Molecular Dynamics Simulations of the TEM-1 β-Lactamase Complexed with Cephalothin

Herein, we present theoretical results aimed at elucidating the origin of the kinetic preference
for penicillins over cephalosporins characteristic of the TEM/SHV subgroup of class A
β-lactamases. First, we study the conformational properties of cephalothin showing that the
C2-down conformer of the dihydrothiazine ring is preferred over the C2-up one by ∼2 kcal/mol
in solution (0.4−1.4 kcal/mol in the gas phase). Second, the TEM-1 β-lactamase complexed
with cephalothin is investigated by carrying out a molecular dynamics simulation. The ΔGbinding
energy is then estimated using molecular mechanics Poisson−Boltzmann surface area
(MM-PBSA) and quantum chemical PBSA (QM-PBSA) computational schemes. The preferential
binding of benzylpenicillin over cephalothin is reproduced by the different energetic calculations,
which predict relative ΔΔGbinding energies ranging from 1.8 to 5.7 kcal/mol. The benzylpenicillin/cephalothin ΔΔGbinding energy is most likely due to the lower efficacy of cephalosporins than
that of penicillins in order to simultaneously bind the “carboxylate pocket” and the “oxyanion
hole” in the TEM-1 active site.