Antituberculosis Libraries

Tuberculosis (TB) is an infectious disease that has always accompanied humanity since its inception and throughout the society's evolution.1,2 Tuberculosis remains in the top 10 causes of death worldwide, while its treatment is a long process that has many side effects. Therefore, the discovery and development of new effective drugs against tuberculosis that target novel biochemical pathways and treat drug-resistant forms of the disease present an urgent need worldwide.

From the molecular-biological point of view, the most appropriate strategy for structure-based drug design (SBDD) is the identification and development of new medicines that target unique proteins of Mycobacterium tuberculosis, which participate in the most fundamental processes within mycobacteria, retaining maximum conservatism while having no direct homologs in humans and animals.3 This approach improves the chances of overcoming side effects related to the inhibition of similar protein targets of the host.

Life Chemicals has designed two Antituberculosis Screening Libraries of over 7,600 drug-like screening compounds aiming at key protein targets to facilitate high-throughput screening (HTS) efforts in anti-TB drug discovery research.

Antituberculosis Focused Library by 2D Similarity

The Library was developed with a 2D fingerprint similarity search against the reference set of 23,734 biologically active compounds (IC50, Ki, etc., less than 10 μM, Inhibition > 25 %), extracted from the Binding and ChEMBL databases. Therapeutically relevant viral assays data both for the Mycobacterium tuberculosis bacterium and the relevant protein targets, protein families were employed:

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Carbonic anhydrase
Cytochrome P450-121 or putative 125 type
Dihydrodipicolinate, 2-C-methyl-D-erythritol
2,4-cyclodiphosphate, and polyketide Pks13 synthase
Dihydrofolateand enoyl-[acyl-carrier-protein] reductase
Epoxide hydrolase and alpha/beta hydrolase fold family
Fructose-bisphosphate aldolase
HTH-type transcriptional regulator EthR
Intracellular chorismate mutase
Lanosterol 14-alpha demethylase
LmbE-related protein
N-acetyltransferase Eis
Pantothenate synthetase
Phosphotyrosine-protein phosphatase PTPB and low molecular weight protein-tyrosine-phosphatase
Polyketide synthase Pks13
Protein RecA
Rv1284/MT1322 protein
Serine/threonine-protein kinase pknB
Thioredoxin reductase
Transmembrane carbonic anhydrase
UDP-galactopyranose mutase

 

Over 4,200 unique structurally diverse small-molecule compounds were selected by filtering and merging their activity type data (Fig. 1).

Compound distribution targeting organism and single protein targets within the Antituberculosis Library.

Figure 1. Compound distribution targeting organism and single protein targets within the Antituberculosis Library.

Antituberculosis Docking Library by Structure-based Approaches

Designed with a receptor-based approach, this Library comprises potential inhibitors of InhA enzyme, M. tuberculosis-specific protein responsible for bacteria cell wall synthesis that is not present in mammals.

The structure of InhA protein and the binding mode of its known inhibitors were studied based on the analysis of crystal structure records in PDB. This information has provided a detailed understanding of the protein-ligand interaction mechanism.

The Life Chemicals HTS Compound Collection was processed according to ADME requirements, and all undesirable chemical groups were filtered out. The resulting drug-like set of compounds was screened by molecular docking using the Glide program (Schrödinger software). 3FNH and 2H7I PDB entries were selected for the docking studies for the most favorable ligand binding and high resolution of the crystal structures. The referent set of active ligands was used for evaluation of the docking procedure4,5. The presence of the NAD+coenzyme was taken into account in virtual screening as it is involved in ligand binding.

A set of around 3,400 potential antituberculosis agents capable of binding with InhA protein was obtained based on the docking results (Fig.2). Compounds have been selected by ligand efficacy and predicted binding mode.

 Ligand F2269-0132 in the binding pocket of InhA.

Figure 2. Ligand F2269-0132 forms a strong hydrogen bond with Tyr158 and protein coenzyme NAD+. High hydrophobic interaction observed between fused aromatic rings and large hydrophobic pocket of InhA.

References

  1. https://www.who.int/tb/publications/2019/consolidated-guidelines-drug-resistant-TB-treatment/en/
  2. Stephani Joy Y. Macalino, Junie B. Billones, Voltaire G. Organo, Maria Constancia O. Carrillo. In Silico Strategies in Tuberculosis Drug Discovery., Molecules. 2020 Feb; 25(3): 665. Published online.
  3. Xiaocui Wu, Jinghui Yang, Guangkun Tan, Haican Liu, Yin Liu, Yinjuan Guo, Rongliang Gao, Baoshan Wan, Fangyou Yu. Drug Resistance Characteristics of Mycobacterium tuberculosis Isolates From Patients With Tuberculosis to 12 Antituberculous Drugs in China., Front Cell Infect Microbiol. 2019; 9: 345. Published online
  4. He X., Alian A., Stroud R., Ortiz de Montellano P. R. J. Med. Chem., 2006, 49, pp. 6308–6323.
  5. Freundlich J. S., Wang F., Vilcheze C., Gulten, G., Langley R., Schiehser G. A., Jacobus D.P., Jacobs W. R., Sacchettini J. C. Chem. Med. Chem., 2009, 4, pp. 241–248.