Peptide Docking Research Articles

Abstract 7384: Regulation of phosphorylated VGLL1 by the positively charged binding pocket on the surface of TEAD4

Abstract Vestigial-like 1 (VGLL1) is a transcriptional co-activator that binds to TEA domain-containing transcription factors (TEADs), regulating hippo pathway. High expression of VGLL1 is associated with gastric cancer, breast cancer, and pancreatic cancers. VGLL1 is transcriptionally regulated by PI3K/β-catenin signaling and is phosphorylated by ribosomal S6 kinase 2 (RSK2) in the presence of TGF-β. It is clear that phosphorylation at S84 of the VGLL1 protein is critical for its interaction with TEAD4 to express their target genes involved in the proliferation and metastasis of cancer cells. In the isothermal titration calorimetry study, we observed S84-phosphorylated VGLL1 peptide bound to TEAD4. However, it is difficult to understand structure-based molecular mechanism of the phosphorylated VGLL1 at S84 due to lack of the detailed human VGLL1-TEAD4 complex structure for rational drug design. In this study, we modeled full-length human VGLL1-TEAD4 or YAP1-TEAD4 complexes and performed MMPBSA calculations or Kd/Ki predictions followed by MD simulations using Pharmaco-Net's CNN-based artificial intelligence model. Our study suggests that a positively charged binding pocket on the surface of TEAD4 can regulate interaction between Trp243 from YAP1 and phosphorylated-Ser84 from VGLL1. The newly identified binding pocket is composed of Lys297, Val414, and Tyr429, which can interact with phosphorylated Ser84 residue and maintain Omega loop-like structure shown in YAP1-TEAD4 complex. The computed binding energy for phosphorylated-VGLL1-TEAD was -134.80 +/- 8.20 Kcal/mol which was a similar binding energy to YAP1-TEAD4 complex. In addition, global peptide docking using S84-containing-VGLL1 peptide (SCVP) indicated that SCVP can bind to the same binding pocket with average 1.39 μM. This suggested that there could be a novel therapeutic approach targeting this interaction with SCVP, an agent that seems to mimic phosphor-VGLL1 interaction and thus demonstrates promise as a potential therapeutic intervention. Nevertheless, further experimental verification and clinical investigations are needed to validate these innovative findings. Citation Format: Jae Mun Choi, Huong Van Le, Young Bin Park, Yu Kyung Yun, Jun Hong Kim, Jonathan Wilianto, Nuzup Shadiev, Chul Sung, Bonsu Ku, Kwan-Young Chang, Misun Won. Regulation of phosphorylated VGLL1 by the positively charged binding pocket on the surface of TEAD4 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7384.

Abstract 4694: In charge: Targeting neddylation of UBE2M for anticancer therapy

Abstract Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules orchestrates a vast number of processes in the cell. Consequently, post-translational modification pathways are considered major targets for therapeutic intervention of many diseases, including cancers. Neddylation is a post-translational mechanism like ubiquitination, but instead of ubiquitin, NEDD8 is conjugated to protein targets via an E1-E2-E3 multi-enzymatic cascade. Neddylation is upregulated in multiple cancer types and the development of therapeutics targeting neddylation pathways are gaining increasing popularity. UBE2M, one of the two E2 neddylation conjugation enzymes, takes part in two types of reactions: transthiolation-transfer of NEDD8 from a thioester to a thiol group and aminolysis-transfer of NEDD8 from a thioester to an amino group. These activities require both a 26-residue N-terminal docking peptide and a conserved E2 catalytic core domain, which is the basis for the transfer of NEDD8. Here, we describe findings in the quest to understand the UBE2M interaction with NEDD8 and effects on cancer cells by modifying UBE2M at the N-terminal docking peptide or at the catalytic site. Cancer cells were transfected with ΔN or catalytic site UBE2M mutant constructs and analyzed by immunoprecipitation for charging of NEDD8 onto UBE2M. The catalytic site mutants are deficient in charging (C111A) or discharging (C111S) of UBE2M by NEDD8, which leads to a decrease in neddylation of downstream substrates, such as CULLIN family members. Elimination of the N-terminal docking peptide by introduction of catalytically competent ΔN UBE2M mutant constructs resulted in reduced reaction kinetics. Structural modeling suggests that the loss of the N-terminal docking region likely weakens protein-protein interactions between UBE2M and the UBA3-APPBP1 E1 complex. Interestingly, ΔN UBE2M mutants were observed to be slightly charged with NEDD8, but appeared to have a defect in NEDD8 discharge, resulting in reduced neddylation of substrates. Moreover, further phenotypic evaluation of UBE2M mutant transfected cancer cells revealed a divergence in phenotypic effect: while both mutant types led to a deficiency in NEDD8 charge or discharge from UBE2M, only the manipulation of the active site of UBE2M led to a DNA re-replication phenotype with subsequent cell death. These observations reveal the complexity of the neddylation cascade and raise the question if slowing down discharge of NEDD8 from UBE2M is a more viable therapeutic option than slowing down the charging of UBE2M. Citation Format: Alex G. Batrouni, Jacob P. Matson, Andressa L. Mota, Archna Ravi, Marcus O'Hara, Micholas D. Smith, Jeremy C. Smith, Vivek K. Vishnudas, Anjan Thakurta, Stephane Gesta, Maria D. Nastke. In charge: Targeting neddylation of UBE2M for anticancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4694.

Purification, identification and molecular docking of dual-functional peptides derived from corn protein hydrolysates with antioxidant and antiadhesive activity against Helicobacter pylori.

More than 50% of the world's population is infected with Helicobacter pylori, which is classified as a group I carcinogen by the World Health Organization (WHO). Corn protein dual-functional peptides were identified and functionally analyzed in vitro and in silico. Two novel dual-functional peptides were identified as Cys-Gln-Asp-Val-Pro-Leu-Leu (CQDVPLL, CQ7) and Thr-Ile-Phe-Pro-Gln-Cys (TIFPQC, TI6) using nanoscale liquid chromatography coupled to tandem mass spectrometry (nano-LC-MS/MS). The antiadhesive effects against H. pylori of CQ7 and TI6 were 45.17 ± 2.41% and 48.62 ± 1.84% at 4 mg mL-1 , respectively. In silico prediction showed that CQ7 and TI6 had good physicochemical properties. Molecular docking demonstrated that CQ7 and TI6 could bind to the adhesins BabA and SabA by hydrophobic interactions and hydrogen bonds, preventing H. pylori infection. Moreover, CQ7 showed strong antioxidant activity due to its unique amino acid composition. The present study demonstrated that the identified peptides, CQ7 and TI6, possess antioxidant and antiadhesive effects, preventing H. pylori infection and alleviating oxidative injury to the gastric mucosa. © 2023 Society of Chemical Industry.

Identification and molecular docking of a novel antidiabetic peptide from protamex-camel milk protein hydrolysates against α-amylase and DPP-IV

Antidiabetic peptides were identified from camel milk protein hydrolysates, and their inhibitory activities against α-amylase and dipeptidyl peptidase-IV (DPP-IV) were determined. The possible binding mechanism between the enzymes and the peptide was elucidated through molecular docking. Camel milk proteins were hydrolyzed using protamex, and the hydrolysates were divided into three fractions (>10, 3–10, and <3 kDa) through ultrafiltration. Fraction <3 kDa was more effective at inhibiting α-amylase and DPP-IV and was purified through gel chromatography and identified through LC-MS/MS. In total, 20 peptides were considered as potential bioactive peptides, mainly derived from β-casein. The novel peptide QEPVPDPVRGL exhibited the most potent antidiabetic activity and spontaneously interacted with α-amylase and DPP-IV through hydrogen bonds, salt bridges, and pi–alkyl, thereby occupying their active cavities. This study indicated that camel milk protein hydrolysates are good sources of peptides with antidiabetic potential.

Evaluation and Simulation of Docking Peptide Labeled with Technetium-99m (Tc-99m) with Human Epidermal Growth Factor Receptor 2 (HER2) in HER2-Positive Breast Cancer Cells

Background: Breast cancer is the first fatal disease in women and the second leading cause of death in humans, after heart disease. In approximately 20% of these patients, breast cancer cells have a higher-than-normal level of a protein called human epidermal growth factor receptor 2 (HER2) on their surface. These cancers, called HER2-positive, tend to grow and spread faster than other breast cancers. Objectives: This study aimed to evaluate the binding of the peptide LTVSPWY labeled with the HER2 receptor compared to the non-labeled peptide and simulate its docking. Methods: The LTVSPWY peptide was first labeled with the 99-radioactive technetium (Tc-99m) and optimized for molecular docking with the HER2 receptor in HyperChem software. Then, the HEX 6 software was used to check how the compounds were connected to the active site of the HER2. Finally, data was analyzed by HEX, LIGPLOT, and other programs. Results: During docking in HEX, the labeled peptide showed a good link with the HER2 protein receptor. The energy of this kind of transplantation was higher than the nonlabeled peptide bond with the HER2 protein receptor. In fact, this combination had the lowest level of connection energy with the receptor, which reflects the success of docking. Conclusions: In the analysis of the post-docking data, we observed the ligand was connected to the HER2 receptor from 5 major sites at different intervals, indicating a suitable bond to the receptor ligand.

Modulation of Structure and Dynamics of Cardiac Troponin by Phosphorylation and Mutations Revealed by Molecular Dynamics Simulations.

Adrenaline acts on β1 receptors in the heart muscle to enhance contractility, increase the heart rate, and increase the rate of relaxation (lusitropy) via activation of the cyclic AMP-dependent protein kinase, PKA. Phosphorylation of serines 22 and 23 in the N-terminal peptide of cardiac troponin I is responsible for lusitropy. Mutations associated with cardiomyopathy suppress the phosphorylation-dependent change. Key parts of troponin responsible for this modulatory system are disordered and cannot be resolved by conventional structural approaches. We performed all-atom molecular dynamics simulations (5 × 1.5 μs runs) of the troponin core (419 amino acids) in the presence of Ca2+ in the bisphosphorylated and unphosphorylated states for both wild-type troponin and the troponin C (cTnC) G159D mutant. PKA phosphorylation affects troponin dynamics. There is significant rigidification of the structure involving rearrangement of the cTnI(1-33)-cTnC interaction and changes in the distribution of the cTnC helix A/B angle, troponin I (cTnI) switch peptide (149-164) docking, and the angle between the regulatory head and ITC arm domains. The familial dilated cardiomyopathy cTnC G159D mutation whose Ca2+ sensitivity is not modulated by cTnI phosphorylation exhibits a structure inherently more rigid than the wild type, with phosphorylation reversing the direction of all metrics relative to the wild type.

Identification and molecular docking of novel chikungunya virus NSP4 inhibitory peptides from camel milk proteins

The chikungunya (CHIK) virus is an arbovirus belonging to the alphavirus (Togaviridae family). Around 85% of infected individuals suffer from symptoms such as high fever and severe joint pain; about 30 to 40% will develop a chronic joint illness. The Nsp4 protease is the most conserved protein in the alphavirus family and serves as an RNA-dependent RNA polymerase (RdRp). Targeting this enzyme might inhibit the CHIKV replication cycle. This work aims to in silico study the CHIKV RdRp inhibitory effect of peptides derived from camel milk protein as antiviral peptides. Various bioinformatics tools were recruited to identify, screen, predict and assess peptides obtained from camel milk as antiviral peptides (AVPs). During this study, CHIKV Nsp4 (polymerase) was used as a target to be inhibited by interaction with peptides derived from camel milk protein. Among 91 putative bioactive peptides, the best predicted 5 were further evaluated. Molecular docking showed that the top 5 AVPs generated better docking scores and interacted well with active sites of Nsp4 by the formation of different hydrogen bonds as well as other bonds. AVP63 and AVP20 showed the best Molecular docking and MD simulation results. The residue 315ASP of the GDD motif (catalytic core) exhibited a favorable interaction with the AVPs. The findings of this study suggest that the AVP20 derived from camel milk protein can be a potential novel CHIKV polymerase inhibitor. Communicated by Ramaswamy H. Sarma

Integrative modeling of diverse protein-peptide systems using CABS-dock.

The CABS model can be applied to a wide range of protein-protein and protein-peptide molecular modeling tasks, such as simulating folding pathways, predicting structures, docking, and analyzing the structural dynamics of molecular complexes. In this work, we use the CABS-dock tool in two diverse modeling tasks: 1) predicting the structures of amyloid protofilaments and 2) identifying cleavage sites in the peptide substrates of proteolytic enzymes. In the first case, simulations of the simultaneous docking of amyloidogenic peptides indicated that the CABS model can accurately predict the structures of amyloid protofilaments which have an in-register parallel architecture. Scoring based on a combination of symmetry criteria and estimated interaction energy values for bound monomers enables the identification of protofilament models that closely match their experimental structures for 5 out of 6 analyzed systems. For the second task, it has been shown that CABS-dock coarse-grained docking simulations can be used to identify the positions of cleavage sites in the peptide substrates of proteolytic enzymes. The cleavage site position was correctly identified for 12 out of 15 analyzed peptides. When combined with sequence-based methods, these docking simulations may lead to an efficient way of predicting cleavage sites in degraded proteins. The method also provides the atomic structures of enzyme-substrate complexes, which can give insights into enzyme-substrate interactions that are crucial for the design of new potent inhibitors.

Identification, flavor characteristics and molecular docking of umami taste peptides of Xuanwei ham

To better understand the palatable properties of Xuanwei ham, the aqueous extract was isolated, analyzed and combin with sensory evaluation. Of umami-tasting activity and umami-enhancing impact, four new peptides (MDAIKKMQ, RKYEEVAR, YVGDEAQSKRG, and VNVDEVGGEALGR) were extracted and identified by ultrafiltration, gel separation, reverse performance liquid chromatography, and nano-LC-MS / MS. Sensory evaluation results showed that all of them had umami activity and enhanced umami taste, among which VNVDEVGGEALGR had the best effect. These peptides' umami taste thresholds ranged from 0.25 to 0.8 mg/mL. The MSG solution's umami taste threshold ranged from 0.125 to 0.5 mg/mL. Molecular docking results showed that the four umami peptides could be embedded into the binding pocket of the T1R3 cavity of the umami taste receptor T1R1/T1R3, wherein the binding sites Asp219, Asp150, and Thr179 may play crucial roles, and Glu222, Asp108, Glu217 and Glu148 play auxiliary roles. Hydrogen bonding and hydrophobic interactions were the most prominent interaction forces. This study helps to clarify the flavor characteristics of Xuanwei ham and could improve new processing technology.

Prediction of ACE‐inhibitory and antioxidant peptides from storage proteins of edible seeds and nuts using in silico approaches

AbstractRecently, plant protein‐derived peptides with diverse bioactivities have gained special attention with regards to health promoting and disease prevention. Among the different plant sources, edible seeds and nuts are known to contribute essential nutritional needs and promote several health benefits. Storage proteins of edible seeds and nuts are known to fulfill the essential nutritional needs and impart several health promoting benefits. In the present study, we attempt to use in silico approaches to divulge storage proteins derived peptides with angiotensin I‐converting enzyme (ACE)‐inhibition and antioxidant properties. In silico hydrolysis of 10 storage proteins using 8 proteases released multiple peptides exhibiting numerous bioactivities. The storage proteins majorly released ACE inhibitory peptides which were subjected for further evaluation (BIOPEP, PeptideRanker, ToxinPred, AllerTOP, and Pepsite2). A total of 25 peptides were considered potential ACE‐inhibitory peptides. Additionally, AnOxPePred webserver was used to evaluate the potential of storage proteins as precursors of antioxidant peptides. As evident from docking analysis (HPEPDOCK), peptides PGCR, GFEWIAFK, GFFYR, and HFR displayed significant interaction with key residues of Kelch‐like ECH‐associated protein 1, a modulator of intracellular oxidant status. Non‐toxic peptide PGCR exhibited both antioxidant and antihypertensive activities and was found to be the most promising peptide. This study opened new avenue for storage proteins of edible seeds and nuts as ingredients in development of nutraceutical formulations.

Elucidation of Short Linear Motif-Based Interactions of the FERM Domains of Ezrin, Radixin, Moesin, and Merlin.

The ERM (ezrin, radixin, and moesin) family of proteins and the related protein merlin participate in scaffolding and signaling events at the cell cortex. The proteins share an N-terminal FERM [band four-point-one (4.1) ERM] domain composed of three subdomains (F1, F2, and F3) with binding sites for short linear peptide motifs. By screening the FERM domains of the ERMs and merlin against a phage library that displays peptides representing the intrinsically disordered regions of the human proteome, we identified a large number of novel ligands. We determined the affinities for the ERM and merlin FERM domains interacting with 18 peptides and validated interactions with full-length proteins through pull-down experiments. The majority of the peptides contained an apparent Yx[FILV] motif; others show alternative motifs. We defined distinct binding sites for two types of similar but distinct binding motifs (YxV and FYDF) using a combination of Rosetta FlexPepDock computational peptide docking protocols and mutational analysis. We provide a detailed molecular understanding of how the two types of peptides with distinct motifs bind to different sites on the moesin FERM phosphotyrosine binding-like subdomain and uncover interdependencies between the different types of ligands. The study expands the motif-based interactomes of the ERMs and merlin and suggests that the FERM domain acts as a switchable interaction hub.

A Structural Network Analysis of Neuronal ArhGAP21/23 Interactors by Computational Modeling.

RhoGTPase-activating proteins (RhoGAPs) play multiple roles in neuronal development; however, details of their substrate recognition system remain elusive. ArhGAP21 and ArhGAP23 are RhoGAPs that contain N-terminal PDZ and pleckstrin homology domains. In the present study, the RhoGAP domain of these ArhGAPs was computationally modeled by template-based methods and the AlphaFold2 software program, and their intrinsic RhoGTPase recognition mechanism was analyzed from the domain structures using the protein docking programs HADDOCK and HDOCK. ArhGAP21 was predicted to preferentially catalyze Cdc42, RhoA, RhoB, RhoC, and RhoG and to downregulate RhoD and Tc10 activities. Regarding ArhGAP23, RhoA and Cdc42 were deduced to be its substrates, whereas RhoD downregulation was predicted to be less efficient. The PDZ domains of ArhGAP21/23 possess the FTLRXXXVY sequence, and similar globular folding consists of antiparalleled β-sheets and two α-helices that are conserved with PDZ domains of MAST-family proteins. A peptide docking analysis revealed the specific interaction of the ArhGAP23 PDZ domain with the PTEN C-terminus. The pleckstrin homology domain structure of ArhGAP23 was also predicted, and the functional selectivity for the interactors regulated by the folding and disordered domains in ArhGAP21 and ArhGAP23 was examined by an in silico analysis. An interaction analysis of these RhoGAPs revealed the existence of mammalian ArhGAP21/23-specific type I and type III Arf- and RhoGTPase-regulated signaling. Multiple recognition systems of RhoGTPase substrates and selective Arf-dependent localization of ArhGAP21/23 may form the basis of the functional core signaling necessary for synaptic homeostasis and axon/dendritic transport regulated by RhoGAP localization and activities.

NCoVDock2: a docking server to predict the binding modes between COVID-19 targets and its potential ligands.

The rapid emergence of SARS-CoV-2 variants with multi-sites mutations is considered as a major obstacle for the development of drugs and vaccines. Although most of the functional proteins essential for SARS-CoV-2 have been determined, the understanding of the COVID-19 target-ligand interactions remains a key challenge. The old version of this COVID-19 docking server was built in 2020, and free and open to all users. Here, we present nCoVDock2, a new docking server to predict the binding modes for targets from SARS-CoV-2. First, the new server supports more targets. We replaced the modeled structures with newly resolved structures and added more potential targets of COVID-19, especially for the variants. Second, for small molecule docking, Autodock Vina was upgraded to the latest version 1.2.0, and a new scoring function was added for peptide or antibody docking. Third, the input interface and molecular visualization were updated for a better user experience. The web server, together with an extensive help and tutorial, are freely available at: https://ncovdock2.schanglab.org.cn.

In silico structure-based design of peptides or proteins as therapeutic tools for obesity or diabetes mellitus: A protocol for systematic review and meta analysis.

In silico studies using dynamic simulation or molecular docking have boosted the screening and identification of molecules and/or targets in studies aimed at treating diseases such as obesity and diabetes mellitus, optimizing the development of new drugs. This study aims to describe a systematic review protocol on peptides and proteins evaluated in silico as potential therapeutic agents for obesity or diabetes mellitus. This protocol followed the Preferred Reporting Items for Systematic Reviews and Meta-analyses Protocols and was registered in the International Prospective Register of Systematic Reviews database (number: CRD42022355540). The databases to be searched will be PubMed, ScienceDirect, Scopus, Web of Science, virtual health library, and EMBASE. It will be included in silico studies that evaluate the simulation by dynamics or molecular docking of proteins or peptides involved in treating obesity or diabetes mellitus. Two independent reviewers will select studies, extract data, and assess methodological quality using the adapted Strengthening the reporting of empirical simulation studies. A narrative synthesis of the included studies will be performed for the systematic reviews. This protocol contemplates the production of 2 systematic reviews to be developed focusing on obesity or diabetes mellitus. The reviews will enable knowledge of peptides and proteins involved in research treating these diseases and will emphasize the importance of in silico studies in this context and for the development of future studies.

Conserved Sites and Recognition Mechanisms of T1R1 and T2R14 Receptors Revealed by Ensemble Docking and Molecular Descriptors and Fingerprints Combined with Machine Learning.

Taste peptides, as an important component of protein-rich foodstuffs, potentiate the nutrition and taste of food. Thereinto, umami- and bitter-taste peptides have been ex tensively reported, while their taste mechanisms remain unclear. Meanwhile, the identification of taste peptides is still a time-consuming and costly task. In this study, 489 peptides with umami/bitter taste from TPDB (http://tastepeptides-meta.com/) were collected and used to train the classification models based on docking analysis, molecular descriptors (MDs), and molecular fingerprints (FPs). A consensus model, taste peptide docking machine (TPDM), was generated based on five learning algorithms (linear regression, random forest, gaussian naive bayes, gradient boosting tree, and stochastic gradient descent) and four molecular representation schemes. Model interpretive analysis showed that MDs (VSA_EState, MinEstateIndex, MolLogP) and FPs (598, 322, 952) had the greatest impact on the umami/bitter prediction of peptides. Based on the consensus docking results, we obtained the key recognition modes of umami/bitter receptors (T1Rs/T2Rs): (1) residues 107S-109S, 148S-154T, 247F-249A mainly form hydrogen bonding contacts and (2) residues 153A-158L, 163L, 181Q, 218D, 247F-249A in T1R1 and 56D, 106P, 107V, 152V-156F, 173K-180F in T2R14 constituted their hydrogen bond pockets. The model is available at http://www.tastepeptides-meta.com/yyds.

Novel Plant-Protein (Quinoa) Derived Bioactive Peptides with Potential Anti-Hypercholesterolemic Activities: Identification, Characterization and Molecular Docking of Bioactive Peptides

Hypercholesterolemia remains a serious global public health concern. Previously, synthetic anti-hypercholesterolemic drugs were used for ameliorating this condition; however, long-term usage presented several side-effects. In this regard, natural products as an adjunct therapy has emerged in recent times. This study aimed to produce novel bioactive peptides with anti-hypercholesterolemic activity (cholesterol esterase (CEase) and pancreatic lipase (PL)) from quinoa protein hydrolysates (QPHs) using three enzymatic hydrolysis methods (chymotrypsin, protease and bromelain) at 2-h hydrolysis intervals (2, 4, and 6 h). Chymotrypsin-generated hydrolysates showed higher CEase (IC50: 0.51 mg/mL at 2 h) and PL (IC50: 0.78 mg/mL at 6 h) inhibitory potential in comparison to other derived hydrolysates and intact quinoa proteins. Peptide profiling by LC-MS QTOF and in silico interaction with target enzymes showed that only four derived bioactive peptides from QPHs could bind in the active site of CEase, whereas twelve peptides could bind in the active site of PL. Peptides QHPHGLGALCAAPPST, HVQGHPALPGVPAHW, and ASNLDNPSPEGTVM were identified to be potential CEase inhibitors, and FSAGGLP, QHPHGLGALCAAPPST, KIVLDSDDPLFGGF, MFVPVPH, and HVQGHPALPGVPAHW were identified as potential PL inhibitors on the basis of the maximum number of reactive residues in these bioactive peptides. In conclusion, QPHs can be considered as an alternative therapy for the treatment of hypercholesterolemia.

AR13 peptide-conjugated liposomes improve the antitumor efficacy of doxorubicin in mice bearing C26 colon carcinoma; in silico, in vitro, and in vivo study

Currently, liposomes have emerged as efficient and safer nano-carriers for targeted therapy in different cancers. This work aimed to employ PEGylated liposomal doxorubicin (Doxil®/PLD), modified with AR13 peptide, to target Muc1 on the surface of colon cancerous cells.We performed molecular docking and simulation studies (using Gromacs package) of AR13 peptide against Muc1 to analyze and visualize the peptide-Muc1 binding combination. For in vitro analysis, the AR13 peptide was post–inserted into Doxil® and verified by TLC, 1H NMR, and HPLC techniques. The zeta potential, TEM, release, cell uptake, competition assay, and cytotoxicity studies were performed. In vivo antitumor activities and survival analysis on mice bearing C26 colon carcinoma were studied.Results showed that after 100 ns simulation, a stable complex between AR13 and Muc1 formed, and molecular dynamics analysis confirmed this interaction. In vitro analysis demonstrated significant enhancement of cellular binding and cell uptake.The results of in vivo study on BALB/c mice bearing C26 colon carcinoma, revealed an extended survival time to 44 days and higher tumor growth inhibition compared to Doxil®. Thus, the AR13 peptide could be explored as a potent ligand for Muc1, improving therapeutic antitumor efficiency in colon cancer cells.

Purification and molecular docking of angiotensin converting enzyme-inhibitory peptides derived from corn gluten meal hydrolysate and from in silico gastrointestinal digestion

Corn gluten meal (CGM) was hydrolyzed by Alcalase with the degree of hydrolysis (DH) and protein recovery of 28.7 % and 67.7 %, respectively. Ultrafiltration revealed that the 3–10 kDa fraction (IC50 =15.98 µg/mL) involved potent ACE inhibitory peptides. The peptides in the fraction were further separated by size exclusion chromatography and reverse-phase chromatography. The novel peptide DLLGCS was identified to be the most active ACE inhibitor (IC50 =39.0 μM). The in silico digested peptide CS was approximately 4.5 times higher than its parent counterpart (IC50 =8.5 µM). Peptides CS and DLLGCS showed an uncompetitive inhibitor characteristic with Ki values of 12.52 and 11.40 µM, respectively. Based on molecular docking, both peptides interacted with the nonactive site of ACE, primarily via hydrogen bonds at Arg522, Asp121, Glu123 and Lys118 residues for DLLCGS and Glu162, Ser147 and Glu349 residues for CS. Therefore, peptides originated from CGM hydrolysates could exhibit a higher degree of inhibition against ACE enzyme upon gastrointestinal digestion, which is likely to be a potential source of bioactive peptides with ACE inhibitory activity.

Investigating In Situ Expression of c-MYC and Candidate Ubiquitin-Specific Proteases in DLBCL and Assessment for Peptidyl Disruptor Molecule against c-MYC-USP37 Complex.

Diffuse Large B-Cell Lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma (NHL). Elevated expression of c-MYC in DLBCL is associated with poor prognosis of the disease. In different cancers, c-MYC has been found regulated by different ubiquitin-specific proteases (USPs), but to date, the role of USPs in c-MYC regulation has not been investigated in DLBCL. In this study, in situ co expression of c-MYC and three candidates USPs, USP28, USP36 and USP37, have been investigated in both the ABC and GCB subtypes of DLBCL. This shows that USP37 expression is positively correlated with the c-MYC expression in the ABC subtype of DLBCL. Structurally, both c-MYC and USP37 has shown large proportion of intrinsically disordered regions, minimizing their chances for full structure crystallization. Peptide array and docking simulations has shown that N-terminal region of c-MYC interacts directly with residues within and in proximity of catalytically active C19 domain of the USP37. Given the structural properties of the interaction sites in the c-MYC-USP37 complex, a peptidyl inhibitor has been designed. Molecular docking has shown that the peptide fits well in the targeted site of c-MYC, masking most of its residues involved in the binding with USP37. The findings could further be exploited to develop therapeutic interventions against the ABC subtype of DLBCL.

Anticancer Activity of Venom Protein Hydrolysis Fraction of Equatorial Spitting Cobra (&lt;i&gt;Naja sumatrana&lt;/i&gt;)

Bioactive peptides play an important role in targeting cancer cells. Venom protein from Naja sumatrana can be explored as a source of bioactive peptides. This research aims to identify and study the molecular docking of bioactive peptides (BPs) from trypsin hydrolysate of N. sumatrana venom protein which was fractionated using an SPE C18 column. The venom of N. sumatrana was hydrolyzed with trypsin enzyme. The protein hydrolysate was then fractionated using an RP-SPE HyperSep Retain PEP column, and the peptide fractions were tested for their anticancer activity against MCF-7 breast cancer cells using the (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method. Identification of peptides in the active fraction was carried out through high-resolution mass spectrometry. The identified peptides were molecularly docked with the EGFR receptor using AutoDock Vina. The results showed that the degree of hydrolysis was 74.7%. The 75% methanol fraction is the active fraction against MCF-7 cells, with an IC50 value of 4.80 μg/mL and a selectivity index of 5.00. Peptide-active anticancer fractions with the sequence of NSLLVK, SSLLVK and TVPVKR were successfully identified and exhibited high binding affinity values, good RMSD values, and the most suitable model for the epidermal growth factor receptor.