The document outlines a presentation on drug metabolism, focusing on the role of cytochrome P450 enzymes in the biochemical modification of drugs. It discusses various phases of drug reactions, including functionalization and conjugation, along with the mechanisms of enzyme inhibition and the significance of molecular interactions. The research objectives include studying the formation of quinone methide metabolites and understanding their impact on cytochrome P450s using quantum chemical methods and molecular docking analyses.

1. SURENDRA JATAV
M.S. (PHARM.) 2ND SEMESTER
DEPT. OF MEDICINAL CHEMISTRY

2. FLOW OF PRESENTATION
Introduction
Work done in our lab
Problem statement
Objectives
Methodology
Work flow
Expected outcomes

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.

4. Catalytic cycle

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

8. . Reaction pathway of quinoneimine
reactive metabolite.

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

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)

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