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DHQase and the Shikimate Pathway of Mycobacterium tuberculosis
Brookfield Central High School
Esha Afreen, Deepti Ajjampore, Brad Bartelt, Krishti Bhowmick, Anthony Fung, Kamya Gopal, Karin Jorgensen, Ramprasad
Karanam, Harshi Mogallapalli, Erik Nesler, Nikil Prasad, Rishi Sachdev, John Scanlon, Hafsa Shereen, and Nikita Sood
Advisor: Mrs. Louise Thompson
Mentor: Sanjib Bhattacharyya, Ph.D., Deputy Laboratory Director at City of Milwaukee Health Department
Abstract
In 2011, nearly 9 million people became sick with tuberculosis, of which 1.4 million died worldwide, according to the World Health Organization. Tuberculosis (TB) is an infectious, airborne disease caused by a pathogenic bacterium, Mycobacterium tuberculosis. This bacterium primarily attacks the lungs and is often
fatal if not treated promptly. 3-dehydroquinate dehydratase (DHQase) is an enzyme that catalyzes the third step of the shikimate pathway, which is essential to M. tuberculosis. The shikimate pathway creates a precursor to the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Inhibition of DHQase will block
the shikimate pathway and the TB bacteria will die. Inhibitors can be used for drug development to treat tuberculosis, especially people affected by multidrug-resistant strains, called MDR-TB. Since DHQase is absent in human cells, the drug will only affect bacteria cells, where the enzyme is inactive until substrate
binds to its active site. 3-dehydroshikimate, a natural ligand, and six inhibitors can interact with DHQase. Effectively inhibiting this enzyme would render tuberculosis harmless. DHQase has a flexible catalytic loop at residues 19–24. Arg19 and Tyr24 are the two key conserved residues. The ligand binding induces
closure of the loop through its interaction with the side-chain atoms of loop residues: Tyr24 and Arg19. DHQase may hold the key to saving the lives of those infected by MDR-TB. The Brookfield Central High School SMART Team (Students Modeling a Research Topic) created physical models of DHQase dodecamer and
monomer to show active-site binding molecules and inhibitors using 3-D modeling printing technology.
DHQase
Introduction: Prevalence
Two years ago, 9 million cases of tuberculosis were
reported worldwide. Of these victims, 1.4 million
died, including several recent cases in the metroMilwaukee area. Tuberculosis (TB) is caused
by the pathogenic bacterium, Mycobacterium
tuberculosis. According to the World Health
Organization (WHO), the TB incidence rate
is rising by 1% each year. Although there is a
common misconception that TB only affects
those living in developing countries, the disease
is becoming increasingly prevalent globally (as
shown in Fig. 1).
Inhibitors for DHQase
Figure 4 shows 3-dehydroquinate dehydratase, or dehydroquinase (DHQase), an enzyme that is
essential to the synthesis of aromatic hydrocarbons. It does so by catalyzing the third step in the
Shikimate pathway, as denoted by the reaction shown in Fig. 3. However, this pathway is not present
in human cells, and the presence of this pathway and enzyme allow M. tuberculosis to thrive. The key
characteristics of DHQase:
• Conserved residues Arg19 and Tyr24 are located on a flexible loop
• Arg19 and Tyr24 are essential for substrate binding, catalysis, and DHQase inhibitor design
There are seven compounds that are known to bind to the active site of DHQase. One of these is a
ligand, which reacts with the enzyme, under normal conditions, to produce the reactants for the next
step in the shikimate pathway. The other six compounds are competitive inhibitors of which four will be
discussed, namely inhibitors 2, 3, 5, and 6 (shown in figure 6). When these inhibitors bind to the active
site, the ligand, 3-dehydroquinate, is not able to bind to DHQase. Inhibitors 3, 5, and 6 are variations
of inhibitor 2. One important factor that determines the potency of the inhibitors is flexibility. Flexibility
refers to the ease with which the inhibitor binds to the active site. Inhibitor 5 is the most flexible,
followed by inhibitors 6, 3, and 2.
C
2
B
3
5
6
Figure 1: Map of tuberculosis cases with MDR-TB
A
A
Pathophysiology
source: textbookofbacteriology.net
B
source: radiopaedia.org
The disease may not manifest itself with evident
symptoms and may remain latent until the illness
becomes fatal; however, if treated in due time,
TB is curable. Symptoms include chronic cough,
fatigue, night sweats, and shortness of breath.
This bacterium primarily targets the lungs (Fig.
2B), but the disease can be spread to any organ
of the body through the bloodstream. Because TB
is an airborne disease, it is extremely contagious.
Each infected person transmits the bacteria to
approximately 10 to 15 others each year (WHO
TB Report, 2012).
Figure 2: A. Mycobacterium tuberculosis (scanning EM, CDC)
B. TB-infected lung
Shikimate Pathway
In Mycobacterium tuberculosis, the Shikimate pathway is critical to the survival of the bacteria. The
diagram of the Shikimate pathway below (Figure 3) consists of seven enzymes that catalyze separate
steps of the pathway. They convert erythrose-4-phosphate and phosphoenol pyruvate to produce
chorismate, an essential precursor of the aromatic compounds that produce the essential amino
acids tryptophan, phenylalanine, and tyrosine. DHQase is the enzyme that catalyzes the third step
in the Shikimate pathway. DHQase catalyzes the reversible conversion of 3-dehydroquinate into
3-dehydroshikimate and water. In the first step of the DHQase reaction, a conserved tyrosine residue
removes the pro-S proton to form the enolate intermediate. At the same time, an asparagine residue
stabilizes the intermediate, and a conserved histidine liberates a water molecule, producing the
3-dehydroshikimate.
Figure 6: Competetive inhibitors 2, 3, 5, and 6 for DHQase
Figure 4: Models of DHQase: A. Dodecamer, B. Monomer, C. Active Site
Competitive Inhibition
Competitive inhibitors structurally mirror the natural substrate and compete for binding with the active
site of an enzyme. If the inhibitor binds to the enzyme, the substrate itself is prevented from binding to
the enzyme, and the enzyme is blocked from performing its normal function.
A
B
C
D
Figure 7 below shows the effect on 3-dehydroquinate activity in a solution of Inhibitor 7 as well as the
natural ligand. Rate of production of 3-dehydroquinate in μM per second along with the concentration
of 3-dehydroquinate in μM when in a solution of Inhibitor 7 of concentration 0 – 300 μM. The graph
shows that Inhibitor 7 acts as a competitive inhibitor of DHQase, as increasing the concentration of
Inhibitor 7 decreases the amount of 3-dehydroquinate produced.
Figure 5: Enzyme, substrate, and inhibitor interaction in competitive inhibition.
A. Enzyme and substrate prepare to bind.
B. Enzyme and substrate are bound.
C. Enzyme has acted on substrate.
D. Substrate cannot bind because inhibitor is already bound to enzyme.
References
Gourley, D. G., Shrive, A. K., Polikarpov, I., Krell, T., Coggins, J. R., Hawkins, A. R., Isaacs, N. W. and Sawyer, L. (1999) The two types of
3-dehydroquinase have distinct structures but catalyze the seme overall reaction. Nat. Struct. Biol. 6, 521–525.
Hopkins, A. L., Groom, C. R. and Alex, A. (2004) Ligand efficiency: a useful metric for lead selection. Drug Discovery Today 9, 430–431.
Marcio V. B. DIAS, William C. SNEE, Karen M. BROMFIELD, Richard J. PAYNE, Satheesh K. PALANINATHAN, Alessio CIULLI, Nigel I.
HOWARD, Chris ABELL, James C. SACCHETTINI and Tom L. BLUNDEL. (2011) Structural investigation of inhibitor designs targeting
3-dehydroquinate dehydratase from the shikimate pathway of Mycobacterium tuberculosis. Biochem. J. (2011) 436, 729–739
Figure 7: Accumulation of 3-dehydroquinate in presence of inhibitor.
Biological Significance
Roszak, A. W., Robinson, D. A., Krell, T., Hunter, I. S., Fredrickson, M., Abell, C., Coggins, J. R. and Lapthorn, A. J. (2002) The structure
and mechanism of the type II dehydroquinase from Streptomyces coelicolor . Structure 10, 493–503.
Tuberculosis is an common disease that is prevalent in third-world countries, but is spreading to more
developed areas. Although less common, multidrug-resistant tuberculosis (MDR-TB) is a more lethal
strain that affects 630,000 people worldwide. Attempts to treat MDR-TB have met with little to no
success. In the future, researchers hope to find a suitable inhibitor for DHQase in order to devolop
drugs that effectively treat MDR-TB.
Skrahina, A., Hurevich, H., Zalutskaya, A., Sahalchyk, E., Astrauko, A., Hoffner, S., & ... Zignol, M. (2013). Multidrug-resistant tuberculosis in Belarus: the size of the problem and associated risk factors. Bulletin Of The World Health Organization, 91(1), 36-45. doi:10.2471/
BLT.12.104588
A SMART Team project supported by the National Institutes of Health Science Education Partnership Award (NIH-SEPA 1R25RR022749) and an NIH
CTSA Award (UL1RR031973).
Robinson, D. A., Stewart, K. A., Price, N. C., Chalk, P. A., Coggins, J. R. and Lapthorn, A. J. (2006) Crystal structure of Helicobacter pylori type II dehydroquinase inhibitor complexes: new directions for inhibitor design. J. Med. Chem. 49, 1282–1290.
Figure 3: The Shikimate pathway which consists of seven enzymes that catalyze separate steps and produce chorismate.
Inhibition of DHQase Activity
A SMART Team project supported by the National Institutes of Health Science Education Partnership Award (NIH-SEPA 1R25RR022749) and an NIH
CTSA Award (UL1RR031973).