4 research outputs found
Δημιουργία φαρμακοφόρου μοντέλου για το ένζυμο της κυτοσολικής φωσφολιπάσης Α2. Χρήση βιβλιοθηκών για την εξεύρεση χημικών οργανικών ενώσεων με υψηλή βαθμονόμηση μοριακής πρόσδεσης
Το ένζυμο κυτοσολική φωσφολιπάση Α2 (cPLA2) παρουσιάζει ως θεμελιώδη λειτουργία
την απελευθέρωση του αραχιδονικού οξέος από τις φωσφολιπιδικές μεμβράνες. Το
αραχιδονικό οξύ αποτελεί την πρόδρομο ένωση για το σχηματισμό των λιπιδικών
μεσολαβητών της φλεγμονής, συμπεριλαμβανομένων και των εικοσανοειδών. Συνεπώς,
το ένζυμο cPLA2 αποτελεί ένα ενδιαφέροντα στόχο για βιοχημικές και δομικές
μελέτες, οι οποίες μπορούν να οδηγήσουν σε μια βαθύτερη γνώση της αντιμετώπισης
της φλεγμονής. Στο πρώτο τμήμα της μεταπτυχιακής εργασίας, περιγράφεται η
δημιουργία συμπλέγματος του ενζύμου με τον αναστολέα ΑΧ074 με τη μεθοδολογία
της επαγόμενης προσαρμογής (Induced Fit). Η ένωση ΑΧ074 παρουσιάζει την
ισχυρότερη βιολογική δράση από τους 2-οξοαμιδικούς αναστολείς που έχουν
συντεθεί από την ομάδα του Καθηγητή κ. Γεώργιου Κόκοτου στο Εργαστήριο
Οργανικής Χημείας του Πανεπιστημίου Αθηνών. Στο δεύτερο τμήμα, περιγράφεται η
δημιουργία φαρμακοφόρου μοντέλου με βάση την πιθανή βιοδραστική διαμόρφωση του
προσδέτη αναφοράς (Ligand-Based) και η διαδικασία της εικονικής σάρωσης με βάση
το φαρμακοφόρο (Pharmacophore-Based Virtual Screening) εμπορικά διαθέσιμων
βιβλιοθηκών ενώσεων. Για τις «ενώσεις κρούσης» (hits) που προκύπτουν από αυτή
τη διαδικασία πραγματοποιήθησαν πειράματα μοριακής πρόσδεσης με σκοπό τη
βαθμονόμηση της πρόσδεσής τους.The fundamental function of enzyme cytosolic phospholipase A2 (cPLA2) is to
release arachidonic acid from the phospholipid membranes. Arachidonic acid is
the precursor for the formation of lipid mediators of inflammation, including
eicosanoids. Therefore, the enzyme is an interesting target for biochemical and
structural studies which can lead to a deeper knowledge of the treatment of
inflammation. In the first part of this thesis, the creation of a complex of
the enzyme and the inhibitor AX074 is described by the Induced Fit methodology.
AX074 presents the strongest biological activity of the 2-oxoamide inhibitors
that have been synthesized by the group of Professor George Kokotos in the
Laboratory of Organic Chemistry of University of Athens. In the second part of
this thesis, a pharmacophore model has been created based on the Ligand-Based
methodology and the process of «Pharmacophore-Based Virtual Screening (VS)» has
been applied to commercially available compound libraries. For «hits» compounds
that emerged from this process, molecular docking experiments have been
performed in order to investigate their docking scoring
Binding conformation of 2-oxoamide inhibitors to group IVA cytosolic phospholipase A2 determined by molecular docking combined with molecular dynamics.
The group IVA cytosolic phospholipase A(2) (GIVA cPLA(2)) plays a central role in inflammation. Long chain 2-oxoamides constitute a class of potent GIVA cPLA(2) inhibitors that exhibit potent in vivo anti-inflammatory and analgesic activity. We have now gained insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA(2) active site through a combination of molecular docking calculations and molecular dynamics simulations. Recently, the location of the 2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA(2) was determined using a combination of deuterium exchange mass spectrometry followed by molecular dynamics simulations. After the optimization of the AX007-GIVA cPLA(2) complex using the docking algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors have been docked in the enzyme active site. The calculated binding affinity presents a good statistical correlation with the experimental inhibitory activity (r(2) = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the design of new compounds with improved inhibitory activity against GIVA cPLA(2)
Binding Conformation of 2-Oxoamide Inhibitors to Group IVA Cytosolic Phospholipase A2 Determined by Molecular Docking Combined with Molecular Dynamics
The group IVA cytosolic phospholipase A2 (GIVA
cPLA2) plays a central role in inflammation. Long chain 2-oxoamides
constitute a class of potent GIVA cPLA2 inhibitors that exhibit potent in
vivo anti-inflammatory and analgesic activity. We have now gained
insight into the binding of 2-oxoamide inhibitors in the GIVA cPLA2
active site through a combination of molecular docking calculations
and molecular dynamics simulations. Recently, the location of the
2-oxoamide inhibitor AX007 within the active site of the GIVA cPLA2
was determined using a combination of deuterium exchange mass
spectrometry followed by molecular dynamics simulations. After the
optimization of the AX007-GIVA cPLA2 complex using the docking
algorithm Surflex-Dock, a series of additional 2-oxoamide inhibitors
have been docked in the enzyme active site. The calculated binding
affinity presents a good statistical correlation with the experimental
inhibitory activity (r
2 = 0.76, N = 11). A molecular dynamics simulation of the docking complex of the most active compound has
revealed persistent interactions of the inhibitor with the enzyme active site and proves the stability of the docking complex and
the validity of the binding suggested by the docking calculations. The combination of molecular docking calculations and
molecular dynamics simulations is useful in defining the binding of small-molecule inhibitors and provides a valuable tool for the
design of new compounds with improved inhibitory activity against GIVA cPLA2