mechanism based inactivation by quinoneimine reactive metabolite
SURENDRA JATAVM.S. (PHARM.) 2ND SEMESTERDEPT. OF MEDICINAL CHEMISTRY
FLOW OF PRESENTATIONIntroductionWork done in our labProblem statementObjectivesMethodologyWork flowExpected outcomes
Drug metabolism is the biochemical modification of drugsthrough specialized enzyme systems (CYPs) to form readilyexcretable hydrophilic metabolites It involves Phase I and Phase II reactions Phase IThese are functionalization reactions.Oxidation (majority of drugs), reduction and hydrolysis . Phase IIConjugation reactions(glucuronidation, sulfation, acetylation, methylation, glutathione conjugation etc.,)3Kalgutkar, et al. Curr. Drug Metab. 2005, 6, 161.
Membrane bound proteins attached to endoplasmic reticulum and arehighly expressed in liver Super family of heme containing monooxygenase enzymes accountingfor 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 catalyticproperties, ex: epoxidation, hydroxylation, heteroatom oxidation, etc. Enzyme’s active site topology and its interaction with substrate areimportant for substrate selectivity, affinity and reactivity5Kalgutkar et aln Risks. J. Med. Chem. 2012, 55, 4896.
CYP inhibition Many drugs may increase or decrease the activity of variousCYPs either by inducing its biosynthesis (enzyme induction) orby directly inhibiting the activity (enzyme inhibition) Inhibition of CYPs – major cause for DDIs Reversible IrreversibleReversible inhibition Competitive/noncompetitive Activity of enzyme can be restored6Bharatam et al. CRIPS. 2010, 11, 62..
Mechanism-Based Inhibition of CYPs RM/ intermediate – covalently modifies amino acid residuesin 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
. Reaction pathway of quinoneiminereactive metabolite.
Work done in our lab MBI by RMs such as nitroso, carbenes have been carried outusing quantum chemical methods Study of mechanistic pathways - provided new molecularinsights behind actual mechanism of MBI by RMs Quantum chemical calculations on TZD class of drugs havebeen reported Molecular level mechanism of MBI of CYP by epoxidemetabolite of furan ring containing compounds has beenrecently determined
Problem statement What is the molecular mechanism for the formation ofquinone methide metabolite from the substrates? What are the nucleophilic residues involved in the interactionwith the quinone methide, leading to MBI of CYPs? What is the energy profile for the whole metabolic pathwayleading to MBI of CYPs by the quinone methideintermediate? What is the effect of the protein environment on thismetabolic pathway?
Objectives To perform comparative crystal structure analysis To perform molecular docking studies with & withoutoxygen atom on Fe in heme porphyrin moiety – to find thenucleophilic residues responsible for covalent adductformation To carry out quantum chemical studies to understand thereaction mechanism and energy profile for MBI byquinoneimine To carry out QM/MM analysis on the whole reactionpathway to study the influence of the surrounding residues
Work flowSearch for compounds in which quinoneiminederivative nucleus is present and show MBIDocking of obtained compounds using Glide andfinding the best pose for quinoneimine formationWith oxygen atom on Fe in heme porphyrin To study the interaction of quinonemethide with heme porphyrinWithout oxygen atom on FeTo find out the nucleophilic residues inactive site that interact with quinone methidePerform quantum chemical studies to understand the quinonemethide generation and formation of covalent adductTo generate energy profile of the metabolic pathway and to study the influence of proteinenvironment on the pathway
MOLECULAR DOCKINGComputational process of searching for a conformation ofthe ligand that is able to fit both geometrically andenergetically in to the binding site of a proteinIt involvesPreparation of ligands/moleculesIdentification of binding siteSearch algorithm to effectively sample the searchspaceScoring functionProcess being with docking algorithms in active siteand explore the conformational search space.METHODOLOGY
Schrodinger Dock Auto dock tools Glide (grid –based ligand docking withenergetic) Gold (genetic optimization for liganddocking) MOE (molecular operating environment)
QUANTUM CHEMICAL METHOD1.Quantum chemical theory explain thepredication of chemical behavior2.Quantum chemical calculation involvethe energies of molecules3.Quantum chemical result includeda. Molecular geometryb. Strength of molecular of molecularbond