3. Drug metabolism is the biochemical modification of drugs
through specialized enzyme systems (CYPs) to form readily
excretable hydrophilic metabolites
It involves Phase I and Phase II reactions
Phase I
These are functionalization reactions.
Oxidation (majority of drugs), reduction and hydrolysis .
Phase II
Conjugation reactions
(glucuronidation, sulfation, acetylation, methylation, glutathio
ne conjugation etc.,)
3
Kalgutkar, et al. Curr. Drug Metab. 2005, 6, 161.
5. Membrane bound proteins attached to endoplasmic reticulum and are
highly expressed in liver
Super family of heme containing monooxygenase enzymes accounting
for Phase I metabolism of nearly 75% of drugs
On the basis of sequence identity, they are categorized into
Families (<40% amino acid identity)
Subfamilies (40 - 50% amino acid sequence)
They differ in substrate specificity and possess diverse catalytic
properties, ex: epoxidation, hydroxylation, heteroatom oxidation, etc.
Enzyme’s active site topology and its interaction with substrate are
important for substrate selectivity, affinity and reactivity
5
Kalgutkar et aln Risks. J. Med. Chem. 2012, 55, 4896.
6. CYP inhibition
Many drugs may increase or decrease the activity of various
CYPs either by inducing its biosynthesis (enzyme induction) or
by directly inhibiting the activity (enzyme inhibition)
Inhibition of CYPs – major cause for DDIs
Reversible
Irreversible
Reversible inhibition
Competitive/noncompetitive
Activity of enzyme can be restored
6
Bharatam et al. CRIPS. 2010, 11, 62..
7. Mechanism-Based Inhibition of CYPs
RM/ intermediate – covalently modifies amino acid residues
in the active site and/or coordinates to heme prosthetic group
Irreversible inactivation of CYPs referred to as Mechanism-
Based inhibition (MBI)
Mechanism based inhibition can be
Quasi-irreversible
Irreversible
9. Work done in our lab
MBI by RMs such as nitroso, carbenes have been carried out
using quantum chemical methods
Study of mechanistic pathways - provided new molecular
insights behind actual mechanism of MBI by RMs
Quantum chemical calculations on TZD class of drugs have
been reported
Molecular level mechanism of MBI of CYP by epoxide
metabolite of furan ring containing compounds has been
recently determined
10. Problem statement
What is the molecular mechanism for the formation of
quinone methide metabolite from the substrates?
What are the nucleophilic residues involved in the interaction
with the quinone methide, leading to MBI of CYPs?
What is the energy profile for the whole metabolic pathway
leading to MBI of CYPs by the quinone methide
intermediate?
What is the effect of the protein environment on this
metabolic pathway?
11. Objectives
To perform comparative crystal structure analysis
To perform molecular docking studies with & without
oxygen atom on Fe in heme porphyrin moiety – to find the
nucleophilic residues responsible for covalent adduct
formation
To carry out quantum chemical studies to understand the
reaction mechanism and energy profile for MBI by
quinoneimine
To carry out QM/MM analysis on the whole reaction
pathway to study the influence of the surrounding residues
12. Work flow
Search for compounds in which quinoneimine
derivative nucleus is present and show MBI
Docking of obtained compounds using Glide and
finding the best pose for quinoneimine formation
With oxygen atom on Fe in heme porphyrin
To study the interaction of quinone
methide with heme porphyrin
Without oxygen atom on Fe
To find out the nucleophilic residues in
active site that interact with quinone methide
Perform quantum chemical studies to understand the quinone
methide generation and formation of covalent adduct
To generate energy profile of the metabolic pathway and to study the influence of protein
environment on the pathway
13.
14.
15. MOLECULAR DOCKING
Computational process of searching for a conformation of
the ligand that is able to fit both geometrically and
energetically in to the binding site of a protein
It involves
Preparation of ligands/molecules
Identification of binding site
Search algorithm to effectively sample the search
space
Scoring function
Process being with docking algorithms in active site
and explore the conformational search space.
METHODOLOGY
16. Schrodinger
Dock
Auto dock tools
Glide (grid –based ligand docking with
energetic)
Gold (genetic optimization for ligand
docking)
MOE (molecular operating environment)
17.
18. QUANTUM CHEMICAL METHOD
1.Quantum chemical theory explain the
predication of chemical behavior
2.Quantum chemical calculation involve
the energies of molecules
3.Quantum chemical result included
a. Molecular geometry
b. Strength of molecular of molecular
bond