Computational tools for exploring peptide-membrane interactions in gram-positive bacteria

• Published in: Computational and structural biotechnology journal Vol. 21; pp. 1995 - 2008
• Main Authors: Kumar, Shreya, Balaya, Rex Devasahayam Arokia, Kanekar, Saptami, Raju, Rajesh, Prasad, Thottethodi Subrahmanya Keshava, Kandasamy, Richard K.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.01.2023; Research Network of Computational and Structural Biotechnology; Elsevier
• Subjects: amino acid composition; biofilm; biomarkers; biotechnology; BIP Inhibitors; computer simulation; digestive system; drugs; gene expression; Gram-positive bacteria; humans; In silico approaches; peptides; prediction; QSP inhibitors; QSP predictors; Quorum sensing peptides; Review; surveys; therapeutics; BFE; RAP; QSPR; GDC; TRG; Gram-positive bacteria; 3-HBA; TRAP; HNP; DT; QSP predictors; MRSA; MD; MDR; BLAST; WHO; ML; QS; AAC; AMP; ROC; AIP; DCH; PSM; H-Kinase; QSCN; IT; Quorum sensing peptides; HGM; RF; OMR; In silico approaches; GNB; PCP; SIT; CADD; ABC; FDA; D; TCS; SAR; H; PTM; OVP; KNN; SVM; PDB; QSHGM; GBM; mRMR; QSIM; CSP; SFS; ACD; QSI; MSL; BIP; MCC; Agr; QSP; PPIs; QSP inhibitors; CTD; HAM; BNB; H-phosphotransferase; RIP; ATP; BIP Inhibitors; AIP, Autoinducing Peptide; SVM, Support Vector Machine; ML, Machine Learning; GNB, Gaussian NB; QS, Quorum Sensing; D, Aspartate; ATP, Adenosine Triphosphate; PSM, Phenol-Soluble Modulin; PPIs, Protein-Protein Interactions; MRSA, Methicillin Resistant S. aureus; QSP, QS Peptides; AAC, Amino Acid Composition; ABC, ATP-binding cassette; CSP, Competence Stimulating Peptide; BLAST, Basic Local Alignment Search Tool; H-Kinase, Histidine Kinase; HGM, Human Gut Microbiota; QSPR, Quantitative Structure Property Relationship; QSIM, QS Interference Molecules; TCS, Two-Component Sensory; TRAP, Target of RAP; OMR, Omargliptin; QSI, QS Inhibitors; HAM, Hamamelitannin; DT, Decision Tree; MD, Molecular Dynamics; RIP, RNAIII-inhibiting peptide; IT, Information Theory Features; MSL, Multiple Sequence Alignment; GBM, Gradient Boosting Machine; H-phosphotransferase, Histidine Phosphotransferase; BNB, Bernoulli Naïve-Bayes; QSCN, QS communication network; SAR, Structure-Activity Relationship; H, Histidine; mRMR, minimum Redundancy and Maximum Relevance; PCP, Physicochemical Properties; SIT, Sitagliptin; CADD, Computer-Aided Drug Design; TRG, Trelagliptin; AMP, Anti-Microbial Peptide; MCC, Mathew Co-relation Coefficient; QSHGM, Quorum Sensing of Human Gut Microbes; 3-HBA, 3–Hydroxybenzoic Acid; DCH, 3,3′-(3,4-dichlorobenzylidene)-bis-(4-hydroxycoumarin); RAP, RNAIII-activating protein; PTM, Post Translational Modification; HNP, Human Neutrophil Peptide; WHO, World Health Organization; PDB, Protein Data Bank; RF, Random Forest; CTD, Composition-Transition-Distribution; OVP, Overlapping Property Features; GDC, g-gap Dipeptide; FDA, Food and Drug Administration; ROC, Receiver Operating Characteristic; Agr, Accessory gene regulator; KNN, K-Nearest Neighbors; BIP, Biofilm Inhibitory Peptides; SFS, Sequential Forward Search; BFE, Binding Free Energy; MDR, Multiple Drug Resistance; ACD, Available Chemicals Database

The vital cellular functions in Gram-positive bacteria are controlled by signaling molecules known as quorum sensing peptides (QSPs), considered promising therapeutic interventions for bacterial infections. In the bacterial system QSPs bind to membrane-coupled receptors, which then auto-phosphorylat...