Abou Alaiwa MH, Reznikov LR, Gansemer ND et al (2014) pH modulates the activity and synergism of the airway surface liquid antimicrobials β-defensin-3 and LL-37. Proc Natl Acad Sci USA 111:18703–18708. https://doi.org/10.1073/pnas.1422091112

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alford RF, Fleming PJ, Fleming KG, Gray JJ (2020) Protein structure prediction and design in a biologically realistic implicit membrane. Biophys J 118:2042–2055. https://doi.org/10.1016/j.bpj.2020.03.006

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alford RF, Samanta R, Gray JJ (2021) Diverse scientific benchmarks for implicit membrane energy functions. J Chem Theory Comput 17:5248–5261. https://doi.org/10.1021/acs.jctc.0c00646

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alpízar-Pedraza D, Roque-Diaz Y, Garay-Pérez H et al (2024) Insights into the adsorption mechanisms of the antimicrobial peptide CIDEM-501 on membrane models. Antibiotics 13:167. https://doi.org/10.3390/antibiotics13020167

Article  CAS  PubMed  PubMed Central  Google Scholar 

An Y, Webb MA, Jacobs WM (2024) Active learning of the thermodynamics-dynamics trade-off in protein condensates. Sci Adv. https://doi.org/10.1126/sciadv.adj2448

Article  PubMed  PubMed Central  Google Scholar 

Andrés MT, Fierro P, Antuña V, Fierro JF (2024) The antimicrobial activity of human defensins at physiological non-permeabilizing concentrations is caused by the inhibition of the plasma membrane H+-ATPases. Int J Mol Sci 25:7335. https://doi.org/10.3390/ijms25137335

Article  CAS  PubMed  PubMed Central  Google Scholar 

Awang T, Chairatana P, Vijayan R, Pongprayoon P (2021) Evaluation of the binding mechanism of human defensin 5 in a bacterial membrane: a simulation study. Int J Mol Sci 22:12401. https://doi.org/10.3390/ijms222212401

Article  CAS  PubMed  PubMed Central  Google Scholar 

Awang T, Chairatana P, Pongprayoon P (2023) Molecular dynamics simulations of human α-defensin 5 (HD5) crossing gram-negative bacterial membrane. PLoS One 18:e0294041. https://doi.org/10.1371/journal.pone.0294041

Article  CAS  PubMed  PubMed Central  Google Scholar 

Banu S, Nagaraj R, Idris MM (2022) Defensins: therapeutic molecules with potential to treat SARS-CoV-2 infection. Indian J Med Res 155:83–85. https://doi.org/10.4103/ijmr.ijmr_2798_21

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bedran TBL, Mayer MPA, Spolidorio DP, Grenier D (2014) Synergistic anti-inflammatory activity of the antimicrobial peptides human beta-defensin-3 (hBD-3) and cathelicidin (LL-37) in a three-dimensional co-culture model of gingival epithelial cells and fibroblasts. PLoS One 9:e106766. https://doi.org/10.1371/journal.pone.0106766

Article  CAS  PubMed  PubMed Central  Google Scholar 

Benfield AH, Henriques ST (2020) Mode-of-action of antimicrobial peptides: membrane disruption vs. intracellular mechanisms. Front Med Technol. https://doi.org/10.3389/fmedt.2020.610997

Article  PubMed  PubMed Central  Google Scholar 

Borenstein LA, Selsted ME, Lehrer RI, Miller JN (1991) Antimicrobial activity of rabbit leukocyte defensins against Treponema pallidum subsp. pallidum. Infect Immun 59:1359–1367. https://doi.org/10.1128/iai.59.4.1359-1367.1991

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brender JR, McHenry AJ, Ramamoorthy A (2012) Does cholesterol play a role in the bacterial selectivity of antimicrobial peptides? Front Immunol. https://doi.org/10.3389/fimmu.2012.00195

Article  PubMed  PubMed Central  Google Scholar 

Brewer A, Zhang L (2021) Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method. Biophys Chem 277:106662. https://doi.org/10.1016/j.bpc.2021.106662

Article  CAS  PubMed  Google Scholar 

Brizuela CA, Liu G, Stokes JM, de la Fuente-Nunez C (2025) ) < scp > AI Methods for antimicrobial peptides: progress and challenges. Microb Biotechnol 18. https://doi.org/10.1111/1751-7915.70072

Broemstrup T, Reuter N (2010) Molecular dynamics simulations of mixed acidic/zwitterionic phospholipid bilayers. Biophys J 99:825–833. https://doi.org/10.1016/j.bpj.2010.04.064

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brooks BR, Brooks CL, Mackerell AD et al (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545–1614. https://doi.org/10.1002/jcc.21287

Article  CAS  PubMed  PubMed Central  Google Scholar 

Browne K, Chakraborty S, Chen R et al (2020) A new era of antibiotics: the clinical potential of antimicrobial peptides. Int J Mol Sci. https://doi.org/10.3390/ijms21197047

Article  PubMed  PubMed Central  Google Scholar 

Chaudhary N, Aparoy P (2020) Application of per-residue energy decomposition to identify the set of amino acids critical for in silico prediction of COX-2 inhibitory activity. Heliyon 6:e04944. https://doi.org/10.1016/j.heliyon.2020.e04944

Article  CAS  PubMed  PubMed Central  Google Scholar 

Choe S (2023) Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method. Sci Rep 13:1168. https://doi.org/10.1038/s41598-023-28493-4

Das S, Nikolaidis N, Goto H et al (2010) Comparative genomics and evolution of the alpha-defensin multigene family in primates. Mol Biol Evol 27:2333–2343. https://doi.org/10.1093/molbev/msq118

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dinata R, Vashisht M, Mandal SM, Baindara P (2025) Repurposing of human defensins as a promising antiviral therapeutics against SARS-CoV-2. The Microbe 7:100388. https://doi.org/10.1016/j.microb.2025.100388

Article  Google Scholar 

Domański J, Hedger G, Best RB et al (2017) Convergence and sampling in determining free energy landscapes for membrane protein association. J Phys Chem B 121:3364–3375. https://doi.org/10.1021/acs.jpcb.6b08445

Article  CAS  PubMed  Google Scholar 

Drab E, Sugihara K (2020) Cooperative function of LL-37 and HNP1 protects mammalian cell membranes from lysis. Biophys J 119:2440–2450. https://doi.org/10.1016/j.bpj.2020.10.031

Article  CAS  PubMed  PubMed Central  Google Scholar 

Drabik D, Chodaczek G, Kraszewski S, Langner M (2020) Mechanical properties determination of DMPC, DPPC, DSPC, and HSPC solid-ordered bilayers. Langmuir 36:3826–3835. https://doi.org/10.1021/acs.langmuir.0c00475

Article  CAS  PubMed  PubMed Central  Google Scholar 

Du B, Fu Y, Han Y et al (2023) The lung-gut crosstalk in respiratory and inflammatory bowel disease. Front Cell Infect Microbiol. https://doi.org/10.3389/fcimb.2023.1218565

Article  PubMed  PubMed Central  Google Scholar 

Ebenhan T, Gheysens O, Kruger HG et al (2014) Antimicrobial peptides: their role as infection-selective tracers for molecular imaging. BioMed Res Int 2014:867381. https://doi.org/10.1155/2014/867381

Article  CAS  PubMed  PubMed Central  Google Scholar 

El Khoury M, Swain J, Sautrey G et al (2017) Targeting bacterial cardiolipin enriched microdomains: an antimicrobial strategy used by amphiphilic aminoglycoside antibiotics. Sci Rep 7:10697. https://doi.org/10.1038/s41598-017-10543-3

Article  CAS  Pu