Molecular docking of the pentapeptide derived from rice bran protein as anticancer agent inhibiting both receptor and non-receptor tyrosine kinases

Gasymov, Oktay K.; Kecel‐Gunduz, Serda; Çeli̇k, Sefa; Akyüz, Sevim; Özel, Ayşen E.; Agaeva, G. A.; Suleymanova, Leman M.; Agaeva, U. T.; Bakhishova, Matanat; Aliyev, Jamil A.

doi:10.1080/07391102.2022.2067234

Journal of Biomolecular Structure and Dynamics

2022

DOI: 10.1080/07391102.2022.2067234

|View full text |Cite

Molecular docking of the pentapeptide derived from rice bran protein as anticancer agent inhibiting both receptor and non-receptor tyrosine kinases

Oktay K. Gasymov¹,

Serda Kecel‐Gunduz

Sefa Çeli̇k

et al.

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...

Citation Types

Supporting

Mentioning

Contrasting

Year Published

2024

Publication Types

Select...

Article3

Relationship

Self Cite0

Independent3

Authors

Journals

Cited by 3 publications

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

Molecular docking and molecular dynamics studies of Glu‐Glu‐Arg, Glu‐Pro‐Arg, and Pro‐Arg‐Pro tripeptides to reveal their anticancer and antiviral potentials

Yilmaz,

Celik,

Erbolukbas Ozel

et al. 2024

J Chinese Chemical Soc

View full text Add to dashboard Cite

Bioactive peptides have been emerging as drug candidates with increasing importance in the last few decades. In this study, to evaluate the anticancer and antiviral properties of EER (Glu‐Glu‐Arg), EPR (Glu‐Pro‐Arg), and PRP (Pro‐Arg‐Pro) tripeptides, firstly their conformation preferences were searched, and the most stable optimized structure of each tripeptide was determined, using the molecular mechanics force field (MMFF) method and the Spartan06 program. Afterwards, each tripeptide was docked to SARS‐CoV‐2 spike protein receptor‐binding domain (6M0J), SARS‐CoV‐2 main protease (6M03, 6LU7), spike glycoprotein (6VXX), DNA (1BNA), integrins (4WK0, 3ZDX, 1JV2) and epidermal growth factor receptor tyrosine kinase (4HJO). Moreover, molecular dynamics (MD) simulations were performed to validate the stability of the EER, EPR and PRP tripeptides docked to SARS‐CoV‐2 main protease, MPro (6M03) and epidermal growth factor receptor tyrosine kinase (4HJO) within 100 ns time scale and ligand‐receptor interactions were evaluated. The metrics root‐mean‐square deviation, root‐mean‐square fluctuation, intermolecular hydrogen bonding, and radius of gyration revealed that the EER, EPR, and PRP tripeptides form energetically stable complexes with the target proteins. The binding free energies were calculated by the combination of Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson‐Boltzmann Surface Area (MM‐PBSA) methods (MM/PB(GB)SA). Principal Component Analysis on MD data was performed to evaluate the energy and structural information of the tripeptide‐protein complexes. Additionally, in‐silico structure‐based pharmacological predictions were made and the anticancer and antibacterial activities of the tripeptides were predicted.

show abstract

Molecular docking and molecular dynamics studies of Glu‐Glu‐Arg, Glu‐Pro‐Arg, and Pro‐Arg‐Pro tripeptides to reveal their anticancer and antiviral potentials

Yilmaz,

Celik,

Erbolukbas Ozel

et al. 2024

J Chinese Chemical Soc

View full text Add to dashboard Cite

show abstract

Binding of Peptides Containing D‐Amino Acids to the Tsg101 Tumor Susceptibility Protein

Perez,

Chapagain,

Gerstman

2024

ChemistrySelect

View full text Add to dashboard Cite

Tsg101 is implicated in tumorigenesis and viral budding, and its inhibition through peptide binding is a potential therapeutic strategy. We utilized the crystal structure of the Tsg101‐PSAP complex from the protein databank in molecular dynamics studies on peptide‐Tsg101 interactions. To enhance peptide stability against enzymatic degradation, we designed peptides with L‐form terminal prolines and D‐form middle amino acids. These peptides also featured acetylated proline at the N‐terminus and amidated C‐terminus, increasing resistance to proteases. Virtual screening of 400 amino acid combinations identified promising peptide candidates and specific binding sites. Subsequent molecular dynamics simulations focused on the peptide PywP, which displayed strong binding stability at a novel Tsg101 site. Further simulations with variations of the D‐form amino acid ′w’ showed that 18 of 21 tested peptides, notably PyeP and PytP, remained firmly bound, highlighting their potential as Tsg101 inhibitors. These peptides also contain hydrophilic residues, potentially improving solubility and therapeutic delivery.

show abstract

Vibrational spectroscopic characterization, quantum chemical, molecular docking and molecular dynamics investigations of cyclo(L-phenylalanyl-L-proline), an anticancer agent

Oktemer,

Celik,

Ozel

et al. 2024

Spectroscopy Letters

View full text Add to dashboard Cite

scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.

Contact Info

customersupport@researchsolutions.com

10624 S. Eastern Ave., Ste. A-614

Henderson, NV 89052, USA

This site is protected by reCAPTCHA and the Google Privacy Policy and Terms of Service apply.

Blog Terms and Conditions API Terms Privacy Policy Contact Cookie Preferences Do Not Sell or Share My Personal Information

Made with 💙 for researchers

Part of the Research Solutions Family.

Molecular docking of the pentapeptide derived from rice bran protein as anticancer agent inhibiting both receptor and non-receptor tyrosine kinases

Cited by 3 publications

References 50 publications

Molecular docking and molecular dynamics studies of Glu‐Glu‐Arg, Glu‐Pro‐Arg, and Pro‐Arg‐Pro tripeptides to reveal their anticancer and antiviral potentials

Molecular docking and molecular dynamics studies of Glu‐Glu‐Arg, Glu‐Pro‐Arg, and Pro‐Arg‐Pro tripeptides to reveal their anticancer and antiviral potentials

Binding of Peptides Containing D‐Amino Acids to the Tsg101 Tumor Susceptibility Protein

Vibrational spectroscopic characterization, quantum chemical, molecular docking and molecular dynamics investigations of cyclo(L-phenylalanyl-L-proline), an anticancer agent

Contact Info

Product

Resources

About