**8. Peptide bond formation by ribosome**

to *L*-ornithine and urea (Fig. 21) is also the final cytosolic step of the urea cycle in mammali‐ an liver. *S*-(2-Boronoethyl)-*L*-cysteine is one of the most effective inhibitor of the enzyme (Fig 21). The specificity determinants of amino acid recognition by arginase were identified by X-Ray structure of human arginase I enzyme complexed with this inhibitor. These stud‐ ies undoubtedly shown that boronate adopts tetrahedral configuration [Cama et al., 2003 & 2003a; Shishova, et al., 2009]. Also aldehydes and sulfonamides similar to boronic acids ap‐

Urease catalyzes hydrolysis of urea in the last step of organic nitrogen mineralization to give ammonia and carbamate, which decomposes to give a second molecule of ammonia and bi‐ carbonate (Fig. 22). The hydrolysis of the reaction products induces an overall pH increase that has negative implications both in human and animal health as well as in the ecosphere. Urease is a virulence factor in infections of urinary (*Proteus mirabilis*, *Ureaplasma urealyticum*) and gastrointestinal tracts (*Helicobacter pylori*), causing severe diseases such as peptic ulcers, stomach cancer, and formation of urinary stones. The efficiency of soil nitrogen fertilization with urea (the most used fertilizer worldwide) decreases due to ammonia volatilization and root damage caused by soil pH increase. Thus, control of the activity of urease through the use of inhibitors could counteract these negative effects [Kosikowska & Berlicki, 2011; Zam‐ belli et al., 2011]. Di- and triamides of phosphoric acid represent a group of urease inhibitors with the highest activity. It is the direct consequence of their similarity to the tetrahedral transition state of the enzymatic reaction of urea hydrolysis. Takeda Chemicals have patent‐ ed a large group of N-acyltriamido phosphates and found over 90 examples with nanomolar activity against *H. pylori* urease, with flurofamide being the most effective (Fig. 22) [Kosi‐

Recently design, synthesis, and evaluation of novel ogranophosphonate inhibitors of bacteri‐ al urease have been described as an attractive alternative to known phosphoramidates. On the basis of the crystal structure of *Bacillus pasteurii* urease, several phosphinic acids and their short peptides have been designed by using the computer-aided techniques. The step‐

peared to be promising inhibitors of arginases [Shin et al., 2004].

344 Drug Discovery

**Figure 21.** Arginase catalyzed reaction and representative inhibitors of the enzyme.

kowska & Berlicki, 2011].

Ribosomes are molecular machines that synthesize proteins in the cell. Recent biochemical analyses and high-resolution crystal structures of the bacterial ribosome have shown that the active site for the formation of peptide bonds – the peptidyl-transferase center – is com‐ posed solely of rRNA. Thus, the ribosome is the largest known RNA catalyst and the only natural ribozyme that has a synthetic activity. Peptide bond formation during ribosomal protein synthesis involves an aminolysis reaction between the aminoacyl α-amino group and the carbonyl ester of the growing peptide via a transition state with a developing nega‐ tive charge - the oxyanion. Therefore the observed intermediates and transition states are similar to those observed in proteinases (Fig. 23). Structural and molecular dynamic studies have suggested that the ribosome may stabilize the oxyanion in the transition state of pep‐ tide bond formation via a highly ordered water molecule [Rodnina et al., 2006; Carrasco et al., 2011].

**Figure 22.** Urease hydrolysed reaction and evolution of the structure of its inhibitors.

To biochemically elucidate how the ribosome stabilizes the developing negative charge in the transition state of peptide bond formation, a series of tetrahedral transition state mimics were synthesized. Their relative binding affinities for the ribosomes also were measured (Fig. 23). The obtained results confirmed high affinity of predicted mechanism of ribosome action [Green & Lorsch, 2002; Weinger et al., 2004; Carrasco, et al., 2011].

**Figure 24.** Mechanism of condensation of two molecules of D-Ala catalyzed by *D*-alanine-*D*-alanine ligase.

teins [Dzekieva et al., 2010; Dzekieva et al., 2012] (Fig. 25).

**Figure 25.** Inhibitors activated by ATP.

**10. Nucleotide deaminases**

Similarly acting inhibitors have been found for glutamine synthetase (phosphinothricin and methionine sulfoximine and their analogs) [Berlicki et al., 2005; Berlicki & Kafarski 2006; Berlicki, 2008], γ-glutamylcysteine synthetase [Hibi et al., 2004], or penicillin binding pro‐

Transition State Analogues of Enzymatic Reaction as Potential Drugs

http://dx.doi.org/10.5772/52504

347

Enzymes of the deaminase superfamily catalyze deamination of bases in nucleotides and nucleic acids across in diverse biological contexts. Representatives that act on free nucleoti‐ des or bases are primarily involved in the salvage of pyrimidines and purines, or in their catabolism in bacteria, eukaryotes and phages. Other members of the deaminase superfami‐ ly catalyze the *in situ* deamination of bases in both RNA and DNA. Such modifications play a central role in RNA editing, which is critical for generating the appropriate anti-codon se‐ quences for decoding the genetic code, modification of the sequences of microRNA and oth‐

**Figure 23.** Transition state analog inhibitor of peptidyl transferase.
