HPEPDOCK: a web server for blind peptide-protein docking based on a hierarchical algorithm

In Silico Identification of Peptides with PPARγ Antagonism in Protein Hydrolysate from Rice (Oryza sativa)

At least half the population in industrialized countries suffers from obesity due to excessive accumulation of adipose tissue. Recently, rice (Oryza sativa) proteins have been considered valuable sources of bioactive peptides with antiadipogenic potential. In this study, the digestibility and bioaccessibility in vitro of a novel protein concentrate (NPC) from rice were determined through INFOGEST protocols. Furthermore, the presence of prolamin and glutelin was evaluated via SDS-PAGE, and their potential digestibility and the bioactivity of ligands against peroxisome proliferator-activated receptor gamma (PPARγ) were explored by BIOPEP UWM and HPEPDOCK. For the top candidates, molecular simulations were conducted using Autodock Vina to evaluate their binding affinity against the antiadipogenic region of PPARγ and their pharmacokinetics and drug-likeness using SwissADME. Simulating gastrointestinal digestion showed a recovery of 43.07% and 35.92% bioaccessibility. The protein banding patterns showed the presence of prolamin (57 kDa) and glutelin (12 kDa) as the predominant proteins in the NPC. The in silico hydrolysis predicts the presence of three and two peptide ligands in glutelin and prolamin fraction, respectively, with high affinity for PPARγ (≤160). Finally, the docking studies suggest that the prolamin-derived peptides QSPVF and QPY (−6.38 & −5.61 kcal/mol, respectively) have expected affinity and pharmacokinetic properties to act as potential PPARγ antagonists. Hence, according to our results, bioactive peptides resulting from NPC rice consumption might have an antiadipogenic effect via PPARγ interactions, but further experimentation and validation in suitable biological model systems are necessary to gain more insight and to provide evidence to support our in silico findings.

SARS-CoV-2 envelope protein attain Kac mediated dynamical interaction network to adopt 'histone mimic' at BRD4 interface

Interface mimicry, achieved by recognition of host-pathogen interactions, is the basis by which pathogen proteins can hijack the host machinery. The envelope (E) protein of SARS-CoV-2 is reported to mimic the histones at the BRD4 surface via establishing the structural mimicry; however, the underlying mechanism of E protein mimicking the histones is still elusive. To explore the mimics at dynamic and structural residual network level an extensive docking, and MD simulations were carried out in a comparative manner between complexes of H3-, H4-, E-, and apo-BRD4. We identified that E peptide is able to attain an 'interaction network mimicry', as its acetylated lysine (Kac) achieves orientation and residual fingerprint similar to histones, including water-mediated interactions for both the Kac positions. We identified Y59 of E, playing an anchor role to escort lysine positioning inside the binding site. Furthermore, the binding site analysis confirms that E peptide needs a higher volume, similar to the H4-BRD4 where both the lysine's (Kac5 and Kac8) can accommodate nicely, however, the position of Kac8 is mimicked by two additional water molecules other than four water-mediated bridging's, strengthening the possibility that E peptide could hijack host BRD4 surface. These molecular insights seem pivotal for mechanistic understanding and BRD4-specific therapeutic intervention. KEY POINTSMolecular mimicry is reported in hijacking and then outcompeting the host counterparts so that pathogens can rewire their cellular function by overcoming the host defense mechanism.The molecular recognition process is the basis of molecular mimicry. The E peptide of SARS-CoV-2 is reported to mimic host histone at the BRD4 surface by utilizing its C-terminally placed acetylated lysine (Kac63) to mimic the N-terminally placed acetylated lysine Kac5GGKac8 histone (H4) by interaction network mimicry identified through microsecond molecular dynamics (MD) simulations and post-processing extensive analysis.There are two steps to mimic: firstly, tyrosine residues help E to anchor at the BRD4 surface to position Kac and increase the volume of the pocket. Secondary, after positioning of Kac, a common durable interaction network N140:Kac5; Kac5:W1; W1:Y97; W1:W2; W2:W3; W3:W4; W4:P82 is established between Kac5, with key residues P82, Y97, N140, and four water molecules through water mediate bridge. Furthermore, the second acetylated lysine Kac8 position and its interaction as polar contact with Kac5 were also mimicked by E peptide through interaction network P82:W5; W5:Kac63; W5:W6; W6:Kac63.The binding event at BRD4/BD1 seems an induced-fit mechanism as a bigger binding site volume was identified at H4-BRD4 on which E peptide attains its better stability than H3-BRD4.We identified the tyrosine residue Y59 of E that acts like an anchor on the BRD4 surface to position Kac inside the pocket and attain the interaction network by using aromatic residues of the BRD4 surface.Communicated by Ramaswamy H. Sarma.

Screening of EWI-2-Derived Peptides for Targeting Tetraspanin CD81 and Their Effect on Cancer Cell Migration

CD81, a transmembrane protein belonging to the tetraspanin family, has recently been suggested as a therapeutic target for cancers. Here, we screened peptides that bind to the tetraspanin CD81 protein, and evaluated their inhibitory activity in cancer cell migration. To screen for CD81-binding peptides (CD81-BP), a peptide array membrane was prepared from the amino acid sequence of the EWI-2 protein, a major partner of CD81, before binding to fluorescently labeled CD81. As a result, four candidate CD81-BPs were identified and characterized. In particular, the CFMKRLRK peptide (called P152 in this study) was found to be the best candidate that preferentially binds to the extracellular loop of CD81, with an estimated dissociation constant of 0.91 µM. Since CD81 was reported to promote cancer cell migration, an initial step in metastasis, the Boyden chamber assay, was next performed to assess the effect of CD81-BP candidates on the migration of MDA-MB-231 human breast cancer cells. Interestingly, our result indicated that P152 could suppress MDA-MB-231 cell migration at the level comparable to that of an anti-human CD81 antibody (5A6). Thus, we propose these CD81-BPs with the anti-migration property against cancer cells for the development of novel therapeutic strategies.

Simultaneous control of infection and inflammation with keratin-derived antibacterial peptides targeting TLRs and co-receptors

Controlling infection-driven inflammation is a major clinical dilemma because of limited therapeutic options and possible adverse effects on microbial clearance. Compounding this difficulty is the continued emergence of drug-resistant bacteria, where experimental strategies aiming to augment inflammatory responses for enhanced microbial killing are not applicable treatment options for infections of vulnerable organs. As with corneal infections, severe or prolonged inflammation jeopardizes corneal transparency, leading to devastating vision loss. We hypothesized that keratin 6a-derived antimicrobial peptides (KAMPs) may be a two-pronged remedy capable of tackling bacterial infection and inflammation at once. We used murine peritoneal neutrophils and macrophages, together with an in vivo model of sterile corneal inflammation, to find that nontoxic and prohealing KAMPs with natural 10- and 18-amino acid sequences suppressed lipoteichoic acid (LTA)- and lipopolysaccharide (LPS)-induced NFκB and IRF3 activation, proinflammatory cytokine production, and phagocyte recruitment independently of their bactericidal function. Mechanistically, KAMPs not only competed with bacterial ligands for cell surface Toll-like receptor (TLR) and co-receptors (MD2, CD14, and TLR2) but also reduced cell surface availability of TLR2 and TLR4 through promotion of receptor endocytosis. Topical KAMP treatment effectively alleviated experimental bacterial keratitis, as evidenced by substantial reductions of corneal opacification, inflammatory cell infiltration, and bacterial burden. These findings reveal the TLR-targeting activities of KAMPs and demonstrate their therapeutic potential as a multifunctional drug for managing infectious inflammatory disease.

In-depth peptidomic profile and molecular simulation studies on ACE-inhibitory peptides derived from probiotic fermented milk of different farm animals

Investigations into ACE inhibitory properties of probiotic fermented bovine, camel, goat, and sheep milk were performed and studied for two weeks of refrigerated storage. Results from the degree of proteolysis suggested higher susceptibility of goat milk proteins, followed by sheep and camel milk proteins, to the probiotic-mediated proteolysis. ACE-inhibitory properties displayed continuous decline in ACE-IC₅₀ values for two weeks of refrigerated storage. Overall, goat milk fermented with Pediococcus pentosaceus caused maximum ACE inhibition (IC₅₀: 262.7 µg/mL protein equivalent), followed by camel milk (IC₅₀: 290.9 µg/mL protein equivalent). Studies related to peptide identification and in silico analysis using HPEPDOCK score revealed presence of 11, 13, 9 and 9 peptides in fermented bovine, goat, sheep, and camel milk, respectively, with potent antihypertensive potential. The results obtained suggest that the goat and camel milk proteins demonstrated higher potential for generating antihypertensive peptides via fermentation when compared to bovine and sheep milk.

Systematic analysis and comparison of peptide specificity and selectivity between their cognate receptors and noncognate decoys

Protein-peptide interactions (PpIs) play an important role in cell signaling networks and have been exploited as new and attractive therapeutic targets. The affinity and specificity are two unity-of-opposite aspects of PpIs (and other biomolecular interactions); the former indicates the absolute binding strength between the peptide ligand and its cognate protein receptor in a PpI, while the latter represents the relative recognition selectivity of the peptide ligand for its cognate protein receptor in a PpI over those noncognate decoys that could be potentially encountered by the peptide in cell. Although the PpI binding affinity has been widely investigated over the past decades, the peptide recognition specificity (and selectivity) still remains largely unexplored to date. In this study, we classified PpI specificity into three types: (i) class-I specificity: peptide selectivity for its cognate wild-type protein receptor over the noncognate mutant decoys of this receptor, (ii) class-II specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are homologous with this receptor, and (iii) class-III specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are the cognate receptors of other peptides. We performed affinity and selectivity analysis for the three types of PpI specificity and revealed that the PpIs generally exhibit a moderate or modest specificity; peptide selectivity increases in the order: class-I < class-II < class-III. All the three types of PpI specificity were observed to have no statistically significant correlation with peptide length and hydrophobicity, but the class-I and class-II specificities can be influenced considerably by peptide secondary structures; the high specificity is preferentially associated with ordered structure types as compared to undefined structure types. In addition, the mutation distribution (for class-I specificity), sequence conservation (for class-II specificity), and structural similarity (for class-III specificity) seem also to address effects on peptide selectivity.

Computational approaches for the design of modulators targeting protein-protein interactions

BACKGROUND

Protein-protein interactions (PPIs) are intriguing targets for designing novel small-molecule inhibitors. The role of PPIs in various infectious and neurodegenerative disorders makes them potential therapeutic targets . Despite being portrayed as undruggable targets, due to their flat surfaces, disorderedness, and lack of grooves. Recent progresses in computational biology have led researchers to reconsider PPIs in drug discovery.

AREAS COVERED

In this review, we introduce in-silico methods used to identify PPI interfaces and present an in-depth overview of various computational methodologies that are successfully applied to annotate the PPIs. We also discuss several successful case studies that use computational tools to understand PPIs modulation and their key roles in various physiological processes.

EXPERT OPINION

Computational methods face challenges due to the inherent flexibility of proteins, which makes them expensive, and result in the use of rigid models. This problem becomes more significant in PPIs due to their flexible and flat interfaces. Computational methods like molecular dynamics (MD) simulation and machine learning can integrate the chemical structure data into biochemical and can be used for target identification and modulation. These computational methodologies have been crucial in understanding the structure of PPIs, designing PPI modulators, discovering new drug targets, and predicting treatment outcomes.

Peptide deregulated in hypertrophic scar-1 alleviates hypertrophic scar fibrosis by targeting focal adhesion kinase and pyruvate kinase M2 and remodeling the metabolic landscape

Hypertrophic scarring is a fibrotic skin disease characterized by excessive deposition of collagens. Emerging evidence has suggested important roles for peptides in fibrosis-related diseases. Here, we demonstrate that a skin-derived endogenous peptide, peptide deregulated in hypertrophic scar-1 (PDHS1), with the sequence IATTTASAATAAAIGATPRAK, inhibits cell proliferation, promotes apoptosis, decreases the proportion of cells in S phase, and decreases collagen synthesis in hypertrophic scar fibroblasts. Additionally, treatment with PDHPS1 alleviates hypertrophic scarring in a rabbit ear model. PDHPS1 was found to bind to focal adhesion kinase (FAK) and to decrease its activity. PDHPS1 was also shown to bind to pyruvate kinase M2 (PKM2) and to decreased its expression. Smad2 phosphorylation is also inhibited by treatment with PDHPS1. Overexpression of FAK rescues the decreased expression of COL3A1 induced by PDHPS1 treatment. Targeted metabolomics revealed that PDHPS1 reprogramed metabolism that related to amino acid synthesis, leading to decreases of the key glycolysis intermediates glucose-6-phosphate and fructose-6-phosphate. These results demonstrated that the endogenous peptide PDHPS1 alleviates hypertrophic scar fibrosis in vitro and in vivo by targeting FAK and PKM2 and remodeling the metabolic landscape. Overall, treatment with PDHPS1 is a potential therapeutic strategy for hypertrophic scarring.

Application of Molecular Simulation Methods in Food Science: Status and Prospects

Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.

The SWIB/MDM2 motif of UBE4B activates the p53 pathway

The tumor suppressor p53 plays a critical role in cancer pathogenesis, and regulation of p53 expression is essential for maintaining normal cell growth. UBE4B is an E3/E4 ubiquitin ligase involved in a negative-feedback loop with p53. UBE4B is required for Hdm2-mediated p53 polyubiquitination and degradation. Thus, targeting the p53-UBE4B interactions is a promising anticancer strategy for cancer therapy. In this study, we confirm that while the UBE4B U box does not bind to p53, it is essential for the degradation of p53 and acts in a dominant-negative manner, thereby stabilizing p53. C-terminal UBE4B mutants lose their ability to degrade p53. Notably, we identified one SWIB/Hdm2 motif of UBE4B that is vital for p53 binding. Furthermore, the novel UBE4B peptide activates p53 functions, including p53-dependent transactivation and growth inhibition, by blocking the p53-UBE4B interactions. Our findings indicate that targeting the p53-UBE4B interaction presents a novel approach for p53 activation therapy in cancer.

Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database

Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.

Targeting KRAS-mutant stomach/colorectal tumors by disrupting the ERK2-p53 complex

KRAS is widely mutated in human cancers, resulting in unchecked tumor proliferation and metastasis, which makes identifying KRAS-targeting therapies a priority. Herein, we observe that mutant KRAS specifically promotes the formation of the ERK2-p53 complex in stomach/colorectal tumor cells. Disruption of this complex by applying MEK1/2 and ERK2 inhibitors elicits strong apoptotic responses in a p53-dependent manner, validated by genome-wide knockout screening. Mechanistically, p53 physically associates with phosphorylated ERK2 through a hydrophobic interaction in the presence of mutant KRAS, which suppresses p53 activation by preventing the recruitment of p300/CBP; trametinib disrupts the ERK2-p53 complex by reducing ERK2 phosphorylation, allowing the acetylation of p53 protein by recruiting p300/CBP; acetylated p53 activates PUMA transcription and thereby kills KRAS-mutant tumors. Our study shows an important role for the ERK2-p53 complex and provides a potential therapeutic strategy for treating KRAS-mutant cancer.

HCovDock: an efficient docking method for modeling covalent protein-ligand interactions

Covalent inhibitors have received extensive attentions in the past few decades because of their long residence time, high binding efficiency and strong selectivity. Therefore, it is valuable to develop computational tools like molecular docking for modeling of covalent protein-ligand interactions or screening of potential covalent drugs. Meeting the needs, we have proposed HCovDock, an efficient docking algorithm for covalent protein-ligand interactions by integrating a ligand sampling method of incremental construction and a scoring function with covalent bond-based energy. Tested on a benchmark containing 207 diverse protein-ligand complexes, HCovDock exhibits a significantly better performance than seven other state-of-the-art covalent docking programs (AutoDock, Cov_DOX, CovDock, FITTED, GOLD, ICM-Pro and MOE). With the criterion of ligand root-mean-squared distance < 2.0 Å, HCovDock obtains a high success rate of 70.5% and 93.2% in reproducing experimentally observed structures for top 1 and top 10 predictions. In addition, HCovDock is also validated in virtual screening against 10 receptors of three proteins. HCovDock is computationally efficient and the average running time for docking a ligand is only 5 min with as fast as 1 sec for ligands with one rotatable bond and about 18 min for ligands with 23 rotational bonds. HCovDock can be freely assessed at http://huanglab.phys.hust.edu.cn/hcovdock/.

Analysis of critical protein-protein interactions of SARS-CoV-2 capping and proofreading molecular machineries towards designing dual target inhibitory peptides

In recent years, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as the cause of the coronavirus disease (COVID-19) global pandemic, and its variants, especially those with higher transmissibility and substantial immune evasion, have highlighted the imperative for developing novel therapeutics as sustainable solutions other than vaccination to combat coronaviruses (CoVs). Beside receptor recognition and virus entry, members of the SARS-CoV-2 replication/transcription complex are promising targets for designing antivirals. Here, the interacting residues that mediate protein-protein interactions (PPIs) of nsp10 with nsp16 and nsp14 were comprehensively analyzed, and the key residues' interaction maps, interaction energies, structural networks, and dynamics were investigated. Nsp10 stimulates both nsp14's exoribonuclease (ExoN) and nsp16's 2'O-methyltransferase (2'O-MTase). Nsp14 ExoN is an RNA proofreading enzyme that supports replication fidelity. Nsp16 2'O-MTase is responsible for the completion of RNA capping to ensure efficient replication and translation and escape from the host cell's innate immune system. The results of the PPIs analysis proposed crucial information with implications for designing SARS-CoV-2 antiviral drugs. Based on the predicted shared protein-protein interfaces of the nsp16-nsp10 and nsp14-nsp10 interactions, a set of dual-target peptide inhibitors was designed. The designed peptides were evaluated by molecular docking, peptide-protein interaction analysis, and free energy calculations, and then further optimized by in silico saturation mutagenesis. Based on the predicted evolutionary conservation of the interacted target residues among CoVs, the designed peptides have the potential to be developed as dual target pan-coronavirus inhibitors.

Identification of a peptide ligand for human ALDH3A1 through peptide phage display: Prediction and characterization of protein interaction sites and inhibition of ALDH3A1 enzymatic activity

Aldehyde dehydrogenase 3A1 (ALDH3A1) by oxidizing medium chain aldehydes to their corresponding carboxylic acids, is involved in the detoxification of toxic byproducts and is considered to play an important role in antioxidant cellular defense. ALDH3A1 has been implicated in various other functions such as cell proliferation, cell cycle regulation, and DNA damage response. Recently, it has been identified as a putative biomarker of prostate, gastric, and lung cancer stem cell phenotype. Although ALDH3A1 has multifaceted functions in both normal and cancer homeostasis, its modes of action are currently unknown. To this end, we utilized a random 12-mer peptide phage display library to identify efficiently human ALDH3A1-interacting peptides. One prevailing peptide (P1) was systematically demonstrated to interact with the protein of interest, which was further validated in vitro by peptide ELISA. Bioinformatic analysis indicated two putative P1 binding sites on the protein surface implying biomedical potential and potent inhibitory activity of the P1 peptide on hALDH3A1 activity was demonstrated by enzymatic studies. Furthermore, in search of potential hALDH3A1 interacting players, a BLASTp search demonstrated that no protein in the database includes the full-length amino acid sequence of P1, but identified a list of proteins containing parts of the P1 sequence, which may prove potential hALDH3A1 interacting partners. Among them, Protein Kinase C Binding Protein 1 and General Transcription Factor II-I are candidates of high interest due to their cellular localization and function. To conclude, this study identifies a novel peptide with potential biomedical applications and further suggests a list of protein candidates be explored as possible hALDH3A1-interacting partners in future studies.

Sequence alterations affect the antidiabetic attributes of hazelnut peptide fractions during the industrial manufacture and simulated digestion of hazelnut paste

Press cakes are by-products of cold press oil manufacture and are characterized by significant protein concentrations. Our group has previously demonstrated potential bioactive attributes of hazelnut protein hydrolysates including their antidiabetic activities. Here, an effort was made to utilize DPP-IV (Dipeptidyl peptidase-IV)-inhibitory hazelnut peptides in industrial food manufacture. Hazelnut protein isolates (approx. 95% protein) were obtained via an alkali extraction-isoelectric precipitation method. Papain, bromelain and pepsin were used in the enzymatic hydrolysis and hydrolysates were fractionated via Fast Protein Liquid Chromatography. As a general observation, although fractionation lead to dilution of the samples, fractions were observed to be more bioactive than the total hydrolysates. In vitro antidiabetic activities of the fractions were tested and 3 antidiabetic fractions were added to hazelnut paste. Afterwards simulated gastrointestinal digestion and antidiabetic activity assays were performed. DPP-IV inhibition was the major antidiabetic mechanism in the fractions and digested paste, while some fractions were characterized by comparable IC50 values as the positive controls. Alpha-glucosidase inhibition was limited by digestion trials, whereas alpha-amylase inhibition was only slight in the digested paste (< %6). In silico analyses predicted partial degradation of the peptides, whereas the interactions between DPP-IV or alpha-glucosidase and hazelnut peptides were predicted to be significant (p < 0.05). Consequently hazelnut press cakes were regarded as a potential source of antidiabetic peptides that can be used in industrial manufacture of functional foods, while food processing conditions or gastrointestinal digestion could largely affect peptide bioactivity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05601-2.

AMPA GluA2 subunit competitive inhibitors for PICK1 PDZ domain: Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and ADME studies

PICK1 (Protein interacting with C kinase-1) plays a key role in the regulation of intracellular trafficking of AMPA GluA2 subunit that is linked with synaptic plasticity. PICK1 is a scaffolding protein and binds numerous proteins through its PDZ domain. Research showed that synaptic plasticity is altered upon disrupting the GluA2-PDZ interactions. Inhibiting PDZ and GluA2 binding lead to beneficial effects in the cure of neurological diseases thus, targeting PDZ domain is proposed as a novel therapeutic target in such diseases. For this, various classes of synthetic peptides were tested. Though small organic molecules have been utilized to prevent these interactions, the number of such molecules is inadequate. Hence, in this study, ten molecular libraries containing large number of molecules were screened against the PDZ domain using pharmacophore-based virtual screening to find the best hits for the PDZ domain. Molecular docking and molecular dynamics simulation studies revealed that Hit_II is a potent inhibitor for the PDZ domain and confirm the allosteric nature of Hit_III. Additionally, ADME analysis suggests the drug-likeness of both Hit_II and Hit_III. This study suggests that tested hits may have potency against the PDZ domain and can be considered effective to treat neurological disorders.Communicated by Ramaswamy H. Sarma.

Detection of the peptidyl epitope for vaccine development against MPV

Background

Monkeypox Virus (MPV) is the cause of zoonotic disease characterized by skin-eruption with pus cell formation and lymphadenopathy. This virus belongs to the Orthopoxvirus genus with DNA as its genetic material. Previously, this infection was reported from Africa and occasionally from USA and UK. However, recently there is a sudden surge of infection in non-epidemic countries and a new strain of MPVhas been discovered. Therefore it is important to revisit the phylogeny of MPV with the addition of new strains. Recently WHO also stressed the need of developing vaccines for new strains. In this scenario we have two objectives for this study -first, to reveal the exact phylogenetic position of the 2022 strain and second, to identify specific peptides which may be used for vaccine development in the future.

Methods

The phylogenetic analysis was done with the help of Bayesian phylogeny. The dN/dS calculation was performed based on DNA polymerase genes of selected MPV strains. The peptidyl-epitope was searched in MPV2022/2 SLO strain with the help of several algorithms implemented in Allergen FP v.1.0, NetMHCII 2.3, MHCpred and Toxin Pred. The structure prediction of the proteins and peptides was performed through Hpepdock. The quality of the structures was validated through the Ramachandran plot. The molecular dynamics and simulation were performed through Gromacs software. The interaction between peptide and protein was assessed through Ligplot software.

Results

The phylogenetic analysis revealed that the considered 2022 MPVstrains were close to the USA strains. The evolutionary analysis showed the volatile nature of the genome. Moreover, 9-mer peptide sequence was identified as an epitope for vaccine development.

Conclusions

The emergence of more virulent strains in near future may not be ruled out. Immunocompromised patients are more susceptible to this virus hence sub-unit vaccine is a better choice than a recombinant or attenuated vaccine against monkeypox. We have identified a small stretch of specific peptide which may be used for developing a subunit vaccine against this virus.

Rational Discovery of Microtubule-Stabilizing Peptides

Microtubule (MT) stabilization is an attractive pharmacological strategy to hamper the progress of neurodegenerative diseases. In this regard, seeking peptides with MT-stabilizing properties has awoken great interest. This work reports the rational discovery of two structurally related MT-stabilizing octapeptides using a combination of protein-peptide docking, conventional molecular dynamics, Gaussian accelerated molecular dynamics (GaMD), and tubulin polymerization assays. FASTA sequences for ∼1000 peptides were crafted from single and double mutants of davunetide (NAP) and docked against the Taxol (TX) site on an octameric MT model representing a portion of the MT wall. Docked peptides were rescored after MM minimization and binding free energy refinement through single-point MM/GBSA calculations. The 60 best-ranked peptides were subjected to 50 ns MD simulations on peptide-MT complexes at the terminal TX site in the octameric Tau-MT model resulting in 11 complexes with occupancies greater than 99% and peptide-protein binding free energies less than -40 kcal/mol. Selected peptides were then examined through 300 ns GaMD simulations in complexes containing two identical ligands at the terminal and intermediate TX sites in the Tau-MT model to account for the differential association of MT-binding peptides to different regions of the MT structure. Six candidates showed a favorable MT-binding potential based on the analysis of interaction frequencies and relative mobilities of the complex components, suggesting a pivotal role of Arg278, Gln281, and Arg369 residues for peptides recognition. Four candidates were predicted to preserve an adequate balance of longitudinal and lateral interactions between tubulin dimers in peptide-MT complexes such that MT-stabilizing effects could be expected. MT polymerization experiments confirmed that four peptides (HAPVSIHQ, NYPVSIHQ, NWPVSIWQ, HAPVSIIQ) exhibit MT-stabilizing activity in vitro with NWPVSIWQ (P43) and HAPVSIIQ (P52) being the most active. Tryptophan quenching assays verified that P43 and P52 bind to nonpolymeric tubulin, whereas viability experiments on HEK cells confirmed their safety to pursue future pharmacological studies. The results herein presented are valuable to making progress in the rational design of MT-stabilizing peptides.

Computer-Aided Screening for Potential Coronavirus 3-Chymotrypsin-like Protease (3CLpro) Inhibitory Peptides from Putative Hemp Seed Trypsinized Peptidome

To control the COVID-19 pandemic, antivirals that specifically target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently required. The 3-chymotrypsin-like protease (3CLpro) is a promising drug target since it functions as a catalytic dyad in hydrolyzing polyprotein during the viral life cycle. Bioactive peptides, especially food-derived peptides, have a variety of functional activities, including antiviral activity, and also have a potential therapeutic effect against COVID-19. In this study, the hemp seed trypsinized peptidome was subjected to computer-aided screening against the 3CLpro of SARS-CoV-2. Using predictive trypsinized products of the five major proteins in hemp seed (i.e., edestin 1, edestin 2, edestin 3, albumin, and vicilin), the putative hydrolyzed peptidome was established and used as the input dataset. To select the Cannabis sativa antiviral peptides (csAVPs), a predictive bioinformatic analysis was performed by three webserver screening programs: iAMPpred, AVPpred, and Meta-iAVP. The amino acid composition profile comparison was performed by COPid to screen for the non-toxic and non-allergenic candidates, ToxinPred and AllerTOP and AllergenFP, respectively. GalaxyPepDock and HPEPDOCK were employed to perform the molecular docking of all selected csAVPs to the 3CLpro of SARS-CoV-2. Only the top docking-scored candidate (csAVP4) was further analyzed by molecular dynamics simulation for 150 nanoseconds. Molecular docking and molecular dynamics revealed the potential ability and stability of csAVP4 to inhibit the 3CLpro catalytic domain with hydrogen bond formation in domain 2 with short bonding distances. In addition, these top ten candidate bioactive peptides contained hydrophilic amino acid residues and exhibited a positive net charge. We hope that our results may guide the future development of alternative therapeutics against COVID-19.

Polypharmacological Cell-Penetrating Peptides from Venomous Marine Animals Based on Immunomodulating, Antimicrobial, and Anticancer Properties

Complex pathological diseases, such as cancer, infection, and Alzheimer's, need to be targeted by multipronged curative. Various omics technologies, with a high rate of data generation, demand artificial intelligence to translate these data into druggable targets. In this study, 82 marine venomous animal species were retrieved, and 3505 cryptic cell-penetrating peptides (CPPs) were identified in their toxins. A total of 279 safe peptides were further analyzed for antimicrobial, anticancer, and immunomodulatory characteristics. Protease-resistant CPPs with endosomal-escape ability in Hydrophis hardwickii, nuclear-localizing peptides in Scorpaena plumieri, and mitochondrial-targeting peptides from Synanceia horrida were suitable for compartmental drug delivery. A broad-spectrum S. horrida-derived antimicrobial peptide with a high binding-affinity to bacterial membranes was an antigen-presenting cell (APC) stimulator that primes cytokine release and naïve T-cell maturation simultaneously. While antibiofilm and wound-healing peptides were detected in Synanceia verrucosa, APC epitopes as universal adjuvants for antiviral vaccination were in Pterois volitans and Conus monile. Conus pennaceus-derived anticancer peptides showed antiangiogenic and IL-2-inducing properties with moderate BBB-permeation and were defined to be a tumor-homing peptide (THP) with the ability to inhibit programmed death ligand-1 (PDL-1). Isoforms of RGD-containing peptides with innate antiangiogenic characteristics were in Conus tessulatus for tumor targeting. Inhibitors of neuropilin-1 in C. pennaceus are proposed for imaging probes or therapeutic delivery. A Conus betulinus cryptic peptide, with BBB-permeation, mitochondrial-targeting, and antioxidant capacity, was a stimulator of anti-inflammatory cytokines and non-inducer of proinflammation proposed for Alzheimer's. Conclusively, we have considered the dynamic interaction of cells, their microenvironment, and proportional-orchestrating-host- immune pathways by multi-target-directed CPPs resembling single-molecule polypharmacology. This strategy might fill the therapeutic gap in complex resistant disorders and increase the candidates' clinical-translation chance.

Identification of a novel peptide ligand for the cancer-specific receptor mutation EGFRvIII using high-throughput sequencing of phage-selected peptides

We report here the selection and characterization of a novel peptide ligand using phage display targeted against the cancer-specific epidermal growth factor tyrosine kinase receptor mutation variant III (EGFRvIII). This receptor is expressed in several kinds of cancer: ovarian cancer, breast cancer and glioblastoma, but not in normal tissues. A 12-mer random peptide library was screened against EGFRvIII. Phage-selected peptides were sequenced in high-throughput by next generation sequencing (NGS), and their diversity was studied to identify highly abundant clones expected to bind with the highest affinities to EGFRvIII. The enriched peptides were characterized and their binding capacity towards stable cell lines expressing EGFRvIII, EGFR wild type (EGFR WT), or a low endogenous level of EGFR WT was confirmed by flow cytometry analysis. The best peptide candidate, VLGREEWSTSYW, was synthesized, and its binding specificity towards EGFRvIII was validated in vitro. Additionally, computational docking analysis suggested that the identified peptide binds selectively to EGFRvIII. The novel VLGREEWSTSYW peptide is thus a promising EGFRvIII-targeting agent for future applications in cancer diagnosis and therapy.

A peptide array pipeline for the development of Spike-ACE2 interaction inhibitors

In humans, coronaviruses are the cause of endemic illness and have been the causative agents of more severe epidemics. Most recently, SARS-CoV-2 was the causative agent of the COVID19 pandemic. Thus, there is a high interest in developing therapeutic agents targeting various stages of the coronavirus viral life cycle to disrupt viral propagation. Besides the development of small-molecule therapeutics that target viral proteases, there is also interest molecular tools to inhibit the initial event of viral attachment of the SARS-CoV-2 Spike protein to host ACE2 surface receptor. Here, we leveraged known structural information and peptide arrays to develop an in vitro peptide inhibitor of the Spike-ACE2 interaction. First, from previous co-crystal structures of the Spike-ACE2 complex, we identified an initial 24-residue long region (sequence: STIEEQAKTFLDKFNHEAEDLFYQ) on the ACE2 sequence that encompasses most of the known contact residues. Next, we scanned this 24-mer window along the ACE2 N-terminal helix and found that maximal binding to the SARS-CoV-2 receptor binding domain (CoV2-RBD) was increased when this window was shifted nine residues in the N-terminal direction. Further, by systematic permutation of this shifted ACE2-derived peptide we identified mutations to the wildtype sequence that confer increased binding of the CoV2-RBD. Among these peptides, we identified binding peptide 19 (referred to as BP19; sequence: SLVAVTAAQSTIEEQAKTFLDKFI) as an in vitro inhibitor of the Spike-ACE2 interaction with an IC₅₀ of 2.08 ± 0.38 μM. Overall, BP19 adds to the arsenal of Spike-ACE2 inhibitors, and this study highlights the utility of systematic peptide arrays as a platform for the development of coronavirus protein inhibitors.

Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction

While deep learning (DL) has brought a revolution in the protein structure prediction field, still an important question remains how the revolution can be transferred to advances in structure-based drug discovery. Because the lessons from the recent GPCR dock challenge were inconclusive primarily due to the size of the dataset, in this work we further elaborated on 70 diverse GPCR complexes bound to either small molecules or peptides to investigate the best-practice modeling and docking strategies for GPCR drug discovery. From our quantitative analysis, it is shown that substantial improvements in docking and virtual screening have been possible by the advance in DL-based protein structure predictions with respect to the expected results from the combination of best pre-DL tools. The success rate of docking on DL-based model structures approaches that of cross-docking on experimental structures, showing over 30% improvement from the best pre-DL protocols. This amount of performance could be achieved only when two modeling points were considered properly: 1) correct functional-state modeling of receptors and 2) receptor-flexible docking. Best-practice modeling strategies and the model confidence estimation metric suggested in this work may serve as a guideline for future computer-aided GPCR drug discovery scenarios.

Jha P, Lupieri A, Nakano T, Passos LS, Rogers MA, Becker-Greene D, Le TD, Decano JL, Ho Lee L, Guimaraes GC, Abdelhamid I, Halu A, Muscoloni A, V. Cannistraci C, Higashi H, Zhang H, Vromman A, Libby P, Keith Ozaki C, Sharma A, Singh SA, Aikawa E, Aikawa M. Proprotein Convertase Subtilisin/Kexin 9 (PCSK9) Promotes Macrophage Activation via LDL Receptor-Independent Mechanisms

BACKGROUND

Activated macrophages contribute to the pathogenesis of vascular disease. Vein graft failure is a major clinical problem with limited therapeutic options. PCSK9 (proprotein convertase subtilisin/kexin 9) increases low-density lipoprotein (LDL)-cholesterol levels via LDL receptor (LDLR) degradation. The role of PCSK9 in macrophage activation and vein graft failure is largely unknown, especially through LDLR-independent mechanisms. This study aimed to explore a novel mechanism of macrophage activation and vein graft disease induced by circulating PCSK9 in an LDLR-independent fashion.

METHODS

We used Ldlr^-/- mice to examine the LDLR-independent roles of circulating PCSK9 in experimental vein grafts. Adeno-associated virus (AAV) vector encoding a gain-of-function mutant of PCSK9 (rAAV8/D377Y-mPCSK9) induced hepatic PCSK9 overproduction. To explore novel inflammatory targets of PCSK9, we used systems biology in Ldlr^-/- mouse macrophages.

RESULTS

In Ldlr^-/- mice, AAV-PCSK9 increased circulating PCSK9, but did not change serum cholesterol and triglyceride levels. AAV-PCSK9 promoted vein graft lesion development when compared with control AAV. In vivo molecular imaging revealed that AAV-PCSK9 increased macrophage accumulation and matrix metalloproteinase activity associated with decreased fibrillar collagen, a molecular determinant of atherosclerotic plaque stability. AAV-PCSK9 induced mRNA expression of the pro-inflammatory mediators IL-1β (interleukin-1 beta), TNFα (tumor necrosis factor alpha), and MCP-1 (monocyte chemoattractant protein-1) in peritoneal macrophages underpinned by an in vitro analysis of Ldlr^-/- mouse macrophages stimulated with endotoxin-free recombinant PCSK9. A combination of unbiased global transcriptomics and new network-based hyperedge entanglement prediction analysis identified the NF-κB (nuclear factor-kappa B) signaling molecules, lectin-like oxidized LOX-1 (LDL receptor-1), and SDC4 (syndecan-4) as potential PCSK9 targets mediating pro-inflammatory responses in macrophages.

CONCLUSIONS

Circulating PCSK9 induces macrophage activation and vein graft lesion development via LDLR-independent mechanisms. PCSK9 may be a potential target for pharmacologic treatment for this unmet medical need.

In Silico Discovery of Anticancer Peptides from Sanghuang

Anticancer peptide (ACP) is a short peptide with less than 50 amino acids that has been discovered in a variety of foods. It has been demonstrated that traditional Chinese medicine or food can help treat cancer in some cases, which suggests that ACP may be one of the therapeutic ingredients. Studies on the anti-cancer properties of Sanghuangporus sanghuang have concentrated on polysaccharides, flavonoids, triterpenoids, etc. The function of peptides has not received much attention. The purpose of this study is to use computer mining techniques to search for potential anticancer peptides from 62 proteins of Sanghuang. We used mACPpred to perform sequence scans after theoretical trypsin hydrolysis and discovered nine fragments with an anticancer probability of over 0.60. The study used AlphaFold 2 to perform structural modeling of the first three ACPs discovered, which had blast results from the Cancer PPD database. Using reverse docking technology, we found the target proteins and interacting residues of two ACPs with an unknown mechanism. Reverse docking results predicted the binding modes of the ACPs and their target protein. In addition, we determined the active part of ACPs by quantum chemical calculation. Our study provides a framework for the future discovery of functional peptides from foods. The ACPs discovered have the potential to be used as drugs in oncology clinical treatment after further research.

Human Claudin-Derived Peptides Block the Membrane Fusion Process of Zika Virus and Are Broad Flavivirus Inhibitors

Zika virus (ZIKV) is a mosquito-borne flavivirus that emerged in the Pacific islands in 2007 and spread to the Americas in 2015. The infection remains asymptomatic in most cases but can be associated with severe neurological disorders. Despite massive efforts, no specific drug or vaccine against ZIKV infection is available to date. Claudins are tight-junction proteins that favor the entry of several flaviviruses, including ZIKV. In this study, we identified two peptides derived from the N-terminal sequences of claudin-7 and claudin-1, named CL7.1 and CL1.1, respectively, that inhibited ZIKV infection in a panel of human cell lines. Using cell-to-cell fusion assays, we demonstrated that these peptides blocked the ZIKV E-mediated membrane fusion. A comparison of the antiviral efficacy of CL1.1 and CL7.1 pointed to the importance of the peptide amphipathicity. Electron microscopic analysis revealed that CL1.1 altered the ultrastructure of the viral particles likely by binding the virus lipid envelope. However, amphipathicity could not fully explain the antiviral activity of CL1.1. In silico docking simulations suggested that CL1.1 may also interact with the E protein, near its stem region. Overall, our data suggested that claudin-derived peptides inhibition may be linked to simultaneous interaction with the E protein and the viral lipid envelope. Finally, we found that CL1.1 also blocked infection by yellow fever and Japanese encephalitis viruses but not by HIV-1 or SARS-CoV-2. Our results provide a basis for the future development of therapeutics against a wide range of endemic and emerging flaviviruses. IMPORTANCE Zika virus (ZIKV) is a flavivirus transmitted by mosquito bites that have spread to the Pacific Islands and the Americas over the past decade. The infection remains asymptomatic in most cases but can cause severe neurological disorders. ZIKV is a major public health threat in areas of endemicity, and there is currently no specific antiviral drug or vaccine available. We identified two antiviral peptides deriving from the N-terminal sequences of claudin-7 and claudin-1 with the latter being the most effective. These peptides block the envelope-mediated membrane fusion. Our data suggested that the inhibition was likely achieved by simultaneously interacting with the viral lipid envelope and the E protein. The peptides also inhibited other flaviviruses. These results could provide the basis for the development of therapies that might target a wide array of flaviviruses from current epidemics and possibly future emergences.

In vitro inhibition of acetylcholinesterase activity by yellow field pea (Pisum sativum) protein-derived peptides as revealed by kinetics and molecular docking

Compounds with structural similarities to the neurotransmitter (acetylcholine) are mostly used to inhibit the activity of acetylcholinesterase (AChE) in Alzheimer’s disease (AD) therapy. However, the existing drugs only alleviate symptoms of moderate to mild conditions and come with side effects; hence, the search is still on for potent and safer options. In this study, High performance liquid chromatography (HPLC) fractionations of AChE-inhibitory pea protein hydrolysates obtained from alcalase, flavourzyme and pepsin digestions were carried out followed by sequence identification of the most active fractions using mass spectrometry. Subsequently, 20 novel peptide sequences identified from the active fractions were synthesized and five peptides, QSQS, LQHNA, SQSRS, ETRSQ, PQDER (IC₅₀ = 1.53 – 1.61 μg/mL) were selected and analyzed for ability to change AChE protein conformation (fluorescence emission and circular dichroism), kinetics of enzyme inhibition, and enzyme-ligand binding configurations using molecular docking. The kinetics studies revealed different inhibition modes by the peptides with relatively low (<0.02 mM and <0.1 mM) inhibition constant and Michaelis constant, respectively, while maximum velocity was reduced. Conformational changes were confirmed by losses in fluorescence intensity and reduced α-helix content of AChE after interactions with different peptides. Molecular docking revealed binding of the peptides to both the catalytic anionic site and the peripheral anionic site. The five analyzed peptides all contained glutamine (Q) but sequences with Q in the penultimate N-terminal position (LQHNA, SQSRS, and PQDER) had stronger binding affinity. Results from the different analysis in this study confirm that the peptides obtained from enzymatic digestion of pea protein possess the potential to be used as novel AChE-inhibitory agents in AD management.

Preparation, In Vitro Affinity, and In Vivo Biodistribution of Receptor-Specific 68Ga-Labeled Peptides Targeting Vascular Endothelial Growth Factor Receptors

As angiogenesis plays a key role in tumor growth and metastasis, the angiogenic process has attracted scientific interest as a target for diagnostic and therapeutic agents. Factors influencing angiogenesis include the vascular endothelial growth factor (VEGF) family and the two associated receptor types (VEGFR-1 and VEGFR-2). VEGFR-1/-2 detection and quantification in cancer lesions are essential for tumor process management. As a result of the advantageous pharmacokinetics and image contrast, peptides radiolabeled with PET emitters have become interesting tools for the visualization of VEGFR-1/-2-positive tumors. In this study, we prepared ⁶⁸Ga-labeled peptides containing 15 (peptide 1) and 23 (peptide 2) amino acids as new PET tracers for tumor angiogenic process imaging.

METHODS

The peptides were conjugated with NODAGA-tris(t-Bu ester) and subsequently radiolabeled with [⁶⁸Ga]Ga-chloride. The prepared [⁶⁸Ga]Ga-NODAGA-peptide 1 and [⁶⁸Ga]Ga-NODAGA-peptide 2 were tested for radiochemical purity and saline/plasma stability. Consequently, the binding affinity toward VEGFRs was assessed in vitro on human glioblastoma and kidney carcinoma cells. The found peptide receptor affinity was compared with the calculated values in the PROtein binDIng enerGY prediction (PRODIGY) server. Finally, the biodistribution study was performed on BALB/c female mice to reveal the basic pharmacokinetic behavior of radiopeptides.

RESULTS

The in vitro affinity testing of [⁶⁸Ga]Ga-NODAGA-peptides 1 and 2 showed retained receptor binding as characterized by equilibrium dissociation constant (K_D) values in the range of 0.5-1.2 μM and inhibitory concentration 50% (IC₅₀) values in the range of 3.0-5.6 μM. Better binding properties of peptide 2 to VEGFR-1/-2 were found in the PRODIGY server. The biodistribution study on mice showed remarkable accumulation of both peptides in the kidneys and urinary bladder with a short half-life after intravenous application. The in vitro plasma stability of [⁶⁸Ga]Ga-NODAGA-peptide 2 was superior to that of [⁶⁸Ga]Ga-NODAGA-peptide 1.

CONCLUSIONS

The obtained results demonstrated a high radiolabeling yield with no need for purification and preserved binding potency of ⁶⁸Ga-labeled peptides 1 and 2 toward VEGFRs in cancer cells. The peptide-receptor protein interaction assessed in protein-peptide docking determined the strongest interaction of peptide 2 with domain 2 of VEGFR-2 in addition to a more acceptable plasma stability (t_1/2 = 120 min) than that for peptide 1. We found both radiolabeled peptides very potent in their receptor binding, which makes them suitable imaging agents. The rapid transition of the radiopeptides into the urinary tract indicates suitable pharmacokinetic characteristics.

In Silico Identification of Potential Insect Peptides against Biofilm-Producing Staphylococcus aureus

Biofilm-producing Staphylococcus aureus (SA) strains are frequently found in medical environments, from surgical/ wound sites, medical devices. These biofilms reduce the efficacy of applied antibiotics during the treatment of several infections, such as cystic fibrosis, endocarditis, or urinary tract infections. Thus, the development of potential therapeutic agents to destroy the extra protective biofilm layers or to inhibit the biofilm-producing enzymes is urgently needed. Advanced and cost-effective bioinformatics tools are advantageous in locating and speeding up the selection of antibiofilm candidates. Based on the potential drug characteristics, we have selected one-hundred thirty-three antibacterial peptides derived from insects to assess for their antibiofilm potency via molecular docking against five putative biofilm formation and regulated target enzymes: the staphylococcal accessory regulator A or SarA (PDB ID: 2FRH), 4,4'-diapophytoene synthase or CrtM (PDB ID: 2ZCQ), clumping factor A or ClfA (PDB ID: 1N67) and serine-aspartate repeat protein C or SdrC (PDB ID: 6LXH) and sortase A or SrtA (PDB ID: 1T2W) of SA bacterium. In this study, molecular docking was performed using HPEPDOCK and HDOCK servers, and molecular interactions were examined using BIOVIA Discovery Studio Visualizer-2019. The docking score (kcal/mol) range of five promising antibiofilm peptides against five targets was recorded as follows: diptericin A (-215.52 to -303.31), defensin (-201.11 to -301.92), imcroporin (-212.08 to -287.64), mucroporin (-228.72 to -286.76), apidaecin II (-203.90 to -280.20). Among these five, imcroporin and mucroporin were 13 % each, while defensin contained only 1 % of positive net charged residues (Arg+Lys) projected through ProtParam and NetWheels tools. Similarly, imcroporin, mucroporin and apidaecin II were 50 %, while defensin carried 21.05 % of hydrophobic residues predicted by the tool PEPTIDE. 2.0. Most of the peptides exhibited potential characteristics to inhibit S. aureus-biofilm formation via disrupting the cell membrane and cytoplasmic integrity. In summary, the proposed hypothesis can be considered a cost-effective platform for selecting the most promising bioactive drug candidates within a limited timeframe with a greater chance of success in experimental and clinical studies.

Computer-Aided Design of Lasso-like Self-Assembling Anticancer Peptides with Multiple Functions for Targeted Self-Delivery and Cancer Treatments

Anticancer peptides are promising drug candidates for cancer treatment, but the short circulation time and low delivery efficiency limit their clinical applications. Herein, we designed several lasso-like self-assembling anticancer peptides (LASAPs) integrated with multiple functions by a computer-aided approach. Among these LASAPs, LASAP1 (CRGDKGPDCGKAFRRFLGALFKALSHLL, 1-9 disulfide bond) was determined to be superior to the others because it can self-assemble into homogeneous nanoparticles and exhibits improved stability in serum. Thus, LASAP1 was chosen for proving the design idea. LASAP1 can self-assemble into nanoparticles displaying iRGD on the surface because of its amphiphilic structure and accumulate to the tumor site after injection because of the EPR effect and iRGD targeting to αVβ3 integrin. The nanoparticles could disassemble in the acidic microenvironment of the solid tumor, and cleaved by the overexpressed hK2, which was secreted by prostate tumor cells, to release the effector peptide PTP-7b (FLGALFKALSHLL), which was further activated by the acidic pH. Therefore, LASAP1 could target the orthotopic prostate tumor in the model mice after intraperitoneal injection and specifically inhibit tumor growth, with low systematic toxicity. Combining the multiple targeting functions, LASAP1 represents a promising design of self-delivery of peptide drugs for targeted cancer treatments.

Accurate Prediction for Protein-Peptide Binding Based on High-Temperature Molecular Dynamics Simulations

The structural characterization of protein-peptide interactions is fundamental to elucidating biological processes and designing peptide drugs. Molecular dynamics (MD) simulations are extensively used to study biomolecular systems. However, simulating the protein-peptide binding process is usually quite expensive. Based on our previous studies, herein, we propose a simple and effective method to predict the binding site and pose of the peptide simultaneously using high-temperature (high-T) MD simulations with the RSFF2C force field. Thousands of binding events (nonspecific or specific) can be sampled during microseconds of high-T MD. From density-based clustering analysis, the structures of all of the 12 complexes (nine with linear peptides and three with cyclic peptides) can be successfully predicted with root-mean-square deviation (RMSD) < 2.5 Å. By directly simulating the process of the ligand binding onto the receptor, our method approaches experimental precision for the first time, significantly surpassing previous protein-peptide docking methods in terms of accuracy.

Design of Three Residues Peptides against SARS-CoV-2 Infection

The continuous and rapid spread of the COVID-19 pandemic has emphasized the need to seek new therapeutic and prophylactic treatments. Peptide inhibitors are a valid alternative approach for the treatment of emerging viral infections, mainly due to their low toxicity and high efficiency. Recently, two small nucleotide signatures were identified in the genome of some members of the Coronaviridae family and many other human pathogens. In this study, we investigated whether the corresponding amino acid sequences of such nucleotide sequences could have effects on the viral infection of two representative human coronaviruses: HCoV-OC43 and SARS-CoV-2. Our results showed that the synthetic peptides analyzed inhibit the infection of both coronaviruses in a dose-dependent manner by binding the RBD of the Spike protein, as suggested by molecular docking and validated by biochemical studies. The peptides tested do not provide toxicity on cultured cells or human erythrocytes and are resistant to human serum proteases, indicating that they may be very promising antiviral peptides.

Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy

MOTIVATION

Cyclization is a common strategy to enhance the therapeutic potential of peptides. Many cyclic peptide drugs have been approved for clinical use, in which the disulfide-driven cyclic peptide is one of the most prevalent categories. Molecular docking is a powerful computational method to predict the binding modes of molecules. For protein-cyclic peptide docking, a big challenge is considering the flexibility of peptides with conformers constrained by cyclization.

RESULTS

Integrating our efficient peptide 3D conformation sampling algorithm MODPEP2.0 and knowledge-based scoring function ITScorePP, we have proposed an extended version of our hierarchical peptide docking algorithm, named HPEPDOCK2.0, to predict the binding modes of the peptide cyclized through a disulfide against a protein. Our HPEPDOCK2.0 approach was extensively evaluated on diverse test sets and compared with the state-of-the-art cyclic peptide docking program AutoDock CrankPep (ADCP). On a benchmark dataset of 18 cyclic peptide-protein complexes, HPEPDOCK2.0 obtained a native contact fraction of above 0.5 for 61% of the cases when the top prediction was considered, compared with 39% for ADCP. On a larger test set of 25 cyclic peptide-protein complexes, HPEPDOCK2.0 yielded a success rate of 44% for the top prediction, compared with 20% for ADCP. In addition, HPEPDOCK2.0 was also validated on two other test sets of 10 and 11 complexes with apo and predicted receptor structures, respectively. HPEPDOCK2.0 is computationally efficient and the average running time for docking a cyclic peptide is about 34 min on a single CPU core, compared with 496 min for ADCP. HPEPDOCK2.0 will facilitate the study of the interaction between cyclic peptides and proteins and the development of therapeutic cyclic peptide drugs.

AVAILABILITY AND IMPLEMENTATION

http://huanglab.phys.hust.edu.cn/hpepdock/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Ligand-based design of peptide entry inhibitors targeting the endosomal receptor binding site of filoviruses

Filoviruses enter cells through micropinocytosis and trafficking into the endosomes in which they bind to the receptor Niemann-Pick C1 protein (NPC1) for membrane fusion and entry into the cytoplasm. The endosomal receptor-binding is critical step for filovirus entry. Designing inhibitors to block receptor binding will prevent viral entry. Using available binding structural information from the co-crystal structures of the viral GP with the receptor NPC1 or with monoclonal antibodies, we have conducted structure-based design of peptide inhibitors to target the receptor binding site (RBS). The designed peptides were tested for their inhibition activity against pseudo-typed or replication-competent viruses in a cell-based assay. The results indicate that these peptides exhibited strong activities against both Ebola and Marburg virus infection. It is expected that these peptides can be further developed for therapeutic use to treat filovirus infection and combat the outbreaks.

Serine O-acetyltransferase derived NV14 peptide reduces cytotoxicity in H2O2 induced MDCK cells and inhibits MCF-7 cell proliferation through caspase gene expression

BACKGROUND

Most of the bioactive peptides exhibit antioxidant effect and do elicit inhibitory effect on proliferation of cancer cells. This study investigates the in-vitro antioxidant and anti-cancer properties of NV14 peptide, derived from serine O-acetyltransferase (SAT) of spirulina, Arthrospira platensis.

METHODS

The anti-cancer effect of the peptide was evaluated using human adenocarcinoma epithelial cells (MCF-7), while the anti-oxidant potential, as in reduction in ROS concentration, has been established using the H₂O₂-exposed, Madin-Darby canine kidney (MDCK) cells. The outcome of the in vitro analyses has been evaluated by in silico molecular docking analyses.

RESULTS

The peptide, dose-dependently, reduced oxidative stress as well as cell proliferation. Besides, based on the binding scores between NV14 peptide and the important proteins associated with apoptosis and antioxidant defense, it is evident that the peptide has antioxidant and anti-cancer effect, in vitro.

CONCLUSIONS

Together, this study demonstrates that NV14 has a potent antioxidant and anti-cancer capability; however, further direction needs to be focused on clinical or pharmacodynamics aspects.

Novel engineered nanobodies specific for N‐terminal region of alpha‐synuclein recognize Lewy‐body pathology and inhibit in‐vitro seeded aggregation and toxicity

Nanobodies (Nbs), the single‐domain antigen‐binding fragments of dromedary heavy‐chain antibodies (HCAb), are excellent candidates as therapeutic and diagnostic tools in synucleinopathies because of their small size, solubility and stability. Here, we constructed an immune nanobody library specific to the monomeric form of alpha‐synuclein (α‐syn). Phage display screening of the library allowed the identification of a nanobody, Nbα‐syn01, specific for α‐syn. Unlike previously developed nanobodies, Nbα‐syn01 recognized the N‐terminal region which is critical for in vitro and in vivo aggregation and contains many point mutations involved in early PD cases. The affinity of the monovalent Nbα‐syn01 and the engineered bivalent format BivNbα‐syn01 measured by isothermal titration calorimetry revealed unexpected results where Nbα‐syn01 and its bivalent format recognized preferentially α‐syn fibrils compared to the monomeric form. Nbα‐syn01 and BivNbα‐syn01 were also able to inhibit α‐syn‐seeded aggregation in vitro and reduced α‐syn‐seeded aggregation and toxicity in cells showing their potential to reduce α‐syn pathology. Moreover, both nanobody formats were able to recognize Lewy‐body pathology in human post‐mortem brain tissue from PD and DLB cases. Additionally, we present evidence through structural docking that Nbα‐syn01 binds the N‐terminal region of the α‐syn aggregated form. Overall, these results highlight the potential of Nbα‐syn01 and BivNbα‐syn01 in developing into a diagnostic or a therapeutic tool for PD and related disorders.

Inhibition mechanism of oligopeptides from soft-shelled turtle egg against α-glucosidase and their gastrointestinal digestive properties

Peptides derived from egg protein hydrolysate have potential hypoglycemic benefits by inhibiting α-glucosidase. Herein, fluorescence spectroscopy and molecular docking were performed to investigate the α-glucosidase inhibitory mechanism of the oligopeptides ARDASVLK and HNKPEVEVR from soft-shelled turtle eggs. Gastrointestinal digestion characteristics of the two oligopeptides were further determined by LC-QTOF-MS/MS. The static fluorescence quenching of α-glucosidase by ARDASVLK and HNKPEVEVR indicated the formation of a stable α-glucosidase-peptide complex, mainly driven by hydrogen bonds and hydrophobic interactions. ARDASVLK and HNKPEVEVR could easily insert into the active pocket of α-glucosidase (docking scores of -157.1 and -158.4, respectively), thereby inhibiting enzyme activity by preventing substrate binding and inducing enzymatic conformation change. After gastrointestinal digestion, 14.3% and 30.4% of ARDASVLK and HNKPEVEVR were maintained intact, respectively, and their digestive products (mainly DASVLK and HNKPEVEV) still showed high inhibitory effects on α-glucosidase (about 35% inhibition). This study sheds light on the mechanism of oligopeptides derived from soft-shelled turtle eggs as a novel α-glucosidase inhibitor for diabetes. PRACTICAL APPLICATIONS: Oligopeptides from egg protein hydrolysate have potential hypoglycemic properties by inhibiting α-glucosidase. This study has provided insights into the inhibitory mechanism of oligopeptides from soft-shelled turtle egg on α-glucosidase. Interestingly, despite the fact that the oligopeptides are largely degraded during gastrointestinal digestion, their digestive metabolites displayed strong α-glucosidase inhibitory activities. Because α-glucosidase is highly expressed in small intestine brush border, our findings support the possibility of these oligopeptides as an attractive health-benefit compound to control glucose without being absorbed by intestinal epithelial cells, unlike other enzyme inhibitors such as ACE inhibitors, which have poor oral bioavailability. This study may facilitate the applications of oligopeptides from soft-shelled turtle egg as α-glucosidase inhibitors and food functional ingredients for the therapy of diabetes.

Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides

At the end of 2019, in China, clinical signs and symptoms of unknown etiology have been reported in several patients whose sample sequencing revealed pneumonia caused by the SARS-CoV-2 virus. COVID-19 is a disease triggered by this virus, and in 2020, the World Health Organization declared it a pandemic. Since then, efforts have been made to find effective therapeutic agents against this disease. Identifying novel natural antiviral drugs can be an alternative to treatment. For this reason, antimicrobial peptides secreted by anurans' skin have gained attention for showing a promissory antiviral effect. Hence, this review aimed to elucidate how and which peptides secreted by anurans' skin can be considered therapeutic agents to treat or prevent human viral infectious diseases. Through a literature review, we attempted to identify potential antiviral frogs' peptides to combat COVID-19. As a result, the Magainin-1 and -2 peptides, from the Magainin family, the Dermaseptin-S9, from the Dermaseptin family, and Caerin 1.6 and 1.10, from the Caerin family, are molecules that already showed antiviral effects against SARS-CoV-2 in silico. In addition to these peptides, this review suggests that future studies should use other families that already have antiviral action against other viruses, such as Brevinins, Maculatins, Esculentins, Temporins, and Urumins. To apply these peptides as therapeutic agents, experimental studies with peptides already tested in silico and new studies with other families not tested yet should be considered.

The Inhibition of DNA Viruses by the Amphibian Antimicrobial Peptide Temporin G: A Virological Study Addressing HSV-1 and JPCyV

Herpes simplex virus type-1 (HSV-1) and John Cunningham polyomavirus (JCPyV) are widely distributed DNA viruses causing mainly asymptomatic infection, but also mild to very severe diseases, especially when these viruses reach the brain. Some drugs have been developed to inhibit HSV-1 replication in host cells, but their prolonged use may induce resistance phenomena. In contrast, to date, there is no cure for JCPyV. The search for alternative drugs that can reduce viral infections without undermining the host cell is moving toward antimicrobial peptides (AMPs) of natural occurrence. These include amphibian AMPs belonging to the temporin family. Herein, we focus on temporin G (TG), showing that it strongly affects HSV-1 replication by acting either during the earliest stages of its life cycle or directly on the virion. Computational studies have revealed the ability of TG to interact with HSV-1 glycoprotein B. We also found that TG reduced JCPyV infection, probably affecting both the earliest phases of its life cycle and the viral particle, likely through an interaction with the viral capsid protein VP1. Overall, our results are promising for the development of short naturally occurring peptides as antiviral agents used to counteract diseases related to HSV-1 and JCPyV.

Seafood Paramyosins as Sources of Anti-Angiotensin-Converting-Enzyme and Anti-Dipeptidyl-Peptidase Peptides after Gastrointestinal Digestion: A Cheminformatic Investigation

Paramyosins, muscle proteins occurring exclusively in invertebrates, are abundant in seafoods. The potential of seafood paramyosins (SP) as sources of anti-angiotensin-converting-enzyme (ACE) and anti-dipeptidyl-peptidase (DPP-IV) peptides is underexplored. This in silico study investigated the release of anti-ACE and anti-DPP-IV peptides from SP after gastrointestinal (GI) digestion. We focused on SP of the common octopus, Humboldt squid, Japanese abalone, Japanese scallop, Mediterranean mussel, Pacific oyster, sea cucumber, and Whiteleg shrimp. SP protein sequences were digested on BIOPEP-UWM, followed by identification of known anti-ACE and anti-DPP-IV peptides liberated. Upon screening for high-GI-absorption, non-allergenicity, and non-toxicity, shortlisted peptides were analyzed via molecular docking and dynamic to elucidate mechanisms of interactions with ACE and DPP-IV. Potential novel anti-ACE and anti-DPP-IV peptides were predicted by SwissTargetPrediction. Physicochemical and pharmacokinetics of peptides were predicted with SwissADME. GI digestion liberated 2853 fragments from SP. This comprised 26 known anti-ACE and 53 anti-DPP-IV peptides exhibiting high-GI-absorption, non-allergenicity, and non-toxicity. SwissTargetPrediction predicted three putative anti-ACE (GIL, DL, AK) and one putative anti-DPP-IV (IAL) peptides. Molecular docking found most of the anti-ACE peptides may be non-competitive inhibitors, whereas all anti-DPP-IV peptides likely competitive inhibitors. Twenty-five nanoseconds molecular dynamics simulation suggests the stability of these screened peptides, including the three predicted anti-ACE and one predicted anti-DPP-IV peptides. Seven dipeptides resembling approved oral-bioavailable peptide drugs in physicochemical and pharmacokinetic properties were revealed: AY, CF, EF, TF, TY, VF, and VY. In conclusion, our study presented in silico evidence for SP being a promising source of bioavailable and safe anti-ACE and anti-DPP-IV peptides following GI digestions.

ERp57 Chaperon Protein Protects Neuronal Cells from Aβ-induced toxicity

Alzheimer's disease (AD) is a neurodegenerative disorder whose main pathological hallmark is the accumulation of Amyloid-β peptide (Aβ) in the form of senile plaques. Aβ can cause neurodegeneration and disrupt cognitive functions by several mechanisms, including oxidative stress. ERp57 is a protein disulfide isomerase involved in the cellular stress response and known to be present in the cerebrospinal fluid of normal individuals as a complex with Aβ peptides, suggesting that it may be a carrier protein which prevents aggregation of Aβ. Although several studies show ERp57 involvement in neurodegenerative diseases, no clear mechanism of action has been identified thus far. In this work we gain insights into the interaction of Aβwith ERp57, with a special focus on the contribution of ERp57 to the defence system of the cell. Here we show that recombinant ERp57 directly interacts with the Aβ_25-35 fragment in vitro with high affinityvia two in silico-predicted main sites of interaction. Furthermore, we used human neuroblastoma cells to show that short-term Aβ_25-35 treatment induces ERp57 decrease in intracellular protein levels, different intracellular localization and ERp57 secretion in the cultured medium. Finally, we demonstrate that recombinant ERp57 counteracts the toxic effects of Aβ_25-35 and restores cellular viability, by preventing Aβ_25-35 aggregation. Overall, the present study shows thatextracellular ERp57 can exert a protective effect from Aβ toxicity and highlights it as a possible therapeutic tool in the treatment of AD.

Potential of antiviral peptide-based SARS-CoV-2 inactivators to combat COVID-19

The appearance of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the lack of effective antiviral therapeutics for coronavirus disease 2019 (COVID-19), a highly infectious disease caused by the virus, demands the search for alternative therapies. Most antiviral drugs known are passive defenders which must enter the cell to execute their function and suffer from concerns such as permeability and effectiveness, therefore in this current study, we aim to identify peptide inactivators that can act without entering the cells. SARS-CoV-2 spike protein is an essential protein that plays a major role in binding to the host receptor angiotensin-converting enzyme 2 and mediates the viral cell membrane fusion process. SARS vaccines and treatments have also been developed with the spike protein as a target. The virtual screening experiment revealed antiviral peptides which were found to be non-allergen, non-toxic and possess good water solubility. U-1, GST-removed-HR2 and HR2-18 exhibit binding energies of -47.8 kcal/mol, -43.01 kcal/mol, and -40.46 kcal/mol, respectively. The complexes between these peptides and spike protein were stabilized through hydrogen bonds as well as hydrophobic interactions. The stability of the top-ranked peptide with the drug-receptor is evidenced by 50-ns molecular dynamics (MD) simulations. The binding of U-1 induces conformational changes in the spike protein with alterations in its geometric properties such as increased flexibility, decreased compactness, the increased surface area exposed to solvent molecules, and an increase in the number of total hydrogen bonds leading to its probable inactivation. Thus, the identified antiviral peptides can be used as anti-SARS-CoV-2 candidates, inactivating the virus’s spike proteins and preventing it from infecting host cells.

Evaluating the structural and immune mechanism of Interleukin-6 for the investigation of goat milk peptides as potential treatments for COVID-19

The function of Immune control, haematopoiesis, and inflammation all depend on the cytokine Interleukin 6 (IL-6), and higher expression of IL-6 is seen in COVID-19 and other diseases. The immune protein IL-6 activation is dependent on binding interactions with IL-6Rα, mIL-6R, and sIL-6R for its cellular function. Termination of these reaction could benefit for controlling the over-expression in COVID-19 patients and that may arise as inhibitors for controlling COVID-19. Traditionally, the goat milk has been prescribed as medicine in ayurvedic practice and through this work, we have explored the benefits of peptides from goat milk as IL-6 inhibitors, and it have the potential of inhibiting the over expression of IL-6 and control the COVID-19 disease. Computational experiments have shown that goat peptides had strong interactions with IL-6, with higher scoring profiles and energy efficiency ranging from −6.00 kcal/mol to −9.00 kcal/mol in docking score and −39.00 kcal/mol in binding energy. Especially the YLGYLEQLLR, VLVLDTDYK and AMKPWIQPK peptides from goat milk holds better scoring and shows strong interactions were identified as the most potential IL-6 inhibitor candidates in this study. Peptides from Goat proteins, which are capable of binding to the IL-6 receptor with strong binding conformations, have no negative effects on other immune system proteins.

Design of melanogenesis regulatory peptides derived from phycocyanin of the microalgae Spirulina platensis

Pigmentation issues are common conditions associated with excessive or insufficient production of melanin. Recently peptides are investigated to discover novel melanogenesis regulators as low molecular weight compounds to regulate skin pigmentation. In this study, an internal library of peptides obtained through in silico enzymatic digestion of phycocyanin from microalgae S. platensis was tested to apprehend their anti-melanogenic effects. Seven peptides were investigated for their inhibitory potential against mushroom and B16-F10 murine tyrosinase enzymes. According to the results, P5 (SPSWY) and P7 (AADQRGKDKCARDIGY) were effective in lowering the activity of mushroom and B16-F10 tyrosinases. P5 was the most potent (IC₅₀ value, 12.1 µM) in mushroom which was followed by P2 (MAACLR, 86.9 µM). Although the peptides were particularly powerful in inhibiting monophenolase activity, only moderate inhibition was observed for diphenolase activity in mushroom tyrosinase assay. Apart from tyrosinase inhibition, P2 and P3 (RCLNGRL) were efficient DPPH radical scavengers at low concentrations (IC₅₀ < 200 µM). In the mammalian assay system, P5 and P7 were noticeably effective to decrease tyrosinase enzyme activity with IC₅₀ values of 48.9 and 34.2 µM, respectively. However, although P4 (RYVTYAVF) was a potent mushroom tyrosinase inhibitor, it increased melanin synthesis up to 3-fold in B16-F10 cells. The results indicate that C-terminal tyrosine residue is important for tyrosinase inhibition. This study shows, for the first time, that microalgae proteins can be regarded as sources for melanogenesis regulation.

Experimental and computational studies on the mechanism of the β-lactoglobulin-derived peptide inhibiting the antigenicity of β-lactoglobulin

In this study, through a combined simulated enzymolysis-molecular docking-molecular simulation-activity determination-action mechanism strategy, we screened a β-LG-derived peptide (VAGTWYSL) to inhibit the antigenicity of β-LG and explored its mechanism of action. Our results indicate that the inhibitory effect of the peptide on the antigenicity of β-LG is affected by different experimental conditions, including pH, reaction time and concentration. Three factors may contribute to the reduced allergenicity of β-LG. First, there must be sufficient forces between the peptide and β-LG, as a result, hydrophobic forces and hydrogen bonds are the main forces to maintain the structural stability of the complex. Second, the binding of the peptide changes the secondary structure of β-LG, especially with an increase in α-helices and a decrease in β-turns. Third, the peptide binds to the hydrophobic region of β-LG, involving the antigenic epitope region Val41-Lys60, which may reduce the antigenicity.