International
Tables for
Crystallography
Volume F
Crystallography of biological macromolecules
Edited by M. G. Rossmann and E. Arnold

© International Union of Crystallography 2006
International Tables for Crystallography (2006). Vol. F. ch. 1.3, pp. 15-21   | 1 | 2 |

Section 1.3.4.2. Resistance

W. G. J. Hola* and C. L. M. J. Verlindea

aBiomolecular Structure Center, Department of Biological Structure, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-7742, USA
Correspondence e-mail:  hol@gouda.bmsc.washington.edu

1.3.4.2. Resistance

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Resistance to drugs in infectious organisms, as well as in cancers, is a fascinating subject, since it demonstrates the action and reaction of biological systems in response to environmental challenges. Life, of course, has been evolving to do just that – and the arrival of new chemicals, termed `drugs', on the scene is nothing new to organisms that are the result of evolutionary processes involving billions of years of chemical warfare. Populations of organisms span a wide range of variation at the genetic and protein levels, and the chance that one of the variants is able to cope with drug pressure is nonzero. The variety of mechanisms observed to be responsible for drug resistance is impressive (Table 1.3.4.4[link]).

Table 1.3.4.4| top | pdf |
Mechanisms of resistance

Overexpress target protein
Mutate target protein
Use other protein with same function
Remove target altogether
Overexpress detoxification enzyme
Mutate detoxification enzyme
Create new detoxification enzyme
Mutate membrane porin protein
Remove or underexpress membrane porin protein
Overexpress efflux pumps
Mutate efflux pumps
Create/steal new efflux pumps
Improve DNA repair
Mutate prodrug conversion enzyme

Crystallography has made major contributions to the detailed molecular understanding of resistance in the case of detoxification, mutation and enzyme replacement mechanisms. Splendid examples are:

  • (a) The beta-lactamases: These beta-lactam degrading enzymes, of which there are four classes, are produced by many bacteria to counteract penicillins and cephalosporins, the most widely used antibiotics on the planet. No less than 53 structures of these enzymes reside in the PDB.

  • (b) HIV protease mutations: Tens of mutations have been characterized structurally. Many alter the active site at the site of mutation, thereby preventing drug binding. Other mutations rearrange the protein backbone, reshaping entire pockets in the binding site (Erickson & Burt, 1996[link]).

  • (c) HIV reverse transcriptase mutations: Via structural studies, at least three mechanisms of drug resistance have been elucidated: direct alteration of the binding sites for the nucleoside analogue or non-nucleoside inhibitors, mutations that change the position of the DNA template, and mutations that induce conformational changes that propagate into the active site (Das et al., 1996[link]; Hsiou et al., 1998[link]; Huang, Chopra et al., 1998[link]; Ren et al., 1998[link]; Sarafianos et al., 1999[link]).

  • (d) Resistance to vancomycin: In non-resistant bacteria, vancomycin stalls the cell-wall synthesis by binding to the D-Ala-D-Ala terminus of the lipid–PP-disaccharide–pentapeptide substrate of the bacterial transglycosylase/transpeptidase, thereby sterically preventing the approach of the substrate. Resistant bacteria, however, have acquired a plasmid-borne transposon encoding for five genes, vanS, vanR, vanH, vanA and vanX, that allows them to synthesise a substrate ending in D-Ala-D-lactate. This minute difference, an oxygen atom replacing an NH, leads to a 1000-fold reduced affinity for vancomycin, explaining the resistance (Walsh et al., 1996[link]). Thus far, the structures of vanX (Bussiere et al., 1998[link]) and D-Ala-D-Ala ligase as a model for vanA (Fan et al., 1994[link]) have been solved. They provide an exciting basis for arriving at new antibiotics against vancomycin-resistant bacteria.

  • (e) DHFR: Some bacteria resort to the `ultimate mutation' in order to escape the detrimental effects of antibiotics. They simply replace the entire targeted enzyme by a functionally identical but structurally different enzyme. A prime example is the presence of a dimeric plasmid-encoded DHFR in certain trimethoprim-resistant bacteria. The structure proved to be unrelated to that of the chromosomally encoded monomeric DHFR (Narayana et al., 1995[link]).

Clearly, the structural insight gained from these studies provides us with avenues towards methods for coping with the rapid and alarming spread of resistance against available antibiotics that threatens the effective treatment of bacterial infections of essentially every person on this planet. This implies that we will constantly have to be aware of the potential occurrence of mono- and also multi-drug resistance, which has profound consequences for drug-design strategies for essentially all infectious diseases. It requires the development of many different compounds attacking many different target proteins and nucleic acids in the infectious agent. It appears to be crucial to use, from the very beginning, several new drugs in combination so that the chances of the occurrence of resistance are minimal. Multi-drug regimens have been spectacularly successful in the case of leprosy and HIV. Obviously, the development of vaccines is by far the better solution, but it is not always possible. Antigenic variation, see e.g. the influenza virus, requires global vigilance and constant re-engineering of certain vaccines every year. Moreover, for higher organisms, and even for many bacterial species like Shigella (Levine & Noriega, 1995[link]), with over 50 serotypes per species, the development of successful vaccines has, unfortunately, proved to be very difficult indeed. For sleeping sickness, the development of a vaccine is generally considered to be impossible. It is most likely, therefore, that world health will depend for centuries on a wealth of therapeutic drugs, together with many other measures, in order to keep the immense number of pathogenic organisms under control.

References

First citation Bussiere, D. E., Pratt, S. D., Katz, L., Severin, J. M., Holzman, T. & Park, C. H. (1998). The structure of VanX reveals a novel amino-dipeptidase involved in mediating transposon-based vancomycin resistance. Mol. Cell, 2, 75–84.Google Scholar
 First citation Das, K., Ding, J., Hsiou, Y., Clark, A. D. Jr, Moereels, H., Koymans, L., Andries, K., Pauwels, R., Janssen, P. A. J., Boyer, P. L., Clark, P., Smith, R. H. Jr, Kroeger Smith, M. B., Michejda, C. J., Hughes, S. H. & Arnold, E. (1996). Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. J. Mol. Biol. 264, 1085–1100.Google Scholar
 First citation Erickson, J. W. & Burt, S. K. (1996). Structural mechanisms of HIV drug resistance. Annu. Rev. Pharmacol. Toxicol. 36, 545–571.Google Scholar
 First citation Fan, C., Moews, P. C., Walsh, C. T. & Knox, J. R. (1994). Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 Å resolution. Science, 266, 439–443.Google Scholar
 First citation Hsiou, Y., Das, K., Ding, J., Clark, A. D. Jr, Kleim, J. P., Rosner, M., Winkler, I., Riess, G., Hughes, S. H. & Arnold, E. (1998). Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. J. Mol. Biol. 284, 313–323.Google Scholar
 First citation Huang, H., Chopra, R., Verdine, G. L. & Harrison, S. C. (1998). Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science, 282, 1669–1675.Google Scholar
 First citation Levine, M. M. & Noriega, F. (1995). A review of the current status of enteric vaccines. Papua New Guinea Med. J. 38, 325–331.Google Scholar
 First citation Narayana, N., Matthews, D. A., Howell, E. E. & Nguyen-huu, X. (1995). A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site. Nature Struct. Biol. 2, 1018–1025.Google Scholar
 First citation Ren, J., Esnouf, R. M., Hopkins, A. L., Jones, E. Y., Kirby, I., Keeling, J., Ross, C. K., Larder, B. A., Stuart, D. I. & Stammers, D. K. (1998). 3-Azido-3′-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes. Proc. Natl Acad. Sci. USA, 95, 9518–9523.Google Scholar
 First citation Sarafianos, S. G., Das, K., Ding, J., Boyer, P. L., Hughes, S. H. & Arnold, E. (1999). Touching the heart of HIV-1 drug resistance: the fingers close down on the dNTP at the polymerase active site. Chem. Biol. 6, R137–R146.Google Scholar
 First citation Walsh, C. T., Fisher, S. L., Park, I. S., Prahalad, M. & Wu, Z. (1996). Bacterial resistance to vancomycin: five genes and one missing hydrogen bond tell the story. Chem. Biol. 3, 21–28.Google Scholar








































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