leu, with IC₅₀ values for ACE of 118.50, 9.40, 0.51, and 26.80 μM, respectively. At a dose of 600 mg PX-5 powder/kg body weight, in spontaneously hypertensive rats PX-5's antihypertensive effect significantly reduced systolic and diastolic blood pressure by 21.9 and 15.5 mm Hg, respectively, after 4 h of oral gavage.