Important structural features of antimicrobial peptides towards specific activity: Trends in the development of efficient therapeutics

Bioorganic Chemistry, Год журнала: 2024, Номер 149, С. 107524 - 107524

Опубликована: Июнь 5, 2024

Язык: Английский

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StackDPPred: Multiclass prediction of defensin peptides using stacked ensemble learning with optimized features

Methods, Год журнала: 2024, Номер 230, С. 129 - 139

Опубликована: Авг. 22, 2024

Host defense or antimicrobial peptides (AMPs) are promising candidates for protecting host against microbial pathogens example bacteria, virus, fungi, yeast. Defensins the type of AMPs that act as potential therapeutic drug agent and perform vital role in various biological process. Conventional Experiments to identify defensin (DPs) time consuming expensive. Thus, shortcomings wet lab experiments leveraged by computational methods accurately predict functional types DPs. In this paper, we aim propose a novel multi-class ensemble-based prediction model called StackDPPred identifying properties The peptide sequences encoded using split amino acid composition (SAAC), segmented position specific scoring matrix (SegPSSM), histogram oriented gradients-based PSSM (HOGPSSM) feature extraction based graphical statistical (FEGS) descriptors. Next, principal component analysis (PCA) is used select best subset attributes. After that, optimized features fed into single machine learning stacking-based ensemble classifiers. Furthermore, ablation study demonstrates robustness efficacy stacking approach reduced predicting DPs their families. proposed method improves overall accuracy 13.41% 7.62% compared existing predictors iDPF-PseRAAC iDEF-PseRAAC, respectively on validation test. Additionally, applied local interpretable model-agnostic explanations (LIME) algorithm understand contribution selected prediction. We believe, could serve valuable tool accelerating screening large-scale peptide-based discovery

Язык: Английский

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Comparative Analysis of pK_a Predictions for Arsonic Acids Using Density Functional Theory-Based and Machine Learning Approaches

ACS Omega, Год журнала: 2025, Номер unknown

Опубликована: Янв. 16, 2025

Arsonic acids (RAsO(OH)2), prevalent in contaminated food, water, air, and soil, pose significant environmental health risks due to their variable ionization states, which influence key properties such as lipophilicity, solubility, membrane permeability. Accurate pK a prediction for these compounds is critical yet challenging, existing models often exhibit limitations across diverse chemical spaces. This study presents comparative analysis of predictions arsonic using support vector machine-based machine learning (ML) approach three density functional theory (DFT)-based models. The DFT evaluated include correlations the maximum surface electrostatic potential (V S,max), atomic charges derived from solvation model (solvation based on density), scaled solvent-accessible method. Results indicate that yielded high mean unsigned errors, rendering it less effective. In contrast, charge-based method conjugated arsonate base provided most accurate predictions. ML-based demonstrated strong predictive performance, suggesting its utility broader obtained values V S,max show weak level, because way predicting related only character molecule. However, influenced by many factors, including molecular structure, solvation, resonance, inductive effects, local environments. cannot fully capture different interactions, gives simplistic view overall field.

Язык: Английский

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Design, synthesis, and photophysical properties of an iridium(III) complex bearing an indolo[3,2,1- jk ]carbazole-decorated NHC ligand

Journal of Coordination Chemistry, Год журнала: 2025, Номер unknown, С. 1 - 15

Опубликована: Янв. 21, 2025

Язык: Английский

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Recent Progress in Terrestrial Biota Derived Antibacterial Agents for Medical Applications

Molecules, Год журнала: 2024, Номер 29(20), С. 4889 - 4889

Опубликована: Окт. 15, 2024

Conventional antibiotic and multidrug treatments are becoming less effective the discovery of new safe antibacterial agents is a global priority. Returning to natural product relatively current trend. Terrestrial biota rich source biologically active substances whose potential has not been fully utilized. The aim this review present state-of-the-art terrestrial biota-derived inspired by treatments. It summarizes most important sources newly identified or modified from last five years. focuses on significance plant- animal- bacteria-derived as powerful alternatives antibiotics, well advantages utilizing molecules alone in combination with antibiotics. main conclusion that products open variety ways for modern improved therapeutic strategies. New known were discovered during 5 years, which under investigation together some long-ago but now experiencing their renaissance development medical use peptides combinational therapy commercial antibiotics outlined promising method treating bacterial infections. In vivo testing clinical trials necessary reach application.

Язык: Английский

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De Novo Design and Characterization of Novel Antimicrobial Peptides, Lk3 and Lk4, Containing Repeating Unit

International Journal of Peptide Research and Therapeutics, Год журнала: 2024, Номер 30(6)

Опубликована: Окт. 1, 2024

Язык: Английский

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Biopreservation strategies using bacteriocins to control meat spoilage and foodborne outbreaks

Italian Journal of Food Safety, Год журнала: 2024, Номер unknown

Опубликована: Окт. 17, 2024

Fresh meat is highly perishable, presenting challenges in spoilage mitigation and waste reduction globally. Despite the efforts, foodborne outbreaks from consumption persist. Biopreservation offers a natural solution to extend shelf life by managing microbial communities. However, include effective diffusion of bacteriocins through matrix potential inhibition starter cultures targeting closely related lactic acid bacteria (LAB). LAB, predominant meat, produce - small, stable peptides with broad antimicrobial properties across varying pH temperature conditions. This review highlights recent advances optimization bacteriocin use, considering its structure mode action. Moreover, strengths weaknesses different techniques for screening, including novel bioengineering methods, are described. Finally, we discuss advantages limitations modes application toward preservation fresh, cured, products.

Язык: Английский

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