Antibacterial Library

Infectious diseases are one of the most critical and urgent health problems in the world. Although the market for antibacterial drugs is nowadays greater than 25 billion US dollars per year, the development and implementation of novel antibacterial medicines are still required due to the developed resistance of many pathogenic bacteria against current antibiotics [1].

Since there are typically several antibacterial agents whose effectiveness against many pathogens is comparable, they can be used empirically and the selection of the treatment approach often depends on various indirect factors, such as pharmacokinetics, side effects, resistance profile, and treatment costs [2]. That is why the development of novel antibacterial drugs that focus on target-activity relationships and belong to structurally different chemical classes is still relevant (Fig. 1) [3].

Life Chemicals has designed its dedicated Antibacterial Screening Library of over 11,100 drug-like screening compounds with potential antibacterial activity as an excellent starting point for high throughput screening (HTS) and high content screening (HCS) projects and hit identification in antibacterial drug discovery.

Custom compound selection based on specific parameters can be performed on request, compound cherry-picking is available. Please, contact us at orders@lifechemicals.com for any details and quotations.

First, a reference set of compounds with reported antibacterial activity against different gram-positive and gram-negative bacteria species (provided below) was prepared. Activity data threshold was chosen < 10 μM, extracted from Binding and ChEMBL databases.

  • Acinetobacter baumannii
  • Actinomadura
  • Actinomyces viscosus
  • Aeromonas hydrophila
  • Agrobacterium tumefaciens
  • Alcaligenes faecalis
  • Alicyclobacillus acidocaldarius
  • Aliivibrio fischeri
  • Aquifex aeolicus
  • Bacillus (B.anthracis, B.cereus, B.megaterium, B.subtilis, B.thermoproteolyticus)
  • Bordetella bronchiseptica
  • Brucella suis
  • Burkholderia cenocepacia
  • Campylobacter jejuni
  • Caulobacter vibrioides
  • Chlamydophila pneumoniae
  • Citrobacter freundii
  • Clavibacter michiganensis
  • Clostridium botulinum
  • Corynebacterium glutamicum
  • Elizabethkingia meningoseptica
  • Enterococcus faecalis
  • Erwinia chrysanthemi
  • Escherichia coli
  • Flavobacterium columnare
  • Francisella tularensis
  • Haemophilus influenzae
  • Helicobacter pylori
  • Klebsiella pneumoniae
  • Lactobacillus casei
  • Listeria innocua
  • Listonella anguillarum
  • Magnetospirillum gryphiswaldense
  • Micrococcus luteus
  • Moraxella catarrhalis
  • Mycobacterium (M.bovis wildlife, M.bovis BCG, M.chelonae, M.fortuitum, M.kansasii, M.peregrinum, M.smegmatis, M.tuberculosis)
  • Mycoplasma gallisepticum
  • Pantoea ananas
  • Peptoclostridium difficile
  • Porphyromonas gingivalis
  • Propionibacterium acnes
  • Proteus vulgaris
  • Pseudomonas (P.aeruginosa, P.putida)
  • Raoultella planticola
  • Salmonella (S.choleraesuis, S.enterica, S.typhimurium)
  • Shigella (S.dysenteriae, S.flexneri)
  • Spiroplasma monobiae
  • Staphylococcus (S.aureus, S.epidermidis)
  • Streptococcus (S.agalactiae, S.mutans, S.pneumoniae, S.pyogenes)
  • Sulfurihydrogenibium 
  • Synechococcus elongatus
  • Thermus aquaticus
  • Thiomicrospira crunogena
  • Vibrio (V.cholerae, V.harveyi)
  • Yersinia (Y.enterocolitica, Y.pestis, Y.pseudotuberculosis)
  • Zymomonas mobil

A 2D fingerprint similarity search (Tanimoto similarity index > 0.80, < 10 analogs per reference to ensure diversity) of the Life Chemicals HTS Compound Collection has resulted in obtaining 4,200 screening compounds effective against bacterial organisms and over 6,900 small-molecule analogues of molecules with known activity against the following bacteria-related protein targets:

  • Streptokinase A
  • ATP-dependent Clp protease
  • 4'-phosphopantetheinyl transferase
  • Protein RecA
  • Anthrax lethal factor
  • Fructose-bisphosphate aldolase
  • Aminotransferase
  • Beta-lactamase (type AmpC, NDM-1, TEM, VIM-2)
  • Enoyl-[acyl-carrier-protein] reductase
  • Replicative DNA helicase
  • DNA gyrase (subunit A, B)
  • UDP-D-alanine ligase
  • Dihydrolipoyl dehydrogenase
  • Probable nicotinate-nucleotide adenylyltransferase
  • Shiga toxin
  • Probable L-lysine-epsilon aminotransferase
  • HTH-type transcriptional regulator Exoenzyme S
  • Histidine protein kinase DivJ
  • Carbonic anhydrase
  • Bifunctional protein GlmU
  • Quinolone resistance protein norA
  • DNA topoisomerase
  • Chorismate synthase
  • UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
  • Pyruvate kinase
  • Botulinum neurotoxin (type A, E, F)
  • Pantothenate synthetase
  • Thymidylate synthase
  • UDP-galactopyranose mutase
  • Peptide deformylase
  • Taq polymerase 1
  • Lanosterol 14-alpha demethylase
  • Acyl-CoA synthase
  • Carbonate dehydratase
  • Inosine-5'-monophosphate dehydrogenase
  • Transcriptional activator (type lasR, luxR, traR)
  • Tyrosine-protein phosphatase PTPB
  • Transcriptional regulator MvfR
  • Beta-galactosidase
  • alpha/beta hydrolase fold family
  • mRNA interferase MazF
  • Dihydrofolate reductase
  • Signal transduction protein TRAP
  • 15-cis-phytoene desaturase
  • Autoinducer 1 sensor kinase/phosphatase luxN
  • Histidine biosynthesis bifunctional protein HisB
  • Tyrosine-protein phosphatase yopH
  • 3-oxoacyl-[acyl-carrier-protein] synthase 3
  • Cereblon isoform 4
  • Epoxide hydrolase
  • GroEL/GroES
  • UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
  • Dihydrodipicolinate synthase
  • Lectin
  • rRNA adenine N-6-methyltransferase
  • Accessory gene regulator protein A
  • Dipeptidyl peptidase IV
  • Heme oxygenase
  • Methionine aminopeptidase
  • Uncharacterized protein Rv1284/MT1322
  • 2-heptyl-4(1H)-quinolone synthase PqsD
  • Chaperone protein dnaK
  • Cytochrome P450
  • Dehydrosqualene desaturase
  • Dihydropteroate synthase
  • Diphosphomevalonate decarboxylase
  • Glutathione-independent formaldehyde dehydrogenase
  • Lycopene cyclase
  • Phenylalanyl-tRNA synthetase Pseudolysin
  • Squalene-hopene cyclase
  • Thermolysin
  • UDP-N-acetylbacillosamine N-acetyltransferase
  • Urease (subunit alpha, beta)
  • Virulence sensor histidine kinase 5-enolpyruvylshikimate-3-phosphate synthase
  • CAI-1 autoinducer sensor kinase/phosphatase CqsS
  • CpG DNA methylase
  • Cystathionine beta-lyase metC
  • D-alanyl-D-alanine carboxypeptidase
  • Dehydrosqualene synthase
  • DNA polymerase III
  • Histidinol dehydrogenase
  • Prolyl endopeptidase
  • Protoporphyrinogen oxidase
  • Thymidylate kinase
  • Toxin B
  • tRNA-guanine transglycosylas

The key cell process and protein targets for commonly used antimicrobial agents.

Pic.1. The key cell process and protein targets for commonly used antimicrobial agents. Picture credit: Yazdankhah, S et al., 2018 [4].

References:

  1. Kaczor AA, Polski A, Sobótka-Polska K, Pachuta-Stec A, Makarska-Bialokoz M, Pitucha M. Novel Antibacterial Compounds and their Drug Targets - Successes and Challenges. Curr Med Chem. 2017;24(18):1948-1982.
  2. ANDRÁS TELEKES, ... ISTVÁN KISS. in Medical Applications of Mass Spectrometry, 2008. https://doi.org/10.1016/B978-0-444-51980-1.X5001-0
  3. Tafere Mulaw Belete. Novel targets to develop new antibacterial agents and novel alternatives to antibacterial agents. Human Microbiome Journal. 2019;11:100052.
  4. Yazdankhah, S.; Grahek-Ogden, D.; Hjeltnes, B.; Langsrud, S.; Lassen, J.; Norström, M.; Sunde, M.; Eckner, K.; Kapperud, G.; Narvhus, J.; Nesbakken, T.; Robertson, L.; Rosnes, J. T.; Skjerdal, O. T.; Skjerve, E.; Vold, L.; Wasteson, Y. Assessment of Antimicrobial Resistance in the Food Chains in Norway. Eur. J. Nutr. Food Saf. 2018, 8 (4), 237–239. https://doi.org/10.9734/ejnfs/2018/43854.
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