Molecular mechanism of the interactions between inhibitory tripeptides and angiotensin-converting enzyme

Angiotensin converting enzyme inhibitors from medicinal plants: a molecular docking and dynamic simulation approach

Angiotensin converting enzyme (ACE) is a key enzyme and mediator in the aetiology of high blood pressure (HBP) and hypertension. As one of the leading cause of untimely death worldwide, there is a lot of research and studies on the management and treatment of hypertension. The usage of medicinal plants in the management of hypertension as alternative to synthetic allopathic drugs is a common practice in folkloric and traditional medicine. Therefore, this study was aimed to investigate the ACE inhibitory activity of some medicinal plants which are commonly used in the treatment of HBP in southwestern part of Nigeria using extensive in-silico approach. Compounds identified in the plants through GC-MS technique, together with Lisinopril were docked against ACE protein. It was observed that only 40 of the compounds had binding affinity ≥ - 6.8 kcal/mol which was demonstrated by the standard drug (lisinopril). Interaction between the compounds and ACE was via conventional hydrogen, carbon hydrogen, alkyl, pi-alkyl, pi-carbon, and Van Der Wall bonds among others. Most of these compounds exhibited drug like properties, without violating majority of the physicochemical descriptors and Lipinski rule of 5. The ADMET evaluation revealed that only 2 compounds (cyclopentadecanone and oxacycloheptadecan-2-one) which were identified in Bacopa florinbunda plant were predicted non-toxic and thus were subjected to molecular dynamics and simulation with ACE. From the molecular dynamics and mechanics analysis, both cyclopentadecanone and oxacycloheptadecan-2-one showed high stability and inhibitory potentials when bound to ACE. Oxacycloheptadecan-2-one was more stable than lisinopril and cyclopentadecanone in the ligand-ACE complex; we therefore suggested its experimental and clinical validation as drug candidates for the treatment of hypertension.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-022-00135-z.

Identification of a novel hypotensive peptide from porcine plasma hydrolysate by in vitro digestion and rat model

•

Porcine plasma was enzymatically hydrolyzed with different times.

•

The hydrolysate with high hydrolysis degree was isolated and purified by G-15 gel chromatography and HPLC.

•

The ace inhibition rates of different purified compounds were determined.

•

The sequence of the polypeptide with best ace inhibition (IFPPKPKDTL) was determined by Q exactive LC-MS / MS.

•

The hypotensive function of synthetic peptide IFPPKPKDTL was also determined in spontaneously hypertensive rat.

We separated a novel functional peptide IFPPKPKDTL from porcine plasma hydrolysate by chromatography, HPLC, and identified by Q Exactive LC-MS/MS. Results showed that IFPPKPKDTL had a significant ability of ACE inhibition (76.6%) likely due to the presence of hydrophobic, aromatic, and acidic amino acids that can inactivate ACE by binding Zn²⁺, providing a hydrogen atom to maintain the link between ACE and the peptide. Furthermore, the ACE inhibition of synthetic IFPPKPKDTL was improved by 15.6% after in vitro digestion. Additionally, the systolic blood pressure and diastolic blood pressure of spontaneously hypertensive rats gavaged by the peptide (30 mg/kg). Thereby, ACE inhibitory peptide IFPPKPKDTL from porcine plasma was stable and has potential functional value.

Exploration of interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide from Wakame (Undaria pinnatifida)

The interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide KNFL from Wakame was explored using isothermal titration calorimetry, multiple spectroscopic techniques and molecular dynamics simulations, and an inhibition model was established based on free energy binding theory. The experiments revealed that the binding of KNFL to ACE was a spontaneous exothermic process driven by enthalpy and entropy and occurred via multiple binding sites to form stable complexes. The complexes may be formed through multiple steps of inducing fit and conformational selection. The peptide KNFL had a fluorescence quenching effect on ACE and its addition not only affected the microenvironment around the ACE Trp and Tyr residues, but also increased the diameter and altered the conformation of ACE. This study should prove useful for improving our understanding of the mechanism of ACE inhibitory peptides.

Novel ACE Inhibitory Peptides Derived from Yeast Hydrolysates: Screening, Inhibition Mechanisms and Effects on HUVECs

The antihypertensive activity of yeast hydrolysate (YH) was confirmed in our previous study. However, the critical peptides in YH and the underlying mechanisms have not been fully elucidated. This study aimed to explore the angiotensin-converting enzyme (ACE) inhibitory peptides in YH and illustrate their molecular and cellular mechanisms. The potential of YH-derived peptides was evaluated by in silico methods, followed by in vitro verification. A new competitive ACE inhibitory peptide, VIPVPFF (V7), with an IC₅₀ value of 10.27 μM, was screened. YH and V7 increased the nitric oxide (NO) levels, upregulated GUCY1A1 gene expression (approximately 15-fold), and functioned in several hypertension-related pathways in human umbilical vein endothelial cells (HUVECs). This study revealed the antihypertensive mechanisms of YH and V7, laying down a theoretical basis for their application.

Correction of diffusion calculations when using two types of non-rectangular simulation boxes in molecular simulations

Although simulation boxes used in molecular dynamics are normally chosen to be cubic or rectangular, two other cell shapes that are very familiar to crystallographers-the truncated octahedron and the rhombic dodecahedron-could also be used because they are also space-filling cells. Due to their spherical nature, these boxes have been intentionally applied in simulations of biomolecular solutions and liquid structures. Indeed, due to the advantages of running many molecular dynamic codes in parallel, simulations based on these non-rectangular boxes have been growing in popularity in recent years. In this work, the effects of using these two types of boxes on diffusion are explored for the first time, and an appropriate correction formula is derived theoretically within the framework of hydrodynamics. In addition, the range of validity for the correction formula is evaluated by performing molecular dynamic simulations on argon at three different densities.

Molecular interactions, bioavailability, and cellular mechanisms of angiotensin-converting enzyme inhibitory peptides

Food-derived angiotensin-converting enzyme inhibitory (ACEi) peptides have gained substantial interest as potential alternatives to synthetic drugs in the management of hypertension. Peptide size and sequence are two critical factors that determine their potency, bioavailability, and cellular mechanisms. Molecular interaction studies between ACE and ACEi peptides support that potent ACEi peptides are generally composed of hydrophobic, positively charged, and aromatic or cyclic amino acid residues at the third, second, and first position from the C-terminus, respectively. Small peptides containing N-terminal Tyr and/or C-terminal Pro could improve their stability against enterocyte peptidases, thus their bioavailability. Different ACEi peptides can reduce aberrant cellular proliferation, excessive inflammation, and oxidative stress but through different mechanisms. Further understanding the structure-activity-bioavailability relationships will help design novel potent ACEi peptides with improved bioavailability and in vivo efficacy. PRACTICAL APPLICATIONS: ACEi peptides have the potential for uses as functional food ingredients against hypertension.

Novel Natural Angiotensin Converting Enzyme (ACE)-Inhibitory Peptides Derived from Sea Cucumber-Modified Hydrolysates by Adding Exogenous Proline and a Study of Their Structure⁻Activity Relationship

Natural angiotensin converting enzyme (ACE)-inhibitory peptides, which are derived from marine products, are useful as antihypertensive drugs. Nevertheless, the activities of these natural peptides are relatively low, which limits their applications. The aim of this study was to prepare efficient ACE-inhibitory peptides from sea cucumber-modified hydrolysates by adding exogenous proline according to a facile plastein reaction. When 40% proline (w/w, proline/free amino groups) was added, the modified hydrolysates exhibited higher ACE-inhibitory activity than the original hydrolysates. Among the modified hydrolysates, two novel efficient ACE-inhibitory peptides, which are namely PNVA and PNLG, were purified and identified by a sequential approach combining a sephadex G-15 gel column, reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS), before we conducted confirmatory studies with synthetic peptides. The ACE-inhibitory activity assay showed that PNVA and PNLG exhibited lower IC₅₀ values of 8.18 ± 0.24 and 13.16 ± 0.39 μM than their corresponding truncated analogs (NVA and NLG), respectively. Molecular docking showed that PNVA and PNLG formed a larger number of hydrogen bonds with ACE than NVA and NLG, while the proline at the N-terminal of peptides can affect the orientation of the binding site of ACE. The method developed in this study may potentially be applied to prepare efficient ACE-inhibitory peptides, which may play a key role in hypertension management.

Graphitized Porous Carbon for Rapid Screening of Angiotensin-Converting Enzyme Inhibitory Peptide GAMVVH from Silkworm Pupa Protein and Molecular Insight into Inhibition Mechanism

A novel hydrophobic hexapeptide with high angiotensin-converting enzyme (ACE) inhibitory activity was screened from silkworm pupa protein (SPP) hydrolysate via graphitized porous carbon and reverse-phase high-performance liquid chromatography methods. Graphitized porous carbon derived from dopamine, possessing high surface area and high graphitic carbon, was used to rapidly screen and enrich hydrophobic peptides from SPP hydrolysate. The ACE inhibition pattern and mechanism of the purified peptide were also systematically studied by the classic Lineweaver-Burk model and by molecular docking/dynamic simulation. The novel hydrophobic hexapeptide was identified as Gly-Ala-Met-Val-Val-His (GAMVVH, IC₅₀ = 19.39 ± 0.21 μM) with good thermal/antidigestive stabilities. Lineweaver-Burk plots revealed that GAMVVH behaved as a competitive ACE inhibitor. It formed hydrogen bonds with S1 and S2 pockets of ACE and established competitive coordination with Zn(II) of ACE. The synergy of hydrogen bonds with active pockets and Zn(II) coordination efficiently changed the three-dimensional structure of ACE and thus inhibited bioactivity of ACE.

Formulation, Characterization and Stability Assessment of a Food-Derived Tripeptide, Leucine-Lysine-Proline Loaded Chitosan Nanoparticles

The chicken- or fish-derived tripeptide, leucine-lysine-proline (LKP), inhibits the angiotensin converting enzyme and may be used as an alternative treatment for prehypertension. However, it has low permeation across the small intestine. The formulation of LKP into a nanoparticle (NP) has the potential to address this issue. LKP-loaded NPs were produced using an ionotropic gelation technique, using chitosan (CL113). Following optimization of unloaded NPs, a mixture amount design was constructed using variable concentration of CL113 and tripolyphosphate at a fixed LKP concentration. Resultant particle sizes ranged from 120 to 271 nm, zeta potential values from 29 to 37 mV, and polydispersity values from 0.3 to 0.6. A ratio of 6:1 (CL113:TPP) produced the best encapsulation of approximately 65%. Accelerated studies of the loaded NPs indicated stability under normal storage conditions (room temperature). Cytotoxicity assessment showed no significant loss of cell viability and in vitro release studies indicated an initial burst followed by a slower and sustained release.

Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair

Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn(2+)-chelated Zn-finger domain of XPA center core portion (i.e., XPA98-210) is the foundation of its biological functionality, while the displacement of the Zn(2+) by toxic metal ions (such as Ni(2+), a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98-210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98-210 Zn-finger after the substitution of Zn(2+) by Ni(2+). The results showed that Ni(2+) dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98-210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98-210's Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni(2+) disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni(2+) binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.