Ferreira M. M. C., Kiralj R., “Chemometric and Molecular Graphics and Modeling Study on Bacterial b-Lactam Efflux Mechanism by Multidrug Resistance AcrB Pump”. Mariehamn, Åland Islands, Finland, 14-18/06/2003: 8th Scandinavian Symposium on Chemometrics (SSC8). Book of Abstracts, O17 (2003). Oral O17.

                Chemometric and Molecular Graphics and Modeling Study on Bacterial
                     b-Lactam Efflux Mechanism by Multidrug Resistance AcrB Pump

                                          Márcia M. C. Ferreira and Rudolf Kiralj

     Instituto de Química, Universidade Estadual de Campinas, Campinas SP, 13083-970, Brazil
 

AcrAB-TolC   is  the  most  important   multidrug  efflux  pump  of   gram-negative  bacteria,  which
excretes  a  variety  of  compounds  from  bacterial  cytoplasm  and  periplasm  directly  to  the  cell
exterior¹. It consists of the transport protein AcrB,  the linker  lipoprotein  AcrA,  and  the  channell-
tunell TolC².  b-Lactam  antibiotics,  the  most  widely  used  antibacterials  which  primarily  inhibit
penicillin-binding  proteins  responsible  for  the  construction  and  maintenance  of the bacterial cell
wall, are also substrates of this pump system.  This fact seriously increases the problems found in the
treatment  of  infectous  diseases.
Hierarchical  Cluster  Analysis   (HCA)   and  Principal  Component  Analysis   (PCA)  on  minimal
inhibitor concentrations  (pMIC)  elevated by  Salmonella typhimurium strains  HN891, SH7616,
SH5014, and of calculated lipophilicity descriptors for  16  b-lactams,  was  performed³.  Molecular
geometries of these  penicillin and  cephalosporin molecules were optimized at  semi-empirical  PM3
level, and various geometric, electronic, hydrogen bond and topological descriptors were calculated.
Quantitative  structure-activity  studies  were  carried  out  to  obtain  Partial  Least  Squares  (PLS)
regression  models  for  estimationn  of  pMICs  from  selected  molecular  descriptors.  Docking  of
selected drugs to a vestibule and the pore of the AcrB transporter crystal structure from Escherichia
coli²  was  also  performed.
HCA  and  PCA on  pMICs  confirmed  that  lipophilicity  and  charges  in  b-lactam  molecules  are
important   in  their  excretion  by   all  bacterial  strains.   The  antibiotics   were  classified  as  good,
moderately good to poor, and bad AcrB substrates. HCA and PCA  on  nine lipophilicity descriptors
revealed a  heterogeneous data set which can be described by  the  first  three  principal  components
and are groupped in several clusters. From QSAR studies parsimonius PLS models (Q² > 0.65, R² >
0.75)  with two lipophilicity parameters  (logP)  in parabolic form,  and two electronic  and hydrogen
bond descriptors,  were obtained.  The  docking  studies  enabled visualization of stereoelectronic b-
lactam  properties  responsible  for  drug – vestibule  and  drug – pore  recognition  mechanism,  thus
confirming  the  chemometric  and  QSAR  results.  This  work  provides a rationale for the multidrug
efflux  mechanism  of b-lactam  antibiotics,  based on  their  molecular  properties  and  drug – AcrB
molecular recognition. The mechanism includes two distinct routes, for lipophilic/amphiphilic and
hydrophilic  drugs.
 

¹ Nikaido, H.;  Basina, M.;  Nguyen, V.;  Rosenberg, E. Y.   J. Bacteriol., 1998,  180,  4686-92.
² Koronakis, V.;  Sharff, A.;  Koronakis, E.;  Luisi, B.;  Hughes, C.  Nature,  2000,  405,  914-9.
³ Ferreira, M. M. C.;  Kiralj, R.   J. Bacteriol.,  submitted.
 

Acknowledgement: The authors acknowledge FAPESP for support.