Bioinformatic methods for the design of antimicrobial peptides

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 3 - 36

Published: Jan. 1, 2025

Language: Английский

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Peptide‑based therapeutic strategies for glioma: current state and prospects

Peptides, Journal Year: 2025, Volume and Issue: 185, P. 171354 - 171354

Published: Feb. 6, 2025

Language: Английский

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Improving the antimicrobial activity of RP9 peptide through theoretical and experimental investigation

Biochemistry and Biophysics Reports, Journal Year: 2025, Volume and Issue: 41, P. 101953 - 101953

Published: Feb. 15, 2025

Language: Английский

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Implications of Artificial Intelligence for Arterial Drug Delivery and Beyond

Published: Jan. 1, 2025

Language: Английский

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Application of computational approaches in biomembranes: From structure to function

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2023, Volume and Issue: 13(6)

Published: July 6, 2023

Abstract Biological membranes (biomembranes) are one of the most complicated structures that allow life to exist. Investigating their structure, dynamics, and function is crucial for advancing our knowledge cellular mechanisms developing novel therapeutic strategies. However, experimental investigation many biomembrane phenomena challenging due compositional structural complexity, as well inherently multi‐scalar features. Computational approaches, particularly molecular dynamics (MD) simulations, have emerged powerful tools addressing atomic details systems, driving breakthroughs in understanding biomembranes roles function. This review presents an overview latest advancements related computational from force fields model construction MD simulations trajectory analysis. We also discussed current hot research topics challenges. Finally, we outline future directions, emphasizing integration field development, enhanced sampling techniques, data‐driven approaches accelerate growth this years come. aim equip readers with promise limitations emerging technologies systems offer valuable recommendations endeavors. article categorized under: Structure Mechanism > Biochemistry Biophysics Molecular Statistical Mechanics Dynamics Monte‐Carlo Methods

Language: Английский

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A prediction model for blood-brain barrier penetrating peptides based on masked peptide transformers with dynamic routing

Briefings in Bioinformatics, Journal Year: 2023, Volume and Issue: 24(6)

Published: Sept. 22, 2023

Abstract Blood-brain barrier penetrating peptides (BBBPs) are short peptide sequences that possess the ability to traverse selective blood-brain interface, making them valuable drug candidates or carriers for various payloads. However, in vivo vitro validation of BBBPs is resource-intensive and time-consuming, driving need accurate silico prediction methods. Unfortunately, scarcity experimentally validated hinders efficacy current machine-learning approaches generating reliable predictions. In this paper, we present DeepB3P3, a novel framework prediction. Our contribution encompasses four key aspects. Firstly, propose deep learning model consisting transformer encoder layer, convolutional network backbone, capsule classification head. This integrated architecture effectively learns representative features from sequences. Secondly, introduce masked as powerful data augmentation technique compensate small training set sizes BBBP Thirdly, develop threshold-tuning method handle imbalanced by approximating optimal decision threshold using set. Lastly, DeepB3P3 provides an estimation uncertainty level associated with each Through extensive experiments, demonstrate achieves state-of-the-art accuracy up 98.31% on benchmarking dataset, solidifying its potential promising computational tool discovery BBBPs.

Language: Английский

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Conjugation of sulpiride with a cell penetrating peptide to augment the antidepressant efficacy and reduce serum prolactin levels

Biomedicine & Pharmacotherapy, Journal Year: 2024, Volume and Issue: 174, P. 116610 - 116610

Published: April 19, 2024

Depression ranks as the fourth most prevalent global disease, with suicide incidents occurring at a younger age. Sulpiride (SUL), an atypical antidepressant drug acting dopamine D2 receptor antagonist and possessing anti-inflammatory properties, exhibits limited ability to penetrate blood brain barrier (BBB). This weak penetration hampers its inhibitory effect on prolactin release in pituitary gland, consequently leading hyperprolactinemia. In order enhance central nervous system efficacy of sulpiride reduce serum levels, we covalently linked VPALR derived from nuclear DNA repair protein ku70. vivo study depressive mice using intraperitoneal injection VPALR-SUL demonstrated significant increase struggle time total distance compared those treated only while also reducing concentration. The pharmacokinetic results showed that prolonged half-life increased bioavailability. conclusion, exhibited potential for enhancing transport across BBB, augmenting effects, levels. laid foundation improving delivery developing novel antidepressants.

Language: Английский

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MolGC: molecular geometry comparator algorithm for bond length mean absolute error computation on molecules

Molecular Diversity, Journal Year: 2024, Volume and Issue: 28(4), P. 1925 - 1945

Published: Aug. 1, 2024

Language: Английский

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Start Me Up: How Can Surrounding Gangliosides Affect Sodium-Potassium ATPase Activity and Steer towards Pathological Ion Imbalance in Neurons?

Biomedicines, Journal Year: 2022, Volume and Issue: 10(7), P. 1518 - 1518

Published: June 27, 2022

Gangliosides, amphiphilic glycosphingolipids, tend to associate laterally with other membrane constituents and undergo extensive interactions proteins in cis or trans configurations. Studies of human diseases resulting from mutations the ganglioside biosynthesis pathway research on transgenic mice same implicate gangliosides pathogenesis epilepsy. Gangliosides are reported affect activity Na+/K+-ATPase, ubiquitously expressed plasma pump responsible for stabilization resting potential by hyperpolarization, firing up action ion homeostasis. Impaired Na+/K+-ATPase has also been hypothesized cause seizures several mechanisms. In this review we present different epileptic phenotypes that caused impaired changed composition. We further discuss how may influence acting as lipid sorting machinery providing optimal stage function. By establishing a distinct environment, together lipids, possibly modulate aid “starting up” “turning off” vital pump. Therefore, structural changes neuronal membranes altered composition can be contributing factor leading aberrant imbalance priming neurons pathological firing.

Language: Английский

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Effects of C-Terminal Lys-Arg Residue of AapA1 Protein on Toxicity and Structural Mechanism

Toxins, Journal Year: 2023, Volume and Issue: 15(9), P. 542 - 542

Published: Sept. 2, 2023

Previous experimental investigations have established the indispensability of C-terminal Lys-Arg residues in toxic activity AapA1 toxin protein. is classified as a type I toxin–antitoxin (TA) bacterial toxin, and precise impact on its structure mechanism action remains elusive. To address this knowledge gap, present study employed molecular dynamics (MD) enhanced sampling Well-tempered Two-dimensional Metadynamics (2D-MetaD) simulations to examine behavior truncated (AapA1-28) within inner membrane Escherichia coli. Specifically, focused elucidation possible conformation states AapA1-28 protein POPE/POPG (3:1) bilayers their interactions between bilayers. The findings our investigation indicate that does not adopt vertical orientation upon insertion; rather, it assumes an angled conformation, with side chain Lys-23 directed toward upper layer membrane. This non-transmembrane impedes ability form pores membrane, resulting reduced toxicity towards These results suggest C-Terminal positively charged are essential for electrostatic binding negatively head group bottom bilayer which stabilize transmembrane conformation. outcomes contribute comprehension functionality membrane-associated proteins, provide improved understanding how sequence influences antimicrobial effect.

Language: Английский

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