Influence of Secondary-Structure Folding on the Mutually Exclusive Folding Process of GL5/I27 Protein: Evidence from Molecular Dynamics Simulations

Screening and evaluation of novel DPP-IV inhibitory peptides in goat milk based on molecular docking and molecular dynamics simulation

Virtual screening techniques have gained much attention as a means of studying bioactive peptides. This study aimed to screen DPP-IV inhibitor peptides in goat milk after simulated digestion in vitro combined with molecular docking and dynamics simulations. By evaluating the docking energy and active sites, and by analyzing RMSD, RMSF, and Rg values, two novel peptides, GPFPLL and LPYPY, were successfully screened and identified. GPFPLL and LPYPY were found to exhibit high inhibitory activity against DPP-IV (IC50 of 130.68 ± 10.38 μM and 179.52 ± 18.89 μM, respectively). Both GPFPLL and LPYPY stably bound to S1 and S1' in DPP-IV, and both demonstrated competitive inhibition of DPP-IV. The inhibition of DPP-IV by GPFPLL and LPYPY after in vitro digestion reached 31.90 % ± 1.80 % and 39.37 % ± 0.90 %, respectively. In a Caco-2 cell experiment, GPFPLL and LPYPY exhibited significant inhibition of DPP-IV, reaching 46.53 % ± 3.48 % and 65.98 % ± 2.87 %, respectively, when the concentration of each peptide was 2 mg/mL. The results of this study suggest that using molecular docking and dynamics simulations to screen novel peptides is an effective approach, and the identified peptides GPFPLL and LPYPY show potential for diabetes management.

Preparation, identification, and inhibitory mechanism of dipeptidyl peptidase IV inhibitory peptides from goat milk whey protein

This study explores potential hypoglycemic mechanisms by preparing and identifying novel dipeptidyl peptidase IV (DPP-IV) inhibitory peptides from goat milk (GM) whey protein. Papain was used to hydrolyze the GM whey protein. After purification by ultrafiltration, the Sephadex column, and preparative RP-HPLC, the peptide inhibited DPP-IV, α-glucosidase, and α-amylase with IC50 of 0.34, 0.37, and 0.72 mg/mL, respectively. To further explore the inhibitory mechanism of peptides on DPP-IV, SPPEFLR, LDADGSY, YPVEPFT, and FNPTY were identified and synthesized for the first time, with IC50 values of 56.22, 52.16, 175.7, and 62.32 µM, respectively. Molecular docking and dynamics results show that SPPEFLR, LDADGSY, and FNPTY bind more tightly to the active pocket of DPP-IV, which was consistent with the in vitro activity. Furthermore, the first three N-terminals of SPPEFLR and FNPTY peptides exhibit proline characteristics and competitively inhibit DPP-IV. Notably, the first N-terminal leucine of LDADGSY may play a key role in inhibiting DPP-IV.

Alpha-cadinol as a potential ACE-inhibitory volatile compound identified from Phaseolus vulgaris L. through in vitro and in silico analysis

Hypertension is a major risk factor of cardiovascular diseases, which is mainly caused due to over activation of renin-angiotensin system. The angiotensin converting enzyme (ACE), which is involved in formation of angiotensin II from angiotensin I, causes the blood vessels to constrict, in turn leading to hypertension. The current study was initiated to understand the role of bioactive volatile compounds from Phaseolus vulgaris L. (common bean), in ACE enzyme inhibition. Beans aqueous extract (BAE) showed maximum ACE inhibition of 88.4 ± 0.8% in comparison to other commonly consumed vegetables like spinach and garlic. The head space gas chromatography-mass spectrometry analysis showed the presence of a number of terpenes and terpenoids, which were present prominently in BAE. In silico molecular docking studies indicated that among the other volatile compounds, alpha-cadinol (-7.27 kcal/mol) and ar-tumerone (-6.44 kcal/mol) have the maximum binding affinity with the active site of ACE, as compared to that of captopril (-6.41 kcal/mol). The molecular dynamic simulation in biological environment, showed that alpha-cadinol forms a stable complex with ACE, with average binding energy of -42 kJ/mol. The ACE:alpha-cadinol complex was found to be stable mainly due to the hydrophobic interactions of alpha-cadinol with active site residues (Tyr523 and Phe457) of ACE. The in silico drug-likeness analysis showed that alpha-cadinol is appropriate for human system with no predicted hepatotoxicity or mutagenicity (AMES toxicity).Communicated by Ramaswamy H. Sarma.

Novel angiotensin-converting enzyme (ACE) inhibitory mechanism of peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2)

This work aimed to identify novel angiotensin-converting-enzyme (ACE) inhibitory peptides from Macadamia integrifolia antimicrobial protein 2 (MiAMP2). The MiAMP2 protein was hydrolyzed through in silico digestion, and the generated peptides were screened for ACE inhibitory activity. The in silico enzyme digestion results revealed that 18 unreported peptides were obtained using AHTPDB and BIOPEP-UWM, and none were thought to be toxic based on absorption, distribution, metabolism, and excretion (ADMET) prediction. PGPR, RPLY, MNPQR, and AAPR were predicted to exhibit good biological activity. The molecular docking results revealed that the four peptides tightly bound to the active pocket of ACE via hydrogen bonds and hydrophobic interactions, among which RPLY and MNPQR bound to ACE more strongly. The in vitro assay results confirmed that RPLY and MNPQR peptides inhibited ACE via competitive manner. These results provide theoretical guidance for the development of novel foodborne antihypertensive peptides from Macadamia nut proteins. PRACTICAL APPLICATIONS: This study provides new insight on the inhibitory potential of Macadamia nut peptides against ACE, which may be further applied to the development of antihypertensive peptides in the medical industry.

Reorienting Mechanism of Harderoheme in Coproheme Decarboxylase-A Computational Study

Coproheme decarboxylase (ChdC) is an important enzyme in the coproporphyrin-dependent pathway (CPD) of Gram-positive bacteria that decarboxylates coproheme on two propionates at position 2 and position 4 sequentially to generate heme b by using H₂O₂ as an oxidant. This work focused on the ChdC from Geobacillus stearothermophilus (GsChdC) to elucidate the mechanism of its sequential two-step decarboxylation of coproheme. The models of GsChdC in a complex with substrate and reaction intermediate were built to investigate the reorienting mechanism of harderoheme. Targeted molecular dynamics simulations on these models validated that harderoheme is able to rotate in the active site of GsChdC with a 19.06-kcal·mol^-1 energy barrier after the first step of decarboxylation to bring the propionate at position 4 in proximity of Tyr145 to continue the second decarboxylation step. The harderoheme rotation mechanism is confirmed to be much easier than the release-rebinding mechanism. In the active site of GsChdC, Trp157 and Trp198 comprise a "gate" construction to regulate the clockwise rotation of the harderoheme. Lys149 plays a critical role in the rotation mechanism, which not only keeps the Trp157-Trp198 "gate" from being closed but also guides the propionate at position 4 through the gap between Trp157 and Trp198 through a salt bridge interaction.

Inhibitory mechanism of angiotensin-converting enzyme inhibitory peptides from black tea

The aim of this work is to discover the inhibitory mechanism of tea peptides and to analyse the affinities between the peptides and the angiotensin-converting enzyme (ACE) as well as the stability of the complexes using in vitro and in silico methods. Four peptide sequences identified from tea, namely peptides I, II, III, and IV, were used to examine ACE inhibition and kinetics. The half maximal inhibitory concentration (IC₅₀) values of the four peptides were (210.03±18.29), (178.91±5.18), (196.31±2.87), and (121.11±3.38) μmol/L, respectively. The results of Lineweaver-Burk plots showed that peptides I, II, and IV inhibited ACE activity in an uncompetitive manner, which requires the presence of substrate. Peptide III inhibited ACE in a non-competitive manner, for which the presence of substrate is not necessary. The docking simulations showed that the four peptides did not bind to the active sites of ACE, indicating that the four peptides are allosteric inhibitors. The binding free energies calculated from molecular dynamic (MD) simulation were -72.47, -42.20, -52.10, and -67.14 kcal/mol (1 kcal=4.186 kJ), respectively. The lower IC₅₀ value of peptide IV may be attributed to its stability when docking with ACE and changes in the flexibility and unfolding of ACE. These four bioactive peptides with ACE inhibitory ability can be incorporated into novel functional ingredients of black tea.

Discovery of Novel Angiotensin-Converting Enzyme Inhibitory Peptides from Todarodes pacificus and Their Inhibitory Mechanism: In Silico and In Vitro Studies

In order to rapidly and efficiently excavate antihypertensive ingredients in Todarodespacificus, its myosin heavy chain was hydrolyzed in silico and the angiotensin-converting enzyme (ACE) inhibitory peptides were predicted using integrated bioinformatics tools. The results showed the degree of hydrolysis (DH) theoretically achieved 56.8% when digested with papain, ficin, and prolyl endopeptidase (PREP), producing 126 ACE inhibitory peptides. By predicting the toxicity, allergenicity, gastrointestinal stability, and intestinal epithelial permeability, 30 peptides were finally screened, of which 21 had been reported and 9 were new. Moreover, the newly discovered peptides were synthesized to evaluate their in vitro ACE inhibition, showing Ile-Ile-Tyr and Asn-Pro-Pro-Lys had strong effects with a pIC₅₀ of 4.58 and 4.41, respectively. Further, their interaction mechanisms and bonding configurations with ACE were explored by molecular simulation. The preferred conformation of Ile-Ile-Tyr and Asn-Pro-Pro-Lys located in ACE were successfully predicted using the appropriate docking parameters. The molecular dynamics (MD) result indicated that they bound tightly to the active site of ACE by means of coordination with Zn(II) and hydrogen bonding and hydrophobic interaction with the residues in the pockets of S₁ and S₂, resulting in stable complexes. In summary, this work proposed a strategy for screening and identifying antihypertensive peptides from Todarodespacificus.