Discovery of a fragment hit compound targeting D-Ala:D-Ala ligase of bacterial peptidoglycan biosynthesis

Abstract Bacterial resistance is an increasing threat to healthcare systems, highlighting the need for discovering new antibacterial agents. An established technique, fragment-based drug discovery, was used to target a bacterial enzyme Ddl involved in the biosynthesis of peptidoglycan. We assembled general and focused fragment libraries that were screened in a biochemical inhibition assay. Screening revealed a new fragment-hit inhibitor of DdlB with a Ki value of 20.7 ± 4.5 µM. Binding to the enzyme was confirmed by an orthogonal biophysical method, surface plasmon resonance, making the hit a promising starting point for fragment development.

[1]  S. Gobec,et al.  Redox active or thiol reactive? Optimization of rapid screens to identify less evident nuisance compounds. , 2022, Drug discovery today.

[2]  Peizhi Ma,et al.  Discovery of novel antibacterial agents: Recent developments in D‐alanyl‐D‐alanine ligase inhibitors , 2021, Chemical biology & drug design.

[3]  G. Wang,et al.  Pharmacomodulations of the benzoyl-thiosemicarbazide scaffold reveal antimicrobial agents targeting d-alanyl-d-alanine ligase in bacterio. , 2020, European journal of medicinal chemistry.

[4]  Q. You,et al.  Medicinal chemistry of metal chelating fragments in metalloenzyme active sites: A perspective. , 2019, European journal of medicinal chemistry.

[5]  B. Joris,et al.  1-(2-Hydroxybenzoyl)-thiosemicarbazides are promising antimicrobial agents targeting d-alanine-d-alanine ligase in bacterio. , 2018, European journal of medicinal chemistry.

[6]  Seth M. Cohen,et al.  Targeting Metalloenzymes for Therapeutic Intervention. , 2018, Chemical reviews.

[7]  M. Raffatellu.  Learning from bacterial competition in the host to develop antimicrobials , 2018, Nature Medicine.

[8]  Roderick E Hubbard,et al.  Using Fragment-Based Approaches to Discover New Antibiotics , 2018, SLAS discovery : advancing life sciences R & D.

[9]  V. Fülöp,et al.  Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine , 2017, Nature Communications.

[10]  Dušanka Janežič,et al.  Discovery of new MurA inhibitors using induced-fit simulation and docking. , 2017, Bioorganic & medicinal chemistry letters.

[11]  Harren Jhoti,et al.  Twenty years on: the impact of fragments on drug discovery , 2016, Nature Reviews Drug Discovery.

[12]  Dean G. Brown,et al.  ESKAPEing the labyrinth of antibacterial discovery , 2015, Nature Reviews Drug Discovery.

[13]  Jayme L. Dahlin,et al.  PAINS in the Assay: Chemical Mechanisms of Assay Interference and Promiscuous Enzymatic Inhibition Observed during a Sulfhydryl-Scavenging HTS , 2015, Journal of medicinal chemistry.

[14]  M. Kinch,et al.  An analysis of FDA-approved drugs for infectious disease: antibacterial agents. , 2014, Drug discovery today.

[15]  S. Gobec,et al.  Inhibitors of the peptidoglycan biosynthesis enzymes MurA-F. , 2014, Bioorganic chemistry.

[16]  Woody Sherman,et al.  Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments , 2013, Journal of Computer-Aided Molecular Design.

[17]  Stanislav Gobec,et al.  6-Arylpyrido[2,3-d]pyrimidines as Novel ATP-Competitive Inhibitors of Bacterial D-Alanine:D-Alanine Ligase , 2012, PloS one.

[18]  Janez Konc,et al.  Function of the D-alanine:D-alanine ligase lid loop: a molecular modeling and bioactivity study. , 2012, Journal of medicinal chemistry.

[19]  S. Conway,et al.  The use of phosphate bioisosteres in medicinal chemistry and chemical biology , 2012 .

[20]  C. Murray,et al.  The rise of fragment-based drug discovery. , 2009, Nature chemistry.

[21]  D. Blanot,et al.  Cytoplasmic steps of peptidoglycan biosynthesis. , 2008, FEMS microbiology reviews.

[22]  Paulette Charlier,et al.  The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis. , 2008, FEMS microbiology reviews.

[23]  Daniel James,et al.  Lessons Learnt from Assembling Screening Libraries for Drug Discovery for Neglected Diseases , 2007, ChemMedChem.

[24]  Jeremy R. Greenwood,et al.  Epik: a software program for pKa prediction and protonation state generation for drug-like molecules , 2007, J. Comput. Aided Mol. Des..

[25]  Federico D. Sacerdoti,et al.  Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters , 2006, ACM/IEEE SC 2006 Conference (SC'06).

[26]  Matthew P. Repasky,et al.  Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. , 2006, Journal of medicinal chemistry.

[27]  Victor Guallar,et al.  Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach , 2005, J. Comput. Chem..

[28]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[29]  E. Brown,et al.  Kinetics, stoichiometry, and identification of the reactive thiolate in the inactivation of UDP-GlcNAc enolpyruvoyl transferase by the antibiotic fosfomycin. , 1994, Biochemistry.

[30]  C. Walsh,et al.  Existence of two D-alanine:D-alanine ligases in Escherichia coli: cloning and sequencing of the ddlA gene and purification and characterization of the DdlA and DdlB enzymes. , 1991, Biochemistry.

[31]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[32]  F C NEUHAUS,et al.  THE ENZYMATIC SYNTHESIS OF D-ALANYL-D-ALANINE. 3. ON THE INHIBITION OF D-ALANYL-D-ALANINE SYNTHETASE BY THE ANTIBIOTIC D-CYCLOSERINE. , 1964, Biochemistry.

[33]  Maurizio Vichi,et al.  Studies in Classification Data Analysis and knowledge Organization , 2011 .

[34]  Thorsten Meinl,et al.  KNIME: The Konstanz Information Miner , 2007, GfKl.