ABC transporter: ATP-binding cassette transporter. It is important for transporting bacteriocines out of bacterial cells. Transporters in the same class also play an important role in AMP sensing and/or detoxification.
Abu-S-Ala: methyl lanthionines (cf. Ala-S-Ala, lanthionines)
AD: Atopic Dermatitis or /Eczema (AE), a diseased condition where expression of AMPs such as hCAP-18/LL-37 is suppressed.
ADME: the processes of a compound is absorbed, distributed, metabolized, and excreted from the human body (or an organism).
AFM: Atomic Force Microscopy
Alarmins: structurally distinct peptide mediators that can recruit and activate antigen-presenting cells (APCs), thereby enhancing immune response. See also DAMP.
Amino acids : A, Ala, alanine; C, Cys, cysteine; D, Asp, asparate; E, Glu, glutamate; F, Phe, phenylallanine; G, Gly, glycine; H, His, histidine; I, Ile, isoleucine; K, Lys,lysine; L, Leu, leucine; M, Met, methionine; N, Asn, asparagine; P, Pro, proline; Q, Gln, glutamine; R, Arg, arginine; S, Ser, serine; T, Thr, threonine; V, Val, valine; W, Trp, tryptophan; and Y, Tyr, tyrosine. SEE ALSO Non-standard AA below.
AMPs : antimicrobial peptides. See also HDP and innate immune peptides
AKT: v-akt murine thymoma viral oncogene homolog 1
AP-1: Activated Protein-1, a transcription factor
APC: Antigen Presenting Cell
APD : The Antimicrobial Peptide Database, or the AMP database
API: Active Pharmaceutical Ingredient
Archaeocins : Proteinaceous antimicrobials from the domain archaea
ATCC: American Type Culture Collection, founded in 1925, is a repository for donated bacterial strains.
Bacteriocins: Proteinaceous antimicrobials from the domain bacteria. For Gram-positive bacteria, class I bacteriocins are lantibiotics whose polypeptide chains are subject to extensive chemical modifications after translation. Type A has an elongated structure while type B has a more rigid and globular structure. Class II bacteriocins possess unmodified polypeptide chains. This class is further divided into class IIa (the pediocin-like bacteriocins), class IIb (the two-peptide chain bacteriocins, class IIc (cyclic peptides), and class IId (the leaderless peptide bacteriocins). Classes III are large proteins with lytic activity (Cotter P et al., 2005 Nature Rev Microbiol 3: 777). Bacteriocins from Gram-negative bacteria are called microcins (Class I < 5 kDa; Class II, 5-10 kDa; and class III(colicins) > 10 kDa (Duquesne et al. 2007 Nat. Prod. Rep. 24: 708-734).
BB codes for peptide binding partners : BBB, peptide self association; BBII, metal ions; BBL, LPS; BBMm, membranes; BBN, nucleic acids; BBPP, protein/enzyme; BBS, sugars. AMPs with such activities can be searched in the name field of the search interface of the APD by entering the code.
BCAA : Branched chain amino acids;
BGCs : biosynthetic gene clusters;
Black death: a plague caused by the deadly bacterium Yersinia pestis.
BLAST: Basic Local Alignment Search Tool
BLP: Bacterial LipoProtein, TLR2/1 ligand (recognizing Gram+ bacterial cell wall). This BLP binding to TLR2/1 upregulates the expression of vitamin D receptor and the vitamin D-1-hydroxylase genes, leading to the induction of human cathelicidin LL-37 to kill Mycobacterium tuberculosis.
Boman Index : Originally called protein-binding potential by Hans Boman. It was renamed as Boman Index when it was introduced into the APD in 2003. Boman index is the sum of the free energies of the respective side chains for transfer from cyclohexane to water taken from Radzeka and Wolfenden and divided by the total number of the residues of an antimicrobial peptide. The calculated values are negative ( except for the hybrid peptide), but the + and - are reversed. A more hydrophobic peptide tends to have a negative index, while a more hydrophilic peptide tends to have a more positive index [Boman, H.G.(2003) J.Inter.Med.254:197-215].
CAPA: Corrective Action, Preventative Action (FDA)
Cathelicidin: a family of antimicrobial peptides that share the common N-terminal cathelin domain in their precursor proteins
CD: Circular Dichroism, especially good at estimating helix formation with the change in conditions.
CDC: US Centers for Disease Control and Prevention
CEM cells: a human CD4+ T-cell line. It has been used to screen for anti-HIV peptides.
CF: Cystic Fibrosis
CFU: Colony-Forming Unit
Chemokines : separated into four subfamilies based on the distinctive pattern of the two N-terminal cysteines: CXC (alpha), CC (beta), C and CX3C classes (nomenclature)
ChIP: Chromatin ImmunoPrecipitation assays
CMC: Critical Micelle Concentration
Colicins : see microcins.
Collectins: Collagenous lectins, which could bind to viruses and thereby protect the host.
COPD: chronic obstructive pulmonary disease, where host defense peptides such as LL-37 may play a role.
Core peptide: in the lantipeptide case, it refers to the C-terminal region of the precursor that becomes the final AMP after processing
. In other cases, it is also used to refer to the critical AMP region that retains antimicrobial activity (e.g., Li et al. 2016).
CpG-ODN: CpG-OligoDeoxyNucleotides (DNA), unmethylated, TLR9 ligand
CQAs: Critical Qaulity Attributes such as viscosity, pH, density, or content uniformity
CNS: Central nervous System
CRE: Carbapenem-resistant Enterobacteriaceae, the "Nightmare bacteria" (CDC director Tom Frieden) detected in over 200 USA hospitals in 2012. Go to the CDC website
Crohn's disease: a chronic inflammatory bowel disease due to a defect in intestinal innate immune responses to bacteria
CT: Computed Tomography
CTD: Common Technical Document
Cyclotides: Plant circular peptides that have no exposed N- or C-terminal residues (listed here).
25D: 25-hydroxyvitamin D3, the major circulating form. Once converted to 1,25D, it can induce LL-37 expression in human cells.
1,25D: 1,25-dihydroxylvitamin D3, the active form of vitamin D that induces the expression of LL-37, hBD-2, and intracellular pattern recognition receptor called NOD2/CARD15 in humans.
DAMP: damage-associated molecular patterns. Examples are alarmins (defensins, cathelicidins, high-mobility group box-1 protein (HMGB1), and iron-binding proteins) and mitochondrial DNA of eukaryotic cells.
DCs: Dendritic Cells
DENV: Dengue virus
Dha: 2,3-didehydroalanine, dehydrated serine (Ser), or occasionally Cys (Claesen and Bibb 2010 PNAS 107:16297)
Dhb: (Z)-2,3-didehydrobutyrine, dehydrated threonine (Thr)
DoD: Department of Defense
dpi: (immunology) days post-infection
Drug compounding: a little-known practice in which pharmacists traditionally alter or recombine drugs to meet the special needs of specific patients, e.g. HIV-1 cocktail therapy
DSC: Differential Scanning Calorimetry
eDNA: extracellullar DNA, i.e. genomic DNA released by bacteria, an important component involved in the formation of bacterial biofilms.
EST: Expressed Sequence Tag
EGFR: Epidermal Growth Factor Receptor
ER: Endoplasmic Reticulum
ESKAPE pathogens: the abbreviation of the six multi-drug resistant bacteria, including Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species.
Eucaryocins : Proteinaceous antimicrobials from the domain eucarya
FACS: Fluorescence-Activated Cell Sorter
FASTA: A universal bioinformatic text-sharing format that begins with a comment followed by single-lettered amino acids or nucleotides.
FDA: US Food and Drug Administration
Firmicutes: the low-G+C-content gram-positive bacterial species, e.g. bacilli & clostridia.
FICI: fractional inhibition concentration index, a number used to gauge synergistic interactions of molecules (FICI < 0.5 synergy; FICI >1, antagonism).
FITC: Fluorescein isothiocyanate, a flurescent probe widely used in tracing the location of antimicrobial peptides in cells.
FPRL1: Formyl Peptide Receptor-Like 1. Human Ll-37 chemoattracts human neutrophils, monocytes, T cells and multipotent mesenchymal stromal cells (stem cells) by binding to this cell surface receptor. This molecular process could be essential for cancer metastasis (see the minireview on the relationship between LL-37 and cancer, Wu W.K.K. et al. 2010 Int J cancer 127:1741-7).
FRET: Fluorescence Resonance Energy Transfer
FT-IR: Fourier Transform InfraRed spectroscopy
GCP: Good Clinical Practice (FDA). See also GLP and GMP.
GLP: Good Laboratory Practice (FDA)
. See also GCP and GMP.
Glycopeptides: glycolated peptides with antimicrobial activity (newly discovered from bacteria in 2011). These are regarded as examples for the class IV peptide (conjugated peptides) originally proposed by Klaenhammer (1993).
GMP: Good Manufacturing Practice (FDA)
GO: Gene Ontology (for instance)
GRAS: Generally Recognized As Safe
hBD: human Beta Defensin (28 genes in humans, most well studied are HBD-1, HBD-2, HBD-3, and HBD-4)
hCAP-18: human Cationic Antimicrobial Protein of 18 kDa (i.e., the precursor of human cathelicidins LL-37 and ALL-38, the mature antimicrobial peptides; originally thought FALL-39). The gene that encodes this protein is referred to as CAMP.
HD5: see "HNP"
HD6: see "HNP"
HDP: see "Host Defense Peptide"
HIV-1: Human immunodeficiency Virus type 1
HNP: Human Neutrophil Protein, HNP-1 to HNP-4 made in granulocytes, and human defensins 5 and 6 (HD-5 and HD-6) made in Paneth cells. All these are human alpha defensins.
GRAVY: Grand average of hydropathicity index. Proteins with a positive GRAVY are more hydrophobic and thereby less soluble, while proteins with a negative GRAVY value are more hydrophilic and tend to be more water soluble (Kyle and Doolittle, 1982).
Host Defense Peptide: An alternative name for antimicrobial peptides that emphasizes the immune modulation activities of AMPs.When needed, a more general term innate immune peptides may also be utilized (See the APD main page).
HSP: Heat Shock Proteins, identified binding targets for Pro-rich AMPs. However, the molecular target could be ribosomes based on recent results (Krizsan A. et al., 2014).
HSV: Herpes Simplex Virus.
IACUC: Institutional Animal Care and Use Committee.
IAV: Influenza A Virus that causes seasonal Flu.
IBC: Institutional Biosafety Committee.
IC50: 50% the maximum Inhibition Concentration
ICK: inhibitor cystine knot found in most spider venom toxins.However, venom peptides with antimicrobial activity appear to be exceptions to this.
IDR: Innate Defence Regulator, which may not kill bacteria directly.
IKK: Inhibitor of Kappa light polypeptide gene enhancer in B-cells, signaling molecules
IMD: another major pathway in Drosophila that regulates the expression of antimicrobial peptides. The imd pathway is induced primarily by Gram-negative bacteria, while the TOLL pathway is induced by Gram-postive bacteria and fungi.
IND: Investigational New Drug (FDA)
Innate immune peptides: a more general term for the antimicrobial peptide field. It basically covers all the functions of such peptides known or to be discovered (Wang G ed. 2017 Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies, CABI). See also AMPs or HDP.
iNOS: inducible Nitric Oxide Synthase
Instability index: This index provides an estimation of peptide stability. It was developed based on the occurance of certain dipeptides in the sequence and reflects in vivo half life of the peptide (Guruprasad K et al., 1990).
IRAK: Interleukin-1 Receptor Associated Kinase
IRB: Institutional Review Board
. A key goal of IRB is to protect human subjects from harm physically, emotionally, or psychologically.
IRF3: Interferon Regulatory Factor 3, a transcription factor (activated by phosphorylation)
ITC: Isothermal Titration Calorimetry
JEV: Japanese Encephalitis Virus that causes brain infection, which spreads via mosquitoes. Pigs and wild birds contain such a virus.
KEGG: Kyoto Encyclopedia of Genes and Genomes
Kinocidins: Chemokines with antimicrobial activity. On the other side of the coin, some antimicrobial peptides such as human LL-37 and HBD-3 are now demonstrated to have chemotactic activity. Search the APD for more.
LAB: Lactic Acid Bacteria that produce lantibiotics useful for food preservation.
LAM: LipoArabinoMannan, a glycolipid associated with the cell wall of Mycobacterium tubercolosis
LanA: the peptide precursor to be processed by lantipeptide modification enzymes
Lantibiotics: lanthionine containing antibiotics which are extensively modified post-translationally.
Lantipeptides: lanthionine containing natural peptides with or without antimicrobial activity.
LBP: LPS-Binding Protein, its complex with LPS binds to CD14 high-affinity LPS receptor on the cell surface and induces cellular response via TLR4, the first mammalian homolog of Drosophila Toll. AMPs such as human LL-37 could compete with LBP, thereby suppressing, at least partially, the lethal effect of LPS-induced immune reponses. The synergistic binding of LPS to human LL-37 may be understood from the two hydrophobic domains due to the existence of Ser9 on the hydrophobic surface of the long amphipathic helix (Wang et al. 2012 Biochemistry 51:653-664). Abstract.
LC50: (50%) Median Lethal Concentration
LC-MS: Liquid Chromatography-Mass Spectrometry
Leader peptide: in the case of lantibiotics, it refers to the N-terminal region of the precursor important for production but unmodified and removed after processing
Lipids: PC, diacyl phosphatidylcholines; PG, diacyl phosphatidylglycerols; PE, diacyl phosphatidylethanolamine
LL-37: a well-studied multifunctional human innate immune peptide with 37 residues and starting with a pair of leucines. This peptide appears to have multiple functions ranging from antimicrobial, chemotactic, and wound healing, to immune modulation.
LPPS: Liquid phase peptide synthesis. See also: SPPS
LPS: LipoPolySaccharides. Also called endotoxin from Gram-negative bacteria. A ligand for TLR4
LRR: Leucine-Rich Repeats
LTA: LipoTeichoic Acid from Gram-positive bacteria
LTP: Lipid Transfer Protein
LUV: Large unilamellar vesicles. e.g. DOPG=1,2-dioleoyl-sn-glycero-3-phosphocholine
MALP-2: Macrophage Activating LipoPeptide-2
MAPK: Mitogen Activated Protein Kinase
MBC: Minimum Bactericidal Concentration
MCP-1: Monocyte Chemotactic Protein-1 (a marker cytokine the level of which is used as an indicator of immune modulation activity of AMPs)
MDR: multidrug resistance
MIC: Minimal Inhibitory Concentration (e.g. against bacteria, fungi, etc)
Microcins : Gene-encoded antibacterial peptides (<10 kDa) produced by enterobacteria to inhibit the growth of closely related species. Note that polypeptides (>10 kDa) are called colicins
Membrane-mimetic models: organic solvents such as TFE (trifluoroethanol), detergent micelles such as SDS (sodium dodecylsulfate) or DPC (dodecylphosphocholine), lipid micelles e.g. D8PG (dioctanoyl phosphatidylglycerol), bicelles, and lipid bilayers
MERS: Middle East Respiratory Syndrome, which belongs to the coronavirus family that includes the common cold and SARS, or severe acute respiratory syndrome that caused 800 deaths in 2003. 2015 MERS OUTBREAK
MOA: Mechanism Of Action. The MOAs of AMPs are complex and usually involve multiple mechanisms, although only one or two can be the lethal processes that cause the death.
MOI: Multiplicity Of Infection. In microbiology, MOI represents the ratio between the infecting microbe (e.g., virus and bacteria) and infected host cells.
Monophosphoryl lipid A: see MPLA below.
MPLA: Monophosphoryl lipid A is a TLR4 agonist. It can be used as a vaccine adjuvant in humans. Further reading
MRI: Magnetic Resonance Imaging (Nobel Prize in 2003)
MRSA: Methicillin-Resistant Staphylococcus aureus, usually containing the antibiotic resistance harboring mec A gene. For instance, community-associated S. aureus strains USA300. Anti-MRSA peptides are annotated in the APD.
MSR: the Macrophage Scavenger Receptor
MTD: the Maximal Tolerance Dose (e.g. 20 mg/kg)
MyD88: Myeloid Differentiation factor 88, a key adaptor protein in the TLR signaling pathways
NDA: New Drug Application
NDM-1: New Delhi metallo-beta-lactamase-1-carrying isolates
NETs: first described in 2004. Neutrophil extracellular traps are a novel extracellular bacterial killing mechanism of neutrophils. NETs contain DNA fibers coated with antimicrobial proteins such as histones, LL-37, neutrophil elastase, cathepsin, and myeloperoxidase.
NETosis: the formation of NETs, which involve two mechanisms: (1) lytic suicide of cells and (2) non-lethal process (no cell lysis is needed, also called vital NETosis).
NFkB: Nuclear Factor kappa B, a transcription factor frequently involved in stress response of cells
NHBE cells: Normal Human Bronchial Epithelial cells
NIH: National Institutes of Health
NLRs: Nod-like receptors
NMR: Nuclear Magnetic Resonance spectroscopy. While solution NMR is the major technique for structural and dynamics studies of membrane-bound AMPs, solid-state NMR provides complementary information such as peptide oligomerization and orientation in the membranes. (Nobel Prizes in 1952, 1991 and 2002)
NO: Nitric Oxide
NOD: nucleotide-binding oligomerization domain, an intracellular receptor responding to LPS
Non-standard amino-acids : Aad, 3-Aminoadipic acid; Abu, 2-Aminobutyric acid; Aib, aminoisobutyric acid; Apm, 3-Aminopimelic acid; Dab, 2,4-diaminobutyric acid; Dap, 2,3-diaminopropionic acid; Hcy, homocysteine; Hse, Homoserine; Hyl, Hydroxylysine; Hyp, Hydroxyproline; aIle, allo-Isoleucine; MeGly, N-methylglycine; NLys, N-(4-aminonutyl) glycine (a peptoid analog of lysine); Nva, Norvaline; Nle, Norleucine; Orn, Ornithine; Pyr, Pyroglutamic acid; Sar, Sarcosine.
NOAEL: No Adverse Effect Level
NSF: National Science Foundation
NRPS: Nonribosomal peptide synthetase
OAK: Oligomers of Acylated Lysines (K)
ORF: Open Reading Frame
Orthologs: genes or gene-coded proteins in different species that evolved from a common ancestral gene, usually with the same function.
PAMPs: Pathogen Associated Molecular Patterns
Paralogs: genes or gene-coded proteins generated by gene duplication within a genome, usually evolving new functions.
PBMC: Peripheral Blood Mononuclear Cells
PBS: Phosphate Buffered Saline
P/C properties: physio-chemical properties
PCR: Polymerase Chain Reaction
PD: Pharmacodynamics, a study of how a compound affects an organism.
pDCs: plasmacytoid Dendritic Cells
Peptaibol: fungi-derived short-length peptides (Pept ~15-20) rich in nonstandard amino acid residues such as aminoisobutyric acid (Aib) usually with a C-terminal hydroxyl group (OH).
Peptoids: poly N-substituted glycines, e.g. NLys and NHis
PGN: PeptidoGlycaN, TLR2 ligand
PGRP: PeptidoGlycan Recognition Protein
PI: propidium iodide, a non-membrane permeating dye frequently used to gauge the membrane damaging effects of antimicrobials. (in grant application, PI means principal investigator).
PK: pharmacokinetics, a study of how an organism influences a drug (e.g., degradation)
PKS: polyketide synthase
PMN: PolyMorphonuclear Neutrophils
PRR: Pattern Recognition Receptors
PTMs: posttranslational modifications
QSAR: Quantitative Structure-Activity Relationship
QTPP: Quality Target Product Profile
RACE: Rapid Amplification of cDNA Ends. This technique produces cDNA from mRNA via reverse transcription, usually followed by PCR amplification.
RANA box: a C-terminal domain connected by a pair of cysteines discovered in amphibian AMPs.
RAR: Retinoic Acid Receptor
RiPP: Ribosomally synthesized and Posttranslationally modified Peptides
ROS: Reactive Oxygen Species
RP-HPLC: Reversed-Phase High-Performance Liquid Chromatography
RSV: Respiratory Syncytial Virus that can cause acute lower respiratory tract infection in young children worldwide.
RT-PCR: Reverse transcriptase polymerase chain reaction
SARS: severe acute respiratory syndrome
SAXS: Small-Angle X-ray Scattering
SCVs: Small colony variants, a more resistant form of bacteria. For example, S. aureus can form SCVs in CF patients. This form is shown to be more resistant to cationic AMPs as well (Gläser R et al., 2014).
Sepsis or septicemia: a systemic inflamatory response syndrome in response to pathogenic bacteria or their components in the blood or tissues
SINE: Short Interspersed Element, or a repetitive DNA element (so called "junk DNA"). Note that such a vitamin D receptor binding element exists only in primate and human genomes.
siRNA: small interfering RNA
SNP: Single Nucleotide Polymorphism
SPPS: Solid phase peptide synthesis; see also LPPS
SPR: Surface Plasmon Resonance
ssRNA: single-stranded RiboNucleic Acid, TLR7 ligand
STAT: the Signal Transducer and Activator of Transcription protein
Structure classification of antimicrobial peptides: alpha (peptides with alpha-helical structures); beta (AMPs with beta-sheet structure); alphabeta (AMPs with both alpha and beta structures; and non-AlphaBeta (AMPs that contain neither alpha nor beta structures) (Wang, G. 2010 Structural studies of AMPs. In Chapter 1, <"Antimicrobial Peptides: Discovery, Design and Novel Therapeutic Strategies" (edited by G. Wang). Read Chapter 1 here.
T2D : type 2 diabetes;
TB: Tuberculosis cuased by the pathogen Mycobacterium tuberculosis. Anti-TB peptides are annotated in the APD.
TCR: T Cell Receptor
TCRS: Two-component regulatory system
TDR-TB: total drug resistant TB
TEM: Transmission Electron Microscopy
Th1: T helper 1
TIR: Toll/Interleukin-1 Receptor domain
TIRAP: Toll-Interleukin 1 Receptor (TIR) domain containing Adaptor Protein; also known as MyD88-adaptor-like protein or Mal
TLRs: Toll-Like Receptors; sensors of both innate and adaptive immune systems for microbial products; 11 in humans. e.g. TLR2 for lipoteichoic acid from Gram-positive bacteria; TLR4 for LPS from Gram-negative bacteria. However, TLR3, TLR7, TLR8, and TLR9 are endosomal Toll-like receptors.
TNF-alpha: Tumor Necrosis Factor alpha, a cytokine. Some AMPs such as human LL-37 can suppress the release of TNF-alpha (part of the immune modulation activity)
TOLL: See IMD
Tollip: Toll-interacting protein
TRAF: TNF Receptor-Associated Factor
TRAIL: TNF-Related Apoptosis Inducing Ligand
TRAM: Toll-like Receptor Adaptor Molecule 2
Tregs: regulatory T cells
TSB: Tryptic Soy Broth
Tyrothricin: a combination of antimicrobial peptides (70-80% tyrocidins and 20-25% gramicidins) produced by B. brevis (Dubos 1939 J Exp Med 70: 249-245). Decade-long use no resistance.
UPLC: Ultra Performance Liquid Chromatography
UTR: UnTranslated Regions
UVB: solar UltraViolet-B
VDR: Vitamin D Receptor
VDRE: Vitamin D Receptor binding Element
Viruses: small particles that can infect host cells and replicate within the host. Some AMPs show antiviral effects against IAV (influenza virus), HIV, and HSV. It's predicted that AMPs can also inactivate Ebola viruses.
VISA: vancomycin intermediate S. aureus strains, which increase basal resistance to vancomycin withour acqusition of any clearly defined resistance determinants.
VRE: Vancomycin-Resistant Enterococcus or Vancomycin-Resistant Enterococci
Wimley-White whole residue hydrophobicity: A more hydrophobic peptide tends to have a more negative value, while a more hydrophilic peptide tends to have a more positive value (Wimley and White, 1996).
WNV: West Nile Virus, an RNA virus similar to ZIKA
XDR: Extensive drug resistance
XX codes for chemical modification: XXA, C-terminal NH2; XXC, cyclization; XXD, D-amino acids; XXG, glycosylation; XXO, oxidation; XXP, peptide phopsphorylation. AMPs with such activities can be searched in the name field of the search interface of the APD by entering the code.
ZIKV: Zika virus
ZZ codes: ZZH, anti-HIV; ZZP, anti-parasital; ZZS, spermicidal; ZZI, insecticidal. AMPs with such activities can be directly searched in the name field of the search interface of the APD by entering the code. Since the end of 2011, the ZZ codes have been replaced by more convenient icon search in the same manner as other activity functions created originally in the database. Additional activities (such anti-MRSA and anti-TB), however, can be searched in the name field.