Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics—quantum and molecular mechanical approaches

Sekar, P.; Paul, D. Meshach; Srinivasan, E.; Rajasekaran, R.

doi:10.1007/s00894-020-04652-6

Cited by 4 publications

(3 citation statements)

References 60 publications

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“…In the protein-peptide interaction analyses of AMPs focusing on S1 Middle East Respiratory Syndrome (MERS) infection, the frog skin AMPs such as Magainin, Brevinin, and Dermaseptin have been documented to be the best docked peptides with high binding affinities [ 22 ]. Moreover, we previously reported the antimicrobial properties of broad spectrum ocellatin peptides [ 23 ], which prompts us to include it in this investigation and to assess its antiviral activity. Based on it, we intended to evaluate the efficacy of potential frog skin alpha-helical AMPs with its closest analogues, such as Brevinin-1BYa (1BYa), Brevinin-1BYc (1BYc), Dermaseptin-S4 (DS4), Dermaseptin-S9 (DS9), Magainin-1 (M1), Magainin-2 (M2), Ocellatin-1 (O1), and Ocellatin-F1 (OF1) that might inhibit spike protein S1 (RDB) of SARS-CoV-2 preserving the low hemolytic activity and high antimicrobial activity.…”

Section: Introductionmentioning

confidence: 99%

“…Magainin peptides (M1 and M2) isolated from the skin of African clawed frogs, Xenopus laevis [ 34 , 35 ] showed an antiviral activity against HSV-1, HSV-2, HIV-1, and SARS-CoV-2 [ 36 – 39 ]. Ocellatin O1 and Ocellatin OF1 peptides were isolated from the skin secretion of Brazilian pepper frogs such as Leptodactylus ocellatus and Leptodactylus labyrinthicus respectively [ 24 ] wherein, both the ocellatin peptides have shown to possess a wide variety of antibacterial, antiviral, and antifungal activities in experimental studies [ 23 , 40 – 42 ]. Synergic antiviral effects between OF1 and alkaloid bufotenine have shown to limit BHK-21 cell lines advanced to rabies viral infection [ 43 ].…”

Section: Introductionmentioning

confidence: 99%

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Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19

et al. 2022

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In COVID-19 infection, the SARS-CoV-2 spike protein S1 interacts to the ACE2 receptor of human host, instigating the viral infection. To examine the competitive inhibitor efficacy of broad spectrum alpha helical AMPs extracted from frog skin, a comparative study of intermolecular interactions between viral S1 and AMPs was performed relative to S1-ACE2p interactions. The ACE2 binding region with S1 was extracted as ACE2p from the complex for ease of computation. Surprisingly, the Spike-Dermaseptin-S9 complex had more intermolecular interactions than the other peptide complexes and importantly, the S1-ACE2p complex. We observed how atomic displacements in docked complexes impacted structural integrity of a receptor-binding domain in S1 through conformational sampling analysis. Notably, this geometry-based sampling approach confers the robust interactions that endure in S1-Dermaseptin-S9 complex, demonstrating its conformational transition. Additionally, QM calculations revealed that the global hardness to resist chemical perturbations was found more in Dermaseptin-S9 compared to ACE2p. Moreover, the conventional MD through PCA and the torsional angle analyses indicated that Dermaseptin-S9 altered the conformations of S1 considerably. Our analysis further revealed the high structural stability of S1-Dermaseptin-S9 complex and particularly, the trajectory analysis of the secondary structural elements established the alpha helical conformations to be retained in S1-Dermaseptin-S9 complex, as substantiated by SMD results. In conclusion, the functional dynamics proved to be significant for viral Spike S1 and Dermaseptin-S9 peptide when compared to ACE2p complex. Hence, Dermaseptin-S9 peptide inhibitor could be a strong candidate for therapeutic scaffold to prevent infection of SARS-CoV-2. Supplementary Information The online version contains supplementary material available at 10.1007/s00894-022-05117-8.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19

et al. 2022

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“…The preference for naturally-derived antimicrobial agents in biomedical applications relies on the fact that microorganisms cannot generate resistance to them as they are natural substances (Kumar, Lee, Beyenal, & Lee, 2020). Naturally-derived antimicrobial agents include vegetal and essential oils, antimicrobial peptides and fatty acids (Aslanli, Lyagin, Stepanov, Presnov, & Efremenko, 2020;Casillas-Vargas et al, 2021;Lalouckova et al, 2021;Pereira dos Santos et al, 2019;Sekar, Paul, Srinivasan, & Rajasekaran, 2021). In this respect, tucumã (Astrocaryum vulgare), an Amazon fruit from which an oil or a butter can be extracted, and its derivatives have been investigated for biomedical applications (Baldissera et al, 2017;Bressa et al, 2021;Cordenonsi et al, 2020;Fernandes, 2015;Rossato et al, 2020Rossato et al, , 2021.…”

Section: Introductionmentioning

confidence: 99%

Bacterial nanocellulose and long-chain fatty acids interaction

Oviedo

Tonel

Filho

et al. 2022

Int J Innov Educ Res

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Chronic wounds are a big challenge in contemporary society, as they lead to a decrease in life-quality, amputations and even death. Infections and biofilm formation might occur with chronic wounds, due to the higher susceptibility to antibiotic multi-resistant bacteria. In this situation, novel wound dressing biomaterials are needed for treatment. Thus, the aim of this research was to evaluate a possible BNC interaction with tucumã oil/butter-derived fatty acids, as this system could be a promising biomaterial for wound treating. The interaction between cellobiose (BNC basic unit) and four fatty acids was evaluated by ab initio simulations and density functional theory (DFT), through SIESTA code. Molecular docking was also used to investigate the effect of a possible releasing of the studied fatty acids to the quorum-sensing proteins of Pseudomonas aeruginosa (gram-negative bacterium) and Staphylococcus aureus (gram-positive bacterium). According to ab initio simulations, the interaction between cellobiose and fatty acids derived from tucumã oil/butter was suggested due to physical adsorption (energy around 0.17-1.33 eV) of the lipidic structures into cellobiose. A great binding affinity (∆G ranging from 4.2-8.2 kcal.mol-1) was observed for both protonated and deprotonated fatty acids against P. aeruginosa (LasI, LasA and Rhlr) and S. aureus (ArgA and ArgC) quorum-sensing proteins, indicating that these bioactive compounds might act as potential antimicrobial and/or antibiofilm agents in the proposed system. Hence, from a theoretical viewpoint, the proposed system could be a promising raw biomaterial in the production of chronic wound dressings.

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Hydrophobic Residues Confer the Helicity and Membrane Permeability of Ocellatin-1 Antimicrobial Peptide Scaffold Towards Therapeutics

Sekar

Chandrasekhar

Rajasekaran

2021

Int J Pept Res Ther

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Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics—quantum and molecular mechanical approaches

Cited by 4 publications

References 60 publications

Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19

Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19

Bacterial nanocellulose and long-chain fatty acids interaction

Hydrophobic Residues Confer the Helicity and Membrane Permeability of Ocellatin-1 Antimicrobial Peptide Scaffold Towards Therapeutics

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