Design and In Silico Evaluation of a Novel Cyclic Disulfide-Rich anti-VEGF Peptide as a Potential Antiangiogenic Drug

Baghban, Roghayyeh; Ghasemali, Samaneh; Farajnia, Safar; Hoseinpoor, Reyhaneh; Andarzi, Sahar; Zakariazadeh, Mostafa; Zarredar, Habib

doi:10.1007/s10989-021-10250-8

Cited by 6 publications

(1 citation statement)

References 52 publications

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“…The frequency could be calculated by several fragments with activity from the protein sequence, and N as the number of protein amino acid residues (Zulvana et al 2019). PeptideRanker consideration in determining the threshold in this ranking is based on the two main components of the location and composition of amino acids in the peptide sequence (Baghban et al 2021). A protein with bioactivity could still have an allergic reaction with the predicted sequences that matched the IgE epitope.…”

Section: Discussionmentioning

confidence: 99%

In Silico Analysis of Protein of Milk, Soybean, and Kefir as Anti- Thrombotic Bioactive Peptide

2022

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Currently, Cardiovascular Diseases (CVDs) cases are increasing significantly in Indonesia and the world. WHO reported that in 2019-related CVD patients accounted for 85%, which increased to 87% in 2021. The cases increased significantly by 2%, which is a significant number as it covered the world population. Stroke is a disease affected by platelets undergoing thrombolysis by the α-thrombin (IIa) receptor with coagulation factors on the heart blood vessel. Chemical or synthesis drugs to treat thrombolytics such as heparin are already available, but they would be harmful if misused. In this study, we focused on the activity, interaction, and prediction of the physicochemical of anti-thrombotic peptides. We found that k-casein from kefir has the highest activity of 0.037 A based on BIOPEP analysis with 17 peptide libraries and molecular docking visualization analysis using PyMol, PyRx, and Discovery Studio for screening the best peptide. ToxinPred and AlgPred showed there are no potentially harmful peptides, but the protein variant of β-conglycinin subunit can be an allergen known to the immune system IgE. In conclusion, the GPR peptide has the highest binding affinity, with a total energy of -6.8 kcal/mol.

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Section: Discussionmentioning

confidence: 99%

In Silico Analysis of Protein of Milk, Soybean, and Kefir as Anti- Thrombotic Bioactive Peptide

2022

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Hybrid Strategy of Bioinformatics Modeling (in silico): Biologically Active Peptides of Milk Protein

Кручинин

Bolshakova

2022

Food Processing: Techniques and Technology

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Bioinformatic analysis methods are an auxiliary tool in the preliminary stage of research into biocatalytic conversion of proteins with predicted release of biologically active peptides. However, there are a number of factors ignored in current strategies for designing biologically active peptides, which prevents the complete prediction of their biological properties. This determines the relevance of the research objective, i.e. developing a hybrid strategy for bioinformatic modeling to study biologically active peptides of milk protein. The new strategy ranks key criteria based on high-performance algorithms of proteomic database. The research featured the scientific publications on in silico methods applied to biologically active peptides. Modern taxonometric methods of information retrieval were applied using the RSCI, Scopus and Web of Science databases. The article introduces and describes step by step the optimal in silico hybrid strategy algorithm for studying biologically active milk protein peptides. The algorithm takes into account the safety assessment of all hydrolysis products, their physicochemical and technological properties. The strategy algorithm relies on analytical data on the protein profile, the amino acid sequence of proteins that make up the raw material, taking into account their polymorphism, and the subsequent identification of bioactive amino acid sites in the protein structure. The algorithm selects optimal enzyme preparations, as well as models the hydrolysis and assesses the peptide bioactivity using proteomic databases. At the preliminary stage of protein hydrolysis, the new in silico strategy scientifically predicts the targeted release of stable peptide complexes of biologically active peptides with proven bioactivity, safety and sensory characteristics. The hybrid algorithm contributes to accumulation of the necessary primary data so as to reduce the time and cost of laboratory experiments.

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Rational Design of Anti-Angiogenic Peptides to Inhibit VEGF/VEGFR2 Interactions for Cancer Therapeutics

Ghasemali

Farajnia

Barzegar

et al. 2022

ACAMC

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Background: Angiogenesis is a critical physiological process that plays a key role in tumor progression, metastatic dissemination, and invasion. In the last two decades, the vascular endothelial growth factor (VEGF) signaling pathway has been the area of extensive researches. VEGF executes its special effects by binding to vascular endothelial growth factor receptors (VEGFRs), particularly VEGFR-2. Objective: The inhibition of VEGF/VEGFR2 interaction is known as an effective cancer therapy strategy. The current study pointed to design and model an anti-VEGF peptide based on VEGFR2 binding regions. Method: The large-scale peptide mutation screening was used to achieve a potent peptide with high binding affinity to VEGF for possible application in inhibition of VEGF/VEGFR2 interaction. The AntiCP and Peptide Ranker servers were used to generate the possible peptides library with anticancer activities and prediction of peptides bioactivity. Then, the interaction of VEGF and all library peptides were analyzed using Hex 8.0.0 and ClusPro tools. A number of six peptides with favorable docking scores were achieved. All of the best docking scores of peptides in complexes with VEGF were evaluated to confirm their stability, using molecular dynamics simulation (MD) with the help of the GROMACS software package. Results: As a result, two antiangiogenic peptides with 13 residues of PepA (NGIDFNRDFFLGL) and PepC (NGIDFNRDKFLFL) were achieved and introduced to inhibit VEGF/VEGFR2 interactions. Conclusions: In summary, this study provided new insights into peptide-based therapeutics development for targeting VEGF signaling pathway in tumor cells. PepA and PepC are recommended as potentially promising anticancer agents for further experimental evaluations.

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Design and In Silico Evaluation of a Novel Cyclic Disulfide-Rich anti-VEGF Peptide as a Potential Antiangiogenic Drug

Cited by 6 publications

References 52 publications

In Silico Analysis of Protein of Milk, Soybean, and Kefir as Anti- Thrombotic Bioactive Peptide

In Silico Analysis of Protein of Milk, Soybean, and Kefir as Anti- Thrombotic Bioactive Peptide

Hybrid Strategy of Bioinformatics Modeling (in silico): Biologically Active Peptides of Milk Protein

Rational Design of Anti-Angiogenic Peptides to Inhibit VEGF/VEGFR2 Interactions for Cancer Therapeutics

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