Molecular docking is a computational technique that predicts how drugs, like methotrexate, interact with the enzyme dihydrofolate reductase (DHFR), impacting drug efficacy and side effects. DHFR's three-dimensional structure has been extensively studied, revealing its active site where ligand binding occurs, crucial for drug design. Methotrexate binds to DHFR, forming key interactions that can inhibit enzyme activity, although its effectiveness is limited by toxicity and drug resistance.

1. MOLECULAR DOCKING AND
DRUG RECEPTOR
INTERACTION, AGENT
ACTING ON DHFR
MO.SHAHNAWAZ
220010226
M.PHARM (PHARMACEUTICAL CHEMISTRY)

2. INTRODUCTION
 Molecular docking is a computational technique used to predict the binding
affinity and orientation of a ligand (such as a drug) to its receptor (such as a
protein) based on their three-dimensional structures.
 Drug receptor interaction refers to the specific molecular interactions that occur
between a drug and its receptor, which ultimately determine the drug's efficacy
and side effects.
 Molecular docking is a valuable tool in drug discovery because it can help
researchers identify potential drug candidates that can be further optimized and
developed into new drugs.

3.  Dihydrofolate reductase (DHFR) is an important enzyme that is involved in the
folate metabolism pathway.
 It catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF), which
is essential for the synthesis of nucleic acids and other important cellular
processes.
 DHFR is a target for several drugs, including methotrexate, trimethoprim, and
pyrimethamine, which are used in the treatment of cancer and bacterial
infections.
 The interaction between DHFR and these drugs is based on their structural
similarity to the natural substrate DHF.

4. Methotrexate, trimethoprim, and pyrimethamine are drugs that target DHFR.
DHFR is an enzyme that catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate
(THF).
Methotrexate and trimethoprim competitively bind to the active site of DHFR, inhibiting its
activity and preventing the reduction of DHF to THF.
The binding of these drugs to DHFR is essential for their therapeutic activity, as it selectively
inhibits cancer cells or pathogens and minimizes side effects in normal cells.

6. MOLECULAR DOCKING AND DRUG RECEPTOR INTERACTION OF
METHOTREXATE
 Dihydrofolate reductase (DHFR) catalyzes the reduction of folic acid to dihydrofolic
acid and to tetrahydrofolic acid, an essential cofactor in the biosynthesis of
thymidylate, purines and glycine.
 The folic acid analogue methotrexate (MTX) has been shown to bind tightly to the
active site of the enzyme, resulting in the death of exposed cells .
 Although MTX has been widely used as a chemotherapeutic agent for the treatment of
many cancers, its lack of specicity for tumor cells and its high toxicity prole for many
types of cancer hamper its effectiveness .
 Additionally, the development of drug resistance is also a limitation to MTX use.

7. RECEPTOR PREPARATION
The three-dimensional structure of DHFR has been extensively studied using
various techniques, such as X-ray crystallography and nuclear magnetic
resonance (NMR) spectroscopy.
The crystal structure of DHFR from Escherichia coli (E. coli) is one of the most
well-known and frequently studied structures. It consists of a single
polypeptide chain composed of 159 amino acid residues. The three-
dimensional structure of DHFR can be visualized as a compact bundle of alpha-
helices and beta-sheets.
The active site of DHFR, where the catalytic reaction takes place, is located in
a cleft on the surface of the protein. It consists of a cofactor-binding pocket
and a substrate-binding pocket.

8. The cofactor-binding pocket accommodates the cofactor NADPH (nicotinamide adenine
dinucleotide phosphate) or NADH (nicotinamide adenine dinucleotide), which is essential
for the enzyme's catalytic activity. The substrate-binding pocket binds dihydrofolate (DHF)
and facilitates its reduction to tetrahydrofolate (THF).

9. LIGAND PREPARATION
The three-dimensional structure of methotrexate is obtained, either from
experimental data or by generating a reasonable structure computationally.
The ligand is prepared by optimizing its geometry, adding necessary hydrogen
atoms, and assigning partial charges.

10. DOCKING SIMULATION
 The receptor and ligand structures are input into a molecular docking
software program.
 The program uses algorithms to explore different orientations and
conformations of the ligand within the binding site of DHFR.
 The ligand is scored based on its complementarity to the receptor, and
different poses are ranked accordingly.
 Key interactions between methotrexate and DHFR are examined, such as
hydrogen bonds, electrostatic interactions, and hydrophobic contacts.
 The binding affinity and binding energy are calculated, providing insights
into the strength of the ligand-receptor interaction.

11.  Methotrexate is known to bind to the active site of DHFR. It forms several key
interactions with the enzyme, including hydrogen bonds and hydrophobic
interactions.
 The pteridine moiety of methotrexate is believed to form hydrogen bonds with
specific amino acid residues within the active site, such as Asp27 and Met20.
 The p-aminobenzoic acid portion of methotrexate establishes hydrophobic contacts
with nearby residues, such as Phe34 and Phe31.
 The ensemble kinetics for the association of methotrexate and DHFR were
measured with a stopped flow by mixing 1 µM enzyme with 2.5–20 µM
methotrexate and monitoring the fluorescence (488-nm excitation, 530-nm cutoff
filter emission) in the same buffer and at the same temperature as the dissociation
constant measurements.

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