Exploring the Role of L10 Loop in New Delhi Metallo-β-lactamase (NDM-1): Kinetic and Dynamic Studies

• Published in: Molecules (Basel, Switzerland) Switzerland), 2021-09, Vol.26 (18), p.5489
• Main Authors: Piccirilli, Alessandra, Criscuolo, Emanuele, Brisdelli, Fabrizia, Mercuri, Paola Sandra, Cherubini, Sabrina, De Sciscio, Maria Laura, Maccarrone, Mauro, Galleni, Moreno, Amicosante, Gianfranco, Perilli, Mariagrazia
• Format: Article
• Language: English
• Subjects: Amino Acid Substitution; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - metabolism; beta-Lactamases - chemistry; beta-Lactamases - genetics; beta-Lactamases - metabolism; Carbapenems; Cefazolin; Cefazolin - chemistry; Cefazolin - metabolism; Cefepime; Cefoxitin; Cefoxitin - chemistry; Cefoxitin - metabolism; Enzymatic activity; Enzyme activity; Enzyme Stability; Enzymes; Hydrogen-Ion Concentration; Imipenem - chemistry; Imipenem - metabolism; kinetic studies; Kinetics; Leucine - genetics; Meropenem - chemistry; Meropenem - metabolism; Metallo-β-lactamase; metallo-β-lactamases; Metallography; molecular dynamic; Molecular dynamics; Molecular Dynamics Simulation; Mutagenesis, Site-Directed; Mutants; NDM-1; Real-Time Polymerase Chain Reaction; Residues; Spectrometry, Fluorescence; Zinc; β Lactamase; β-Lactam antibiotics
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules26185489

Four NDM-1 mutants (L218T, L221T, L269H and L221T/Y229W) were generated in order to investigate the role of leucines positioned in L10 loop. A detailed kinetic analysis stated that these amino acid substitutions modified the hydrolytic profile of NDM-1 against some β-lactams. Significant reduction of k values of L218T and L221T for carbapenems, cefazolin, cefoxitin and cefepime was observed. The stability of the NDM-1 and its mutants was explored by thermofluor assay in real-time PCR. The determination of T B and T D demonstrated that NDM-1 and L218T were the most stable enzymes. Molecular dynamic studies were performed to justify the differences observed in the kinetic behavior of the mutants. In particular, L218T fluctuated more than NDM-1 in L10, whereas L221T would seem to cause a drift between residues 75 and 125. L221T/Y229W double mutant exhibited a decrease in the flexibility with respect to L221T, explaining enzyme activity improvement towards some β-lactams. Distances between Zn1-Zn2 and Zn1-OH- or Zn2-OH- remained unaffected in all systems analysed. Significant changes were found between Zn1/Zn2 and first sphere coordination residues.