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Antibacterial Screening Compound Libraries

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 still remains a pressing matter (Fig. 1) [3].

Life Chemicals has developed dedicated Antibacterial Screening Compound Libraries of over 18,000 drug-like screening compounds with potential bacterial inhibitory activity as excellent starting points for high throughput screening (HTS) and high content screening (HCS) projects, as well as hit identification in antibacterial drug discovery:

These two non-overlapping Screening Sets were carefully selected with both ligand-based (2D fingerprint similarity search) and structure-based (virtual screening, molecular docking) approaches.

The compound selection can be customized based on your requirements, cherry picking is available.

Please, contact us at for any additional information and price quotations.

In their pre-plated format the Sets can be found within our exceptional collection of Pre-plated Focused Libraries.

You can also be interested in the following related products:

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

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

Antibacterial Focused Library

A 2D fingerprint similarity search (Tanimoto similarity index > 0.80, < 10 analogs per reference to ensure diversity) of the Life Chemicals HTS Compound Collection allowed us to select around 15,500 drug-like screening compounds with potential antibacterial activity.

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. As a result, we picked around 8,900 screening compounds effective against bacterial organisms and over 6,900 small-molecule analogues of compounds 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 transglycosylase

Bacterial species cited in the reference compound set:

  • 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

Additionally, approved antibacterial compounds for systemic use and their analogs were also included:

  • Azithromycin
  • Ceftezole
  • Ceftizoxime
  • Cinoxacin
  • Ciprofloxacin
  • Flumequine
  • Linezolid
  • Mandelic acid
  • Metronidazole
  • Nalidixic acid
  • Nitroxoline
  • Oxolinic acid
  • Pefloxacin
  • Procaine benzylpenicillin
  • Rosoxacin
  • Roxithromycin
  • Sulfadimethoxine
  • Sulfamerazine
  • Sulfamethazine
  • Sulfamethizole
  • Sulfamethoxazole
  • Sulfametomidine
  • Sulfanilamide
  • Sulfapyridine
  • Sulfathiazole
  • Sulfathiourea
  • Sulfisomidine
  • Sulfisoxazole
  • Trimethoprim

Antibacterial Pharmacophore Screening Library

Due to the persistent spread of the epidemic of coronavirus infection, more and more attention is being paid to the research of the causative agents of respiratory tract diseases and the development of effective medicines against them.

Neisseria meningitidis and Streptococcus pneumoniae represent the causative agents of invasive bacterial infections, manifested by a wide range of diseases, such as meningitis and septicemia [5-7]. Klebsiella pneumoniae is the causative agent of both pneumonia and nosocomial human infections, characterized by high virulence and resistance to antibiotics, especially carbapenem class [8, 9]. These pathogens are commonly spread worldwide and can lead to fatal consequences in case of a severe course of the disease.

Addressing these urgent problems, our cheminformatics team has designed this Screening Set of around 2,700 structurally-diverse screening compounds with potential biological activity. The molecules were picked out by virtual molecular screening against the most relevant pneumonia-causing bacterial drug targets important for viability, virulence, and resistance of the above-mentioned microorganisms:

N-acetylneuraminate synthase (NeuB)

N-acetylneuraminate synthase (NeuB) is a bacterial sialic acid synthase, vital for neuroinvasive bacteria, such as Neisseria meningitidis, enabling them to synthesize N-acetylneuraminate (NeuNAc) to evade the host immune system. This makes NeuB a highly relevant drug target for antibacterial drug development [10].

Key features:

  • Method: high-throughput virtual screening (pharmacophore hypothesis)
  • X-Ray data used: 6PPY
  • Filters used: QikProp properties and descriptors
  • Number of compounds selected: 586

The pharmacophore hypothesis by 6PPY and examples of lead compounds.

Figure 2. The pharmacophore hypothesis by 6PPY and examples of lead compounds.

Metallo-β-lactamase (MBL)

Antimicrobial therapy is threatened by the global rise of resistance, especially in Gram-negative bacteria, where resistance to β-lactams is largely mediated by β-lactamases. Carbapenems, which evade most β-lactamases, are hydrolyzed by metallo-β-lactamases (MBLs), as well as by a few active-site serine β-lactamases (SBLs), that contributes to the resistance against them of such  enterobacteria  as Klebsiella pneumoniae. Despite a significant progress in the development of beta-lactamase inhibitors, effective Metallo-β-lactamase inhibitors still remain a challenge [11].

Key features:

  • Method: high-throughput virtual screening (pharmacophore hypothesis)
  • X-Ray data used: 6V1M
  • Filters used: QikProp properties and descriptors
  • Number of compounds selected: 1674

The pharmacophore hypothesis by 6V1M and examples of lead compounds.

Figure 3. The pharmacophore hypothesis by 6V1M and examples of lead compounds.


Neuraminidases (sialidases) are important in the pathogenicity of bacteria and the virulence of influenza. They are key enzymes in obtaining nutrients by Streptococcus pneumoniae, as they are able to break down sugars on the surface of host cells, thus causing respiratory tract damage. The above makes NanB a potential drug target to inhibit bacterial infections [12].

Key features:

  • Method: high-throughput virtual screening (pharmacophore hypothesis)
  • X-Ray data used: 4XHB
  • Filters used: QikProp properties and descriptors
  • Number of compounds selected: 856

The pharmacophore hypothesis by 4XHB and examples of lead compounds.

Figure 4. The pharmacophore hypothesis by 4XHB and examples of lead compounds.


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  2. ANDRÁS TELEKES, ... ISTVÁN KISS. in Medical Applications of Mass Spectrometry, 2008.
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  7. McIntosh, E., Feemster, K., & Rello, J. (2022). Protecting adults at risk of pneumococcal infection and influenza from exposure to SARS-CoV-2. Human vaccines & immunotherapeutics, 18(1), 1–7.
  8. Hua, Y., Wang, J., Huang, M., Huang, Y., Zhang, R., Bu, F., Yang, B., Chen, J., Lin, X., Hu, X., Zheng, L., & Wang, Q. (2022). Outer membrane vesicle-transmitted virulence genes mediate the emergence of new antimicrobial-resistant hypervirulent Klebsiella pneumoniae. Emerging microbes & infections, 11(1), 1281–1292.
  9. Tian, D., Liu, X., Chen, W., Zhou, Y., Hu, D., Wang, W., Wu, J., Mu, Q., & Jiang, X. (2022). Prevalence of hypervirulent and carbapenem-resistant Klebsiella pneumoniae under divergent evolutionary patterns. Emerging microbes & infections, 11(1), 1936–1949.
  10. Popović, V., Morrison, E., Rosanally, A. Z., Balachandran, N., Senson, A. W., Szabla, R., Junop, M. S., & Berti, P. J. (2019). NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB. Biochemistry, 58(41), 4236–4245.
  11. Hecker, S. J., Reddy, K. R., Lomovskaya, O., Griffith, D. C., Rubio-Aparicio, D., Nelson, K., Tsivkovski, R., Sun, D., Sabet, M., Tarazi, Z., Parkinson, J., Totrov, M., Boyer, S. H., Glinka, T. W., Pemberton, O. A., Chen, Y., & Dudley, M. N. (2020). Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-β-lactamases. Journal of medicinal chemistry, 63(14), 7491–7507.
  12. Janesch, P., Rouha, H., Badarau, A., Stulik, L., Mirkina, I., Caccamo, M., Havlicek, K., Maierhofer, B., Weber, S., Groß, K., Steinhäuser, J., Zerbs, M., Varga, C., Dolezilkova, I., Maier, S., Zauner, G., Nielson, N., Power, C. A., & Nagy, E. (2018). Assessing the function of pneumococcal neuraminidases NanA, NanB and NanC in vitro and in vivo lung infection models using monoclonal antibodies. Virulence, 9(1), 1521–1538.
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