Predictive modelling of angiotensin converting enzyme inhibitory dipeptides

In vitro, ex vivo and in vivo antihypertensive evaluation of enzymatic hydrolysates of Californian red worm (Eisenia fetida) proteins

Hypertension is an important risk factor concomitant with cardiovascular disease (CVD) states, which is why we set out to evaluate Californian red worm hydrolysates on antihypertensive activity both in vitro, ex vivo, using rabbit aortic rings and in vivo using hypertensive induced rats. The worms were manually separated, washed with water, purged for 4 h with 4 % sodium bicarbonate, sacrificed with 7 % saline, and finally washed with drinking water. The in vitro antihypertensive capacity was performed by measuring angiotensin-converting enzyme inhibition; for the ex vivo assays, rabbit aorta was used to measure relaxation; for the in vivo assays, rats with induced hypertension were used to perform acute (hypotension) and chronic assays, using captopril as a control in all assays. With respect to angiotensin-converting enzyme (ACE) inhibition, the EC50 value of the worm hydrolysate was found to be 358 ppm; with respect to the analysis in aortic rings, it was found that the mechanisms of action of the hydrolysate are endothelium-dependent, presenting a maximum relaxation of 35 %. With respect to the in vivo assays, the hypotensive test showed that the hydrolysate can reduce blood pressure by up to 32 % in only 2 h, while the chronic analysis showed that the hydrolysate at 150 ppm did not present statistically significant differences with the control (captopril) during the 15 days of analysis. The Red Californian earthworm hydrolysate presents bioactive compounds identified with antihypertensive activities in vitro, ex vivo and in vivo in different isolated and animal models. The study demonstrates the efficacy of the hydrolysate to be used as an alternative in the treatment and prevention of hypertension, and it can be implemented in functional foods or nutraceutical foods. Antihypertensive peptides, particularly those that inhibit angiotensin-converting enzyme (ACE), hold significant importance in medical research, specifically in the context of cardiovascular disease treatment, particularly hypertension. The focus on these peptides and the potential implications of their results in medical research can be summarized through several key points: 1) Mechanisms of Action-Antihypertensive peptides function by inhibiting ACE or renin, crucial enzymes in blood pressure regulation. 2)Alternatives to Synthetic Drugs, 3) Additional Health Benefits, and various other factors.

Extraction and Characterization of Protein Concentrates from Limpets (Patella vulgata) and Peptide Release Following Gastrointestinal Digestion

This study investigated the characterization of proteins from the Irish limpet (Patella vulgata) and assessed the in vitro biological activities of hydrolysates obtained following gastrointestinal digestion (INFOGEST) of a limpet protein concentrate (LPC). The physicochemical properties and the digestibility of the LPC were investigated, along with the angiotensin-converting enzyme (ACE) inhibition and antioxidant activities of the LPC-digested samples. All the digested samples examined outperformed the LPC in terms of activity. Peptides were identified using LC-MS/MS after digestion. A total of 38 and 19 peptides were identified in LPC-G and LPC-GI, respectively, using a database search and a de novo approach. Most of the identified peptides had hydrophobic amino acids, which may contribute to their antioxidant and ACE inhibitory activities. The findings of this study showed that LPC has high nutritional quality with good digestibility and could serve as a potential source of antioxidative and ACE inhibitory peptides following gastrointestinal digestion.

Biological Functions of Antioxidant Dipeptides

In the history of modern nutritional science, understanding antioxidants is one of the major topics. In many cases, food-derived antioxidants have π conjugate or thiol group in their molecular structures because π conjugate stabilizes radical by its delocalization and two thiol groups form a disulfide bond in its antioxidative process. In recent years, antioxidant peptides have received much attention because for their ability to scavenge free radicals, inhibition of lipid peroxidation, chelation of transition metal ions, as well as their additional nutritional value. Among them, dipeptides are attracting much interest as post-amino acids, which have residues in common with amino acids, but also have different physiological properties and functions from those of amino acids. Especially, dipeptides containing moieties of several amino acid (tryptophan, tyrosine, histidine, cysteine, and methionine) possess potent antioxidant activity. This review summarizes previous details of structural property, radical scavenging activity, and biological activity of antioxidant dipeptide. Hopefully, this review will help provide a new insight into the study of the biological functions of antioxidant dipeptides.

In vitro angiotensin-converting enzyme and dipeptidyl peptidase-IV inhibitory, and antioxidant activity of blue mussel (Mytilus edulis) byssus collagen hydrolysates

Large quantities of mussel byssus are generated annually as a co-product of the mussel-processing industry. This fibrous material is a rich source of collagen, which when extracted has potential uses as an alternative source of collagen for food applications. However, due the complex structure of the material, the extraction of the collagenous components using food-friendly strategies has proved challenging to date. An enzyme-aided method, using a proline endoproteinase, was employed for the extraction of collagen from mussel byssus yielding 138.82 ± 2.25 mg collagen/g dry weight. Hydrolysates of the collagen extract were generated using five food-grade enzyme preparations with Corolase® PP giving the highest extent of hydrolysis. Reversed-phase and gel permeation high-performance liquid chromatography of the extracted collagen and its enzymatic hydrolysates showed significant hydrolysis of collagen. The hydrolysates generated with Corolase® PP showed the highest in vitro bioactivities: angiotensin-converting enzyme (ACE) IC50 = 0.79 ± 0.17 mg/ml, dipeptidyl peptidase-IV (DPP-IV) IC50 = 0.66 ± 0.17 mg/ml and oxygen radical absorbance capacity (ORAC) activity = 311.23 ± 13.41 µmol trolox equivalents (TE)/g. The results presented herein indicate that in addition to acting as an alternative source of collagen for food applications, mussel byssus collagen-derived hydrolysates have potential applications as functional food ingredients for the management of metabolic diseases such as type II diabetes and hypertension.

In-silico identification of lysine residue for α-Amylase immobilization on dialdehyde cellulose

Enzymes are the precious gift of nature to humans. The wise utilization of enzymes may reduce energy needs of humans and the Immobilization technique can help a lot in this regard. This aspect overcomes limitations of the enzymes, therefore providing an opportunity to explore enzymatic chemistry further. In the present context, it is quite cumbersome & costly to identify the amino acid of enzymes involved in the covalent mode of Immobilization. In the present study, molecular modeling techniques were used to do this difficult task. The present work used molecular modeling methods to extract information about the immobilization of α-Amylase (E.C.3.2.1.1) on Dialdehyde Cellulose. The Lysine residue is the most probable residue to interact with Dialdehyde Cellulose. In the present work, a total of 23 lysine residues were used to study covalent binding behavior with α-Amylase. It was found that if Lys142 is involved in binding with Dialdehyde Cellulose then binding affinity (-6.1 & -5.9 kcal mol-1), as well as the involvement of amino acids of both free α-Amylase and Lys142 immobilized α-Amylase with the starch substrate, were found to be similar. The technique reported here is used for the identification of amino acid residue for the Immobilization of enzymes.

Design, synthesis and bioactive evaluation of geniposide derivatives for antihyperuricemic and nephroprotective effects

Hyperuricemia is a principal factor mediating gout and kidney damage, and xanthine oxidase (XOD) is a key enzyme in the pathogenesis of hyperuricemia. In this context, a series of geniposide derivatives were designed and synthesized, and antihyperuricemic and nephroprotective effects of all derivatives was evaluated in vitro and in vivo. Compound 2e emerged as the most potent XOD inhibitor, with an IC₅₀ value of 6.67 ± 0.46 µM. Simultaneously, cell viability, ROS generation, and SOD levels assay showed that compound 2e could repair the damage of HKC cells by inhibiting the oxidative stress response. The results of the study indicated compound 2e significantly decreased uric acid levels by inhibiting the XOD activity, and repaired kidney damage by inhibiting the expression of TLR4/TLR2/MyD88/NF-κB and NALP3/ASC/caspase-1 signaling pathways. Enzyme inhibition kinetics suggested that compound 2e functioned via reversible mixed competitive inhibition. Moreover, a molecular docking study was performed to gain insight into the binding mode of compound 2e with XOD. These results suggest that geniposide derivatives were potential to be developed into a novel medicine to reveal healthy benefits in natural prevention and reduction risk of hyperuricemia and kidney damage.

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.

Identification and Characterization of Gastrointestinal-Resistant Angiotensin-Converting Enzyme Inhibitory Peptides from Egg White Proteins

Egg proteins are recognized as excellent sources of bioactive peptides, such as angiotensin-converting enzyme inhibitory (ACEi) peptides. Oral administration of a thermolysin-digested egg white hydrolysate (T-EWH) caused a significant blood pressure reduction in spontaneously hypertensive rats; a further ACEi assay implied that its ACEi activity was enhanced after in vitro gastrointestinal (GI) digestion. These results indicated that T-EWH contained ACEi peptides resisting GI digestion and/or being further released during GI digestion. Therefore, the objective of this study was to identify these responsible ACEi peptides from T-EWH. The conventionally activity-guided fractionation was applied, coupled with a synchronized GI digestion throughout, during which both peptide yield and ACEi activity before and after the GI digestion were measured. Finally, six ACEi peptides (LAPYK, LKISQ, LKYAT, INKVVR, LFLIKH, and LGHWVY) with good GI resistance were identified with IC₅₀ values <20 μM, especially LKYAT (0.09 μM). The structure-activity relationship of these peptides was discussed. The discovery of GI-resistant ACEi peptides could further support the application of egg white proteins as functional food ingredients.

Computational Opportunities and Challenges in Finding Cyclic Peptide Modulators of Protein-Protein Interactions

Peptide cyclization can improve stability, conformational constraint, and compactness. However, apart from beta-turn structures, which are well incorporated into cyclic peptides (CPs), many primary peptide structures and functions are markedly altered by cyclization. Accordingly, to mimic linear peptide interfaces with cyclic peptides, it can be beneficial to screen combinatorial cyclic peptide libraries. Computational methods have been developed to screen CPs, but face a number of challenges. Here, we review methods to develop in silico computational libraries, and the potential for screening naturally occurring libraries of CPs. The simplest and most rapid computational pharmacophore methods that estimate peptide three-dimensional structures to be screened versus targets are relatively easy to implement, and while the constraint on structure imposed by cyclization makes them more effective than the same approaches with linear peptides, there are a large number of limiting assumptions. In contrast, full molecular dynamics simulations of cyclic peptide structures not only are costly to implement, but also require careful attention to interpretation, so that not only is the computation time rate limiting, but the interpretation time is also rate limiting due to the analysis of the typically complex underlying conformational space of CPs. A challenge for the field of computational cyclic peptide screening is to bridge this gap effectively. Natural compound libraries of short cyclic peptides, and short cyclized regions of proteins, encoded in the genomes of many organisms present a potential treasure trove of novel functionality which may be screened via combined computational and experimental screening approaches.

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.

Enhancing bioactive peptide release and identification using targeted enzymatic hydrolysis of milk proteins

Milk proteins have been extensively studied for their ability to yield a range of bioactive peptides following enzymatic hydrolysis/digestion. However, many hurdles still exist regarding the widespread utilization of milk protein-derived bioactive peptides as health enhancing agents for humans. These mostly arise from the fact that most milk protein-derived bioactive peptides are not highly potent. In addition, they may be degraded during gastrointestinal digestion and/or have a low intestinal permeability. The targeted release of bioactive peptides during the enzymatic hydrolysis of milk proteins may allow the generation of particularly potent bioactive hydrolysates and peptides. Therefore, the development of milk protein hydrolysates capable of improving human health requires, in the first instance, optimized targeted release of specific bioactive peptides. The targeted hydrolysis of milk proteins has been aided by a range of in silico tools. These include peptide cutters and predictive modeling linking bioactivity to peptide structure [i.e., molecular docking, quantitative structure activity relationship (QSAR)], or hydrolysis parameters [design of experiments (DOE)]. Different targeted enzymatic release strategies employed during the generation of milk protein hydrolysates are reviewed herein and their limitations are outlined. In addition, specific examples are provided to demonstrate how in silico tools may help in the identification and discovery of potent milk protein-derived peptides. It is anticipated that the development of novel strategies employing a range of in silico tools may help in the generation of milk protein hydrolysates containing potent and bioavailable peptides, which in turn may be used to validate their health promoting effects in humans. Graphical abstract The targeted enzymatic hydrolysis of milk proteins may allow the generation of highly potent and bioavailable bioactive peptides.

Peptide identification in a salmon gelatin hydrolysate with antihypertensive, dipeptidyl peptidase IV inhibitory and antioxidant activities

Salmon gelatin (Salmo salar, SG) enzymatic hydrolysates were generated using Alcalase 2.4L, Alcalase 2.4L in combination with Flavourzyme 500L, Corolase PP, Promod 144MG and Brewer's Clarex. The hydrolysate generated with Corolase PP for 1h (SG-C1) had the highest angiotensin converting enzyme (ACE, IC₅₀=0.13±0.05mgmL^-1) and dipeptidyl peptidase IV (DPP-IV, IC₅₀=0.08±0.01mgmL^-1) inhibitory activities, and oxygen radical absorbance capacity (ORAC, 540.94±9.57μmolTEg^-1d.w.). The in vitro bioactivities of SG-C1 were retained following simulated gastrointestinal digestion. Administration of SG and SG-C1 (50mgkg^-1 body weight) to spontaneously hypertensive rats (SHR) lowered heart rate along with systolic, diastolic and mean arterial blood pressure. The SG-C1 hydrolysate was fractionated using semi-preparative RP-HPLC and the fraction with highest overall in vitro bioactivity (fraction 25) was analysed by UPLC-MS/MS. Four peptide sequences (Gly-Gly-Pro-Ala-Gly-Pro-Ala-Val, Gly-Pro-Val-Ala, Pro-Pro and Gly-Phe) and two free amino acids (Arg and Tyr) were identified in this fraction. These peptides and free amino acids had potent ACE and DPP-IV inhibitory, and ORAC activities. The results show that SG hydrolysates have potential as multifunctional food ingredients particularly for the management of hypertension.

The Ig VH complementarity-determining region 3-containing Rb9 peptide, inhibits melanoma cells migration and invasion by interactions with Hsp90 and an adhesion G-protein coupled receptor

The present work aims at investigating the mechanism of action of the Rb9 peptide, which contains the V_HCDR 3 sequence of anti-sodium-dependent phosphate transport protein 2B (NaPi2B) monoclonal antibody RebMab200 and displayed antitumor properties. Short peptides corresponding to the hypervariable complementarity-determining regions (CDRs) of immunoglobulins have been associated with antimicrobial, antiviral, immunomodulatory and antitumor activities regardless of the specificity of the antibody. We have shown that the CDR derived peptide Rb9 induced substrate hyperadherence, inhibition of cell migration and matrix invasion in melanoma and other tumor cell lines. Rb9 also inhibited metastasis of murine melanoma in a syngeneic mouse model. We found that Rb9 binds to and interferes with Hsp90 chaperone activity causing attenuation of FAK-Src signaling and downregulation of active Rac1 in B16F10-Nex2 melanoma cells. The peptide also bound to an adhesion G-protein coupled receptor, triggering a concentration-dependent synthesis of cAMP and activation of PKA and VASP signaling as well as IP-3 dependent Ca²⁺ release. Hsp90 is highly expressed on the cell surface of melanoma cells, and synthetic agents that target Hsp90 are promising cancer therapeutic drugs. Based on their remarkable antitumor effects, the CDR-H3-derived peptides from RebMab200, and particularly the highly soluble and stable Rb9, are novel candidates to be further studied as potential antitumor drugs, selectively acting on cancer cell motility and invasion.

Bioactive peptides from Atlantic salmon (Salmo salar) with angiotensin converting enzyme and dipeptidyl peptidase IV inhibitory, and antioxidant activities

The pH shift method was utilised for the recovery of proteins from salmon trimmings (ST), yielding 93% (w/w) protein. ST protein (STP) hydrolysates were generated with different enzyme preparations. STP incubated with Corolase PP for 1h (STP-C1) had the most potent angiotensin converting enzyme (ACE) and dipeptidyl peptidase IV (DPP-IV) inhibitory and oxygen radical absorbance capacity (ORAC) activities. Analysis of fractions of STP-C1 using UPLC-MS/MS identified sixteen peptides/amino acids. Tyr-Pro had the highest ACE inhibitory activity (ACE IC₅₀=5.21±0.94μM). The highest DPP-IV inhibitory activity was found with the amino acid Tyr (DPP-IV IC₅₀=75.15±0.84μM). Val-Pro had the highest ORAC activity (19.45±2.15μmol of TEg^-1). To our knowledge, the peptides Gly-Pro-Ala-Val, Val-Cys, and Phe-Phe have not been previously identified to have the activities tested in this study. These results indicate that STP hydrolysates are potential sources of bioactive peptides.

Milk proteins as a source of tryptophan-containing bioactive peptides

Tryptophan (W) is an essential amino acid which is primarily required for protein synthesis. It also acts as a precursor of key biomolecules for human health (serotonin, melatonin, tryptamine, niacin, nicotinamide adenine dinucleotide (NAD), phosphorylated NAD (NADP), quinolinic acid, kynureric acid, etc.). Among dietary proteins, milk proteins are particularly rich in W. W residues within milk proteins may be released by proteolytic/peptidolytic enzymes either as a free amino acid or as part of peptide sequences. Different W-containing peptides originating from milk proteins have been shown in vitro to display a wide range of bioactivities such as angiotensin converting enzyme (ACE) inhibition along with antioxidant, antidiabetic and satiating related properties. Free W has been shown in certain instances to have an effect on cognition and the aforementioned bioactive properties. However, a higher bioactive potency has generally been observed with specific W-containing peptides compared to free W. Since W is thermolabile, the impact of processing on the stability of W-containing peptides needs to be considered. Milk protein-derived W-containing peptides may have significant potential as natural health promoting agents in humans.

In vitro assessment of the multifunctional bioactive potential of Alaska pollock skin collagen following simulated gastrointestinal digestion

BACKGROUND

Dietary mineral deficiency, hypertension and diabetes have become serious human health problems. Dietary approaches are increasingly being investigated to address these issues. Identification of food-derived biological peptides has become an important approach to control such diseases. Peptides generated from aquatic byproducts have been shown to possess biological activities.

RESULTS

Significantly higher copper-chelating activity was observed on simulated hydrolysis of intact collagen. The collagen hydrolysate generated in the gastric stage exhibited moderate angiotensin-converting enzyme (ACE)-inhibitory activity with an IC50 value of 2.92 ± 0.22 mg mL(-1), which significantly decreased to 0.49 ± 0.02 mg mL(-1) after intestinal digestion. The dipeptidyl peptidase (DPP) IV-inhibitory potency of the collagen hydrolysate generated directly following simulated gastrointestinal digestion (SGID) (IC50 2.59 ± 0.04 mg mL(-1)) was significantly lower than that of the collagen tryptic hydrolysate (CTH) (IC50 1.53 ± 0.01 mg mL(-1)). The antioxidant activities of collagen and CTH using the ferric-reducing antioxidant power (FRAP) assay were 0.87 ± 0.10 and 1.27 ± 0.03 µmol Trolox equivalent (TE) g(-1) respectively after SGID.

CONCLUSION

This study identifies collagen as a good and inexpensive substrate for the generation of biologically active peptides with potential applications as functional ingredients in the management of chronic illness and mineral deficiency problems.

Computational approaches to developing short cyclic peptide modulators of protein-protein interactions

Cyclic peptides are a promising class of bioactive molecules potentially capable of modulating "difficult" targets, such as protein-protein interactions. Cyclic peptides have long been used as therapeutics derived from natural product derivatives, but remain an underexplored class of compounds from the perspective of rational drug design, possibly due to the known weaknesses of peptide drugs in general. While cyclic peptides are non"druglike" by the accepted empirical rules, their unique structure may lend itself to both membrane permeability and proteolytic resistance-the main barriers to oral delivery. The constrained shape of cyclic peptides also lends itself better to virtual screening approaches, and new tools and successes in this area have been recently noted. An increasing number of strategies are available, both to generate and screen cyclic peptide libraries, and best practises and current successes are described within. This chapter will describe various computational strategies for virtual screening cyclic peptides, along with known implementations and applications. We will explore the generation and screening of diverse combinatorial virtual libraries, incorporating a range of cyclization strategies and structural modifications. More advanced approaches covered include evolutionary algorithms designed to aid in screening large structural libraries, machine learning approaches, and harnessing bioinformatics resources to bias cyclic peptide virtual libraries towards known bioactive structures.

Hypotensive effects and angiotensin-converting enzyme inhibitory peptides of reishi (Ganoderma lingzhi) auto-digested extract

Reishi (Ganoderma lingzhi) has been used as a traditional medicine for millennia. However, relatively little is known about this mushroom’s proteins and their bioactivities. In this study, we used reishi’s own proteases to hydrolyze its protein and obtained auto-digested reishi (ADR) extract. The extract was subjected to in vitro assays and administered to spontaneous hypertensive rats (SHRs) to determine its potential for use as a hypotensive medication. Bioassay-guided fractionation and de novo sequencing were used for identifying the active compounds. After 4 h administration of ADR, the systolic pressure of SHRs significantly decreased to 34.3 mmHg (19.5% change) and the effect was maintained up to 8 h of administration, with the decrease reaching as low as 26.8 mmHg (15% reduction–compare to base line a decrease of 26.8 mmHg is less than a decrease of 34.3 mmHg so it should give a smaller % reduction). Eleven peptides were identified and four of them showed potent inhibition against ACE with IC₅₀ values ranging from 73.1 μM to 162.7 μM. The results showed that ADR could be a good source of hypotensive peptides that could be used for antihypertensive medication or incorporation into functional foods.

Docking ligands into flexible and solvated macromolecules. 6. Development and application to the docking of HDACs and other zinc metalloenzymes inhibitors

Metalloenzymes are ubiquitous proteins which feature one or more metal ions either directly involved in the enzymatic activity and/or structural properties (i.e., zinc fingers). Several members of this class take advantage of the Lewis acidic properties of zinc ions to carry out their various catalytic transformations including isomerization or amide cleavage. These enzymes have been validated as drug targets for a number of diseases including cancer; however, despite their pharmaceutical relevance and the availability of crystal structures, structure-based drug design methods have been poorly and indirectly parametrized for these classes of enzymes. More specifically, the metal coordination component and proton transfers of the process of drugs binding to metalloenzymes have been inadequately modeled by current docking programs, if at all. In addition, several known issues, such as coordination geometry, atomic charge variability, and a potential proton transfer from small molecules to a neighboring basic residue, have often been ignored. We report herein the development of specific functions and parameters to account for zinc-drug coordination focusing on the above-listed phenomena and their impact on docking to zinc metalloenzymes. These atom-type-dependent but atomic charge-independent functions implemented into Fitted 3.1 enable the simulation of drug binding to metalloenzymes, considering an acid-base reaction with a neighboring residue when necessary with good accuracy.

Measuring angiotensin-I converting enzyme inhibitory activity by micro plate assays: comparison using marine cryptides and tentative threshold determinations with captopril and losartan

To determine the angiotensin-I converting enzyme (ACE) inhibitory activity of marine cryptides, different methods were tested. ACE inhibition was measured using two synthetic substrates, (N-[3-(2-furyl) acryloyl]-Phe-Gly-Gly (FAPGG) and N-hippuryl-His-Leu hydrate salt (HHL)), and a natural one, angiotensin-I. The IC50 value (defined as the concentration of inhibitory molecule needed to inhibit 50% of the ACE activity) of the reference synthetic inhibitor captopril was in the nanomolar range (1.79-15.1 nM) when synthetic substrates were used, whereas it exhibited IC50 of micromolar range (16.71 μM) with angiotensin-I. We chose losartan, an antagonist of angiotensin-II receptor as negative control for the ACE inhibition. Losartan was also able to inhibit ACE whatever the substrate tested, with IC50 of micromolar range (17.13-146 μM). We defined this value as a limit above which molecules are not showing in vitro ACE inhibitory activity. Val-Trp (VW), Val-Tyr (VY), Lys-Tyr (KY), Lys-Trp (KW), Ile-Tyr (IY), Ala-Pro (AP), Val-Ile-Tyr (VIY), Leu-Lys-Pro (LKP), Gly-Pro-Leu (GPL), Ala-Lys-Lys (AKK), and Val-Ala-Pro (VAP) were tested as inhibitors of ACE with synthetic and natural substrates. IC50 displayed were substrate-dependent. With FAPGG as substrate, IW, VAP, KY, IY, AP, AKK, and VIY show IC50 values over the IC50 value of losartan and should not be considered as inhibitors of ACE. VY, VW, KW, and LKP exhibited IC50 value lower than the IC50 value of losartan for all substrates tested and were thus considered as good candidates for effectively decreasing hypertension. It appears that the comparison of IC50 is not consistent when IC50 values are obtained with different substrates and different methods. In vitro ACE inhibitory activity assays should always include various ACE substrates and references such as captopril and a negative control to obtain data reliable to discriminate ACE inhibitory peptides.

Food protein hydrolysates as a source of dipeptidyl peptidase IV inhibitory peptides for the management of type 2 diabetes

The prevalence of type 2 diabetes mellitus (T2DM) is increasing and it is estimated that by 2030 approximately 366 million people will be diagnosed with this condition. The use of dipeptidyl peptidase IV (DPP-IV) inhibitors is an emerging strategy for the treatment of T2DM. DPP-IV is a ubiquitous aminodipeptidase that cleaves incretins such as glucagon like peptide 1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP), resulting in a loss in their insulinotropic activity. Synthetic DPP-IV drug inhibitors are being used to increase the half-life of the active GLP-1 and GIP. Dietary intervention is accepted as a key component in the prevention and management of T2DM. Therefore, identification of natural food protein-derived DPP-IV inhibitors is desirable. Peptides with DPP-IV inhibitory activity have been identified in a variety of food proteins. This review aims to provide an overview of food protein hydrolysates as a source of the DPP-IV inhibitory peptides with particular focus on milk proteins. In addition, the proposed modes of inhibition and structure-activity relationship of peptide inhibitors are discussed. Milk proteins and associated peptides also display insulinotropic activity and help regulate blood glucose in healthy and diabetic subjects. Therefore, milk protein derived peptide inhibitors may be a unique multifunctional peptide approach for the management of T2DM.

Predicting binding within disordered protein regions to structurally characterised peptide-binding domains

Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif) containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58).Next, we trained a bidirectional recurrent neural network (BRNN) using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72) showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods) clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.