Transition state analogs (transition state analogues), are

chemical compound A chemical compound is a chemical substance composed of many identical molecules (or molecular entities) containing atoms from more than one chemical element held together by chemical bonds. A molecule consisting of atoms of only one element ...

s with a

chemical structure A chemical structure of a molecule is a spatial arrangement of its atoms and their chemical bonds. Its determination includes a chemist's specifying the molecular geometry and, when feasible and necessary, the electronic structure of the target m ...

that resembles the

transition state In chemistry, the transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest potential energy along this reaction coordinate. It is often marked w ...

of a substrate molecule in an enzyme-catalyzed

chemical reaction A chemical reaction is a process that leads to the chemistry, chemical transformation of one set of chemical substances to another. When chemical reactions occur, the atoms are rearranged and the reaction is accompanied by an Gibbs free energy, ...

. Enzymes interact with a substrate by means of strain or distortions, moving the substrate towards the transition state. Transition state analogs can be used as inhibitors in enzyme-catalyzed reactions by blocking the active site of the enzyme. Theory suggests that enzyme inhibitors which resembled the transition state structure would bind more tightly to the enzyme than the actual substrate. Examples of

drug A drug is any chemical substance other than a nutrient or an essential dietary ingredient, which, when administered to a living organism, produces a biological effect. Consumption of drugs can be via insufflation (medicine), inhalation, drug i ...

s that are transition state analog inhibitors include flu medications such as the neuraminidase inhibitor oseltamivir and the HIV protease inhibitors saquinavir in the treatment of AIDS.

Transition state analogue

The

of a structure can best be described in regards to

statistical mechanics In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. Sometimes called statistical physics or statistical thermodynamics, its applicati ...

where the energies of bonds breaking and forming have an equal probability of moving from the transition state backwards to the reactants or forward to the products. In enzyme-catalyzed reactions, the overall activation energy of the reaction is lowered when an enzyme stabilizes a high energy transition state intermediate. Transition state analogs mimic this high energy intermediate but do not undergo a catalyzed chemical reaction and can therefore bind much stronger to an enzyme than simple substrate or product analogs.

Designing transition state analogue

To design a transition state analogue, the pivotal step is the determination of transition state structure of substrate on the specific enzyme of interest with experimental method, for example, kinetic isotope effect. In addition, the transition state structure can also be predicted with computational approaches as a complementary to KIE. We will explain these two methods in brief.

Kinetic isotope effect

Kinetic isotope effect (KIE) is a measurement of the reaction rate of

isotope Isotopes are distinct nuclear species (or ''nuclides'') of the same chemical element. They have the same atomic number (number of protons in their Atomic nucleus, nuclei) and position in the periodic table (and hence belong to the same chemica ...

-labeled reactants against the more common natural substrate. Kinetic isotope effect values are a ratio of the turnover number and include all steps of the reaction. Intrinsic kinetic isotope values stem from the difference in the bond vibrational environment of an atom in the reactants at ground state to the environment of the atom's transition state. Through the kinetic isotope effect much insight can be gained as to what the transition state looks like of an enzyme-catalyzed reaction and guide the development of transition state analogs.

Computational simulation

Computational approaches have been regarded as a useful tool to elucidate the mechanism of action of enzymes.

Molecular mechanics Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...

itself can not predict the electron transfer which is the fundamental of

organic reaction Organic reactions are chemical reactions involving organic compounds. The basic organic chemistry reaction types are addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions, mechanistic organ ...

but the

molecular dynamics Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamics ( ...

simulation provide sufficient information considering the flexibility of protein during catalytic reaction. The complementary method would be combined molecular mechanics/ quantum mechanics simulation ( QM/MM)methods. With this approach, only the atoms responsible for enzymatic reaction in the catalytic region will be reared with

quantum mechanics Quantum mechanics is the fundamental physical Scientific theory, theory that describes the behavior of matter and of light; its unusual characteristics typically occur at and below the scale of atoms. Reprinted, Addison-Wesley, 1989, It is ...

and the rest of the atoms were treated with

molecular mechanics Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemi ...

Examples of transition state analogue design

After determining the transition state structures using either KIE or computation simulations, the inhibitor can be designed according to the determined transition state structures or intermediates. The following three examples illustrate how the inhibitors mimic the transition state structure by changing functional groups correspond to the geometry and electrostatic distribution of the transition state structures.

Methylthioadenosine nucleosidase inhibitor

Methylthioadenosine nucleosidase are enzymes that catalyse the hydrolytic deadenylation reaction of 5'-methylthioadenosine and S-adenosylhomocysteine. It is also regarded as an important target for antibacterial drug discovery because it is important in the metabolic system of bacteria and only produced by bacteria. Given the different distance between nitrogen atom of adenine and the ribose anomeric carbon (see in the diagram in this section), the transition state structure can be defined by early or late dissociation stage. Based on the finding of different transition state structures, Schramm and coworkers designed two transition state analogues mimicking the early and late dissociative transition state. The early and late transition state analogue shown binding affinity (Kd) of 360 and 140 pM, respectively.

Thermolysin inhibitor

Thermolysin is an enzyme produced by ''Bacillus thermoproteolyticus'' that catalyses the hydrolysis of peptides containing hydrophobic amino acids. Therefore, it is also a target for antibacterial agents. The enzymatic reaction mechanism starts form the small peptide molecule and replaces the zinc binding water molecule towards Glu143 of thermolysin. The water molecule is then activated by both the zinc ion and the Glu143 residue and attacks the carbonyl carbon to form a tetrahedral transition state (see figure). Holden and coworkers then mimicked that tetrahedral transition state to design a series of phosphonamidate peptide analogues. Among the synthesized analogues, R = L-Leu possesses the most potent inhibitory activity (''K''_i = 9.1 nM).

Arginase inhibitor

Arginase is a binuclear manganese metalloprotein that catalyses the hydrolysis of L-

arginine Arginine is the amino acid with the formula (H2N)(HN)CN(H)(CH2)3CH(NH2)CO2H. The molecule features a guanidinium, guanidino group appended to a standard amino acid framework. At physiological pH, the carboxylic acid is deprotonated (−CO2−) a ...

to L-

ornithine Ornithine is a non-proteinogenic α-amino acid that plays a role in the urea cycle. It is not incorporated into proteins during translation. Ornithine is abnormally accumulated in the body in ornithine transcarbamylase deficiency, a disorder of th ...

and

urea Urea, also called carbamide (because it is a diamide of carbonic acid), is an organic compound with chemical formula . This amide has two Amine, amino groups (–) joined by a carbonyl functional group (–C(=O)–). It is thus the simplest am ...

. It is also regarded as a drug target for the treatment of

asthma Asthma is a common long-term inflammatory disease of the airways of the lungs. It is characterized by variable and recurring symptoms, reversible airflow obstruction, and easily triggered bronchospasms. Symptoms include episodes of wh ...

. The mechanism of hydrolysis of L-arginine is carried out via nucleophilic attack on the guanidino group by water, forming a tetrahedral intermediate. Studies shown that a boronic acid moiety adopts a tetrahedral configuration and serves as an inhibitor. In addition, the

sulfonamide In organic chemistry, the sulfonamide functional group (also spelled sulphonamide) is an organosulfur group with the Chemical structure, structure . It consists of a sulfonyl group () connected to an amine group (). Relatively speaking this gro ...

functional group can also mimic the transition state structure. Evidence of boronic acid mimics as transition state analogue inhibitors of human arginase I was elucidated by x-ray crystal structures.

References

{{reflist Enzyme kinetics Chemical nomenclature he:אנלוג של סובסטרט