First Food-Derived Peptide Inhibitor of the Protein-Protein Interaction between Gain-of-Function PCSK9D374Y and the Low-Density Lipoprotein Receptor

Pulse Proteins and Their Hydrolysates: A Comprehensive Review of Their Beneficial Effects on Metabolic Syndrome and the Gut Microbiome

Pulses, as an important part of the human diet, can act as a source of high-quality plant proteins. Pulse proteins and their hydrolysates have shown promising results in alleviating metabolic syndrome and modulating the gut microbiome. Their bioactivities have become a focus of research, with many new findings added in recent studies. This paper comprehensively reviews the anti-hypertension, anti-hyperglycemia, anti-dyslipidemia and anti-obesity bioactivities of pulse proteins and their hydrolysates in recent in vitro and in vivo studies, which show great potential for the prevention and treatment of metabolic syndrome. In addition, pulse proteins and their hydrolysates can regulate the gut microbiome, which in turn can have a positive impact on the treatment of metabolic syndrome. Furthermore, the beneficial effects of some pulse proteins and their hydrolysates on metabolic syndrome have been supported by clinical studies. This review might provide a reference for the application of pulse proteins and their hydrolysates in functional foods or nutritional supplements for people with metabolic syndrome.

Plant bioactive peptides for cardiovascular disease prevention

Cardiovascular disease (CVD) is a major cause of deaths in industrialized countries and a constantly growing cause of morbidity and mortality worldwide Hypercholesterolemia is one of the main risk factors for CVD progression that may be prevented by lifestyle changes, including diet. This chapter will discuss the role of peptides from plants (soybean, lupin, cowpea, hempseed, and rice bran) sources with pleotropic activity for the prevention of CVD. Overall, the bioactivity that will be mainly discussed it is the hypocholesterolemic one. The very diversified structures of the hypocholesterolemic peptides so far identified explains the reason why they exert their activity through different mechanisms of action that will be extensively described in this review. Doubtlessly, their potential use in nutritional application is desirable, however, only few of them have been tested in vivo. Therefore, more efforts need to be pursued for singling out good candidates for the development of functional foods or dietary supplements.

Computational Design, Synthesis, and Biological Evaluation of Diimidazole Analogues Endowed with Dual PCSK9/HMG-CoAR-Inhibiting Activity

Proprotein convertase subtilisin/kexin 9 (PCSK9) is responsible for the degradation of the hepatic low-density lipoprotein receptor (LDLR), which regulates circulating cholesterol levels. Consequently, the PCSK9 inhibition is a valuable therapeutic approach for the treatment of hypercholesterolemia and cardiovascular diseases. In our studies, we discovered Rim13, a polyimidazole derivative reducing the protein-protein interaction between PCSK9 and LDLR with an IC₅₀ of 1.6 μM. The computational design led to the optimization of the shape of the PCSK9/ligand complementarity, enabling the discovery of potent diimidazole derivatives. In fact, carrying out biological assays to fully characterize the cholesterol-lowering activity of the new analogues and using both biochemical and cellular techniques, compound Dim16 displayed improved PCSK9 inhibitory activity (IC₅₀ 0.9 nM). Interestingly, similar to other lupin-derived peptides and their synthetic analogues, some compounds in this series showed dual hypocholesterolemic activity since some of them complementarily inhibited the 3-hydroxy-3-methylglutaryl coenzyme A reductase.

Recent Update on the Development of PCSK9 Inhibitors for Hypercholesterolemia Treatment

The proprotein convertase subtilisin/kexin-type 9 (PCSK9) binds to low-density lipoprotein receptors (LDLR), thereby trafficking them to lysosomes upon endocytosis and enhancing intracellular degradation to prevent their recycling. As a result, the levels of circulating LDL cholesterol (LDL-C) increase, which is a prominent risk factor for developing atherosclerotic cardiovascular diseases (ASCVD). Thus, PCSK9 has become a promising therapeutic target that offers a fertile testing ground for new drug modalities to regulate plasma LDL-C levels to prevent ASCVD. In this review, we have discussed the role of PCSK9 in lipid metabolism and briefly summarized the current clinical status of modalities targeting PCSK9. In particular, a detailed overview of peptide-based PCSK9 inhibitors is presented, which emphasizes their structural features and design, therapeutic effects on patients, and preclinical cardiovascular disease (CVD) models, along with PCSK9 modulation mechanisms. As a promising alternative to monoclonal antibodies (mAbs) for managing LDL-C, anti-PCSK9 peptides are emerging as a prospective next generation therapy.

In vitro display evolution of unnatural peptides spontaneously cyclized via intramolecular nucleophilic aromatic substitutions

We report novel, ribosomally incorporatable, and intramolecularly cysteine-reactive fluorobenzoic acid-derived linkers for SELEX of mRNA-displayed unnatural peptides, which spontaneously cyclized via intramolecular nucleophilic aromatic substitutions forming thioethers. With this strategy we identified several novel PCSK9-binding peptides.

Computational Design and Biological Evaluation of Analogs of Lupin Peptide P5 Endowed with Dual PCSK9/HMG-CoAR Inhibiting Activity

(1) Background: Proprotein convertase subtilisin/kexin 9 (PCSK9) is responsible for the degradation of the hepatic low-density lipoprotein receptor (LDLR), which regulates the circulating cholesterol level. In this field, we discovered natural peptides derived from lupin that showed PCSK9 inhibitory activity. Among these, the most active peptide, known as P5 (LILPHKSDAD), reduced the protein-protein interaction between PCSK9 and LDLR with an IC₅₀ equals to 1.6 µM and showed a dual hypocholesterolemic activity, since it shows complementary inhibition of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoAR). (2) Methods: In this study, by a computational approach, the P5 primary structure was optimized to obtain new analogs with improved affinity to PCSK9. Then, biological assays were carried out for fully characterizing the dual cholesterol-lowering activity of the P5 analogs by using both biochemical and cellular techniques. (3) Results: A new peptide, P5-Best (LYLPKHSDRD) displayed improved PCSK9 (IC₅₀ 0.7 µM) and HMG-CoAR (IC₅₀ 88.9 µM) inhibitory activities. Moreover, in vitro biological assays on cells demonstrated that, not only P5-Best, but all tested peptides maintained the dual PCSK9/HMG-CoAR inhibitory activity and remarkably P5-Best exerted the strongest hypocholesterolemic effect. In fact, in the presence of this peptide, the ability of HepG2 cells to absorb extracellular LDL was improved by up to 254%. (4) Conclusions: the atomistic details of the P5-Best/PCSK9 and P5-Best/HMG-CoAR interactions represent a reliable starting point for the design of new promising molecular entities endowed with hypocholesterolemic activity.

Lupin-Derived Bioactive Peptides: Intestinal Transport, Bioavailability and Health Benefits

There is a renewed interest on the reliance of food-based bioactive compounds as sources of nutritive factors and health-beneficial chemical compounds. Among these food components, several proteins from foods have been shown to promote health and wellness as seen in proteins such as α/γ-conglutins from the seeds of Lupinus species (Lupin), a genus of leguminous plant that are widely used in traditional medicine for treating chronic diseases. Lupin-derived peptides (LDPs) are increasingly being explored and they have been shown to possess multifunctional health improving properties. This paper discusses the intestinal transport, bioavailability and biological activities of LDPs, focusing on molecular mechanisms of action as reported in in vitro, cell culture, animal and human studies. The potentials of several LDPs to demonstrate multitarget mechanism of regulation of glucose and lipid metabolism, chemo- and osteoprotective properties, and antioxidant and anti-inflammatory activities position LDPs as good candidates for nutraceutical development for the prevention and management of medical conditions whose etiology are multifactorial.

The emerging landscape of peptide-based inhibitors of PCSK9

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a clinically validated target for treating cardiovascular disease (CVD) due to its involvement in cholesterol metabolism. Although approved monoclonal antibodies (alirocumab and evolocumab) that inhibit PCSK9 function are very effective in lowering cholesterol, their limitations, including high treatment costs, have so far prohibited widespread use. Accordingly, there is great interest in alternative drug modalities to antibodies. Like antibodies, peptides are valuable therapeutics due to their high target potency and specificity. Furthermore, being smaller than antibodies means they have access to more drug administration options, are less likely to induce adverse immunogenic responses, and are better suited to affordable production. This review surveys the current peptide-based landscape aimed towards PCSK9 inhibition, covering pre-clinical to patented drug candidates and comparing them to current cholesterol lowering therapeutics. Classes of peptides reported to be inhibitors include nature-inspired disulfide-rich peptides, combinatorially derived cyclic peptides, and peptidomimetics. Their functional activities have been validated in biophysical and cellular assays, and in some cases pre-clinical mouse models. Recent efforts report peptides with potent sub-nanomolar binding affinities to PCSK9, which highlights their potential to achieve antibody-like potency. Studies are beginning to address pharmacokinetic properties of PCSK9-targeting peptides in more detail. We conclude by highlighting opportunities to investigate their biological effects in pre-clinical models of cardiovascular disease. The anticipation concerning the PCSK9-targeting peptide landscape is accelerating and it seems likely that a peptide-based therapeutic for treating PCSK9-mediated hypercholesterolemia may be clinically available in the near future.

Engineered EGF-A Peptides with Improved Affinity for Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9)

The epidermal growth-factor-like domain A (EGF-A) of the low-density lipoprotein (LDL) receptor is a promising lead for therapeutic inhibition of proprotein convertase subtilisin/kexin type 9 (PCSK9). However, the clinical potential of EGF-A is limited by its suboptimal affinity for PCSK9. Here, we use phage display to identify EGF-A analogues with extended bioactive segments that have improved affinity for PCSK9. The most potent analogue, TEX-S2_03, demonstrated ∼130-fold improved affinity over the parent domain and had a reduced calcium dependency for efficient PCSK9 binding. Thermodynamic binding analysis suggests the improved affinity of TEX-S2_03 is enthalpically driven, indicating favorable interactions are formed between the extended segment of TEX-S2_03 and the PCSK9 surface. The improved affinity of TEX-S2_03 resulted in increased activity in competition binding assays and more efficient restoration of LDL receptor levels with clearance of extracellular LDL cholesterol in functional cell assays. These results confirm that TEX-S2_03 is a promising therapeutic lead for treating hypercholesterolemia. Many EGF-like domains are involved in disease-related protein-protein interactions; therefore, our strategy for engineering EGF-like domains has the potential to be broadly implemented in EGF-based drug design.

In vitro selection generates RNA aptamer that antagonizes PCSK9-LDLR interaction and recovers cellular LDL uptake

Proprotein convertase subtilisin/kexin type 9 (PCSK9) induces low-density lipoprotein (LDL)-receptor (LDLR) degradation, increasing plasma LDL-cholesterol levels and causing hypercholesterolemia. Therefore, inhibition of PCSK9-LDLR interaction is an attractive therapeutic target for hypercholesterolemia treatment. In this study, we have identified a novel RNA aptamer that binds specifically to PCSK9 by in vitro selection, also known as systematic evolution of ligands by exponential enrichment (SELEX). The binding kinetics of the PCSK9-binding RNA aptamer was measured by biolayer interferometry assay, showing that the aptamer has higher affinity compared to PCSK9-LDLR interaction. Competitive inhibition assay using chemiluminescence detection revealed that the RNA aptamer inhibits PCSK9-LDLR interaction. In cellular LDL-uptake assays with HepG2 cells, the RNA aptamer recovered LDL uptake in the PCSK9-treated cells, demonstrating its anti-PCSK9 antagonistic activity. These results indicated that the PCSK9-binding RNA aptamer has the potential to be an affinity reagent for PCSK9 protein analysis and a therapeutic reagent for hypercholesterolemia treatment.

Exploring Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Autoproteolysis Process by Molecular Simulations: Hints for Drug Design

Proprotein convertase subtilisin/kexin 9 (PCSK9) is a notable target for the treatment of hypercholesterolemia because it regulates the population of the low-density lipoprotein receptor (LDLR) on liver cells. The PCSK9 zymogen is a serine protease that spontaneously undergoes a double self-cleavage step. Available X-ray structures depict the PCSK9 mature state, but the atomic details of the zymogen state of the enzyme are still unknown. Additionally, why the protease activity of PCSK9 is blocked after the second autoprocessing step remains unclear, as this deviates from other members of the PCSK family. By performing constant-pH molecular dynamics (MD) simulations, we investigated the protonation state of the catalytic triad of PCSK9 and found that it strongly influences the catalytic properties of the enzyme. Moreover, we determined the final step of the maturation process by classical and steered MD simulations. This study could facilitate the identification of ligands capable of interfering with the PCSK9 maturation process.

How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs

The early and late development of new anticancer drugs, small molecules or peptides can be slowed down by some issues such as poor selectivity for the target or poor ADME properties. Computer-aided drug design (CADD) and target drug delivery (TDD) techniques, although apparently far from each other, are two research fields that can give a significant contribution to overcome these problems. Their combination may provide mechanistic understanding resulting in a synergy that makes possible the rational design of novel anticancer based therapies. Herein, we aim to discuss selected applications, some also from our research experience, in the fields of anticancer small organic drugs and peptides.

Lupin Peptide T9 (GQEQSHQDEGVIVR) Modulates the Mutant PCSK9D374Y Pathway: in vitro Characterization of its Dual Hypocholesterolemic Behavior

GQEQSHQDEGVIVR (T9) is a peptide originated by the tryptic digestion of lupin β-conglutin that is absorbed in human intestinal Caco-2 cells. A previous study has shown that T9 impairs the protein–protein interaction between mutant D374Y Proprotein Convertase Subtilisin/Kexin 9 (PCSK9^D374Y) and the low-density lipoprotein receptor (LDLR), thus exerting a hypocholesterolemic effect. Moreover, a bioinformatic study predicting that T9 may potentially act as an inhibitor of 3-hydroxy-3-methylglutaryl CoA reductase (HMGCoAR), has suggested a complementary cholesterol-lowering activity. The present study demonstrates that T9 inhibits in vitro the HMGCoAR functionality with an IC₅₀ value of 99.5 ± 0.56 µM. Through the inhibition of either HMGCoAR or PCSK9^D374Y activities, T9 enhances the LDLR protein levels leading to an improved ability of HepG2 cells transfected with the mutant PCSK9^D374Y-FLAG plasmid to uptake extracellular LDL with a final cholesterol-lowering effect. In addition, T9 modulates the PCSK9^D374Y signaling pathway in transfected HepG2 cells leading to a decrease of PCSK9^D374Y and HNF-1α protein levels. All these results indicate that the hypocholesterolemic effects of T9 are due to a dual mechanism of action involving either the modulation of the PCSK9^D374Y or LDLR pathways. This may represent an added value from a therapeutic point of view.

Soybean Peptides Exert Multifunctional Bioactivity Modulating 3-Hydroxy-3-Methylglutaryl-CoA Reductase and Dipeptidyl Peptidase-IV Targets in Vitro

This study was aimed at evaluating the cellular mechanism through which peptic (P) and tryptic (T) soybean hydrolysates modulate the targets involved in hypocholesterolemic pathways in HepG2 and antidiabetic pathways in Caco-2 cells. Both hydrolysates (tested in the concentration range of 0.5-2.5 mg/mL) inhibited the 3-hydroxy-3-methylglutaryl-CoA reductase activity in HepG2 cells. In addition, Soybean P increased LDLR protein levels on HepG2 membranes by 51.5 ± 11.6% and 63.0 ± 6.9% (0.5-1.0 mg/mL) whereas Soybean T increased them by 55.2 ± 9.7% and 85.8 ± 21.5% (0.5-1.0 mg/mL) vs the control, with a final improved HepG2 capacity in the uptake of extracellular LDL. Soybean P reduced in vitro the dipeptidyl peptidase-IV activity by 16.3 ± 3.0% and 31.4 ± 0.12% (1.0 and 2.5 mg/mL), whereas Soybean T reduced it by 15.3 ± 11.0% and 11.0 ± 0.30% (1.0 and 2.5 mg/mL) vs the control. Finally, both hydrolysates inhibited dipeptidyl peptidase-IV activity in situ in human intestinal Caco-2 cells. This investigation may help to explain the activities observed in experimental and clinical studies.

Inhibition of PCSK9D374Y/LDLR Protein-Protein Interaction by Computationally Designed T9 Lupin Peptide

The inhibition of the PCSK9/LDLR protein-protein interaction is a promising strategy for developing new hypocholesterolemic agents. Familial hypercholesterolemia is linked to specific PCSK9 mutations: the D374Y is the most potent gain-of-function (GOF) PCSK9 mutation among clinically relevant ones. Recently, a lupin peptide (T9) showed inhibitory effects on this mutant PCSK9 form, being also capable to increase liver uptake of low density lipoprotein cholesterol. In this Letter, aiming to improve the potency of this peptide, the T9 residues mainly responsible for the interaction with PCSK9^D374Y (hot spots) were computationally predicted. Then, the "non-hot" residues were suitably substituted by new amino acids capable to theoretically increase the structural complementarity between T9 and PCSK9^D374Y. The outcomes of this study were confirmed by in vitro biochemical assays and cellular investigations, showing that a new T9 analog is able to increase the LDLR expression on the liver cell surface by 84% at the concentration of 10 μM.