SEMINAR IZ MOLEKULSKEGA MODELIRANJA PRI FARMACEVTSKI KEMIJI III
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1 SEMIAR IZ MOLEKULSKEGA MODELIRAJA PRI FARMACEVTSKI KEMIJI III 2. DEL PREDSTAVITEV PROGRAMOV ZA DELO A SEMIARJU doc. dr. Andrej Perdih andrej.perdih@ki.si
2 LITERATURA 1. TEMELJA: POGLAVJE O OSOVAH MOLEKULSKEGA MODELIRAJA 2. ZA VSE KI BI ŽELELI ZVEDETI VEČ O PODROČJU Dostopno v knjižnici FFA
3 Seminar pri farmacevtski kemiji 3 CILJ SEMIARJA: PRAKTIČO SPOZATI BIOLOŠKO AKTIVE MOLEKULE KOT TRIDIMEZIOALE ETITETE. 1. aloga: 3D modeli molekul in računanje osnovnih lastnosti 2. aloga: Torzijski potencial in lastnosti konformacij 3. aloga: Prileganje dveh molekul s primerljivo biološko aktivnostjo 4. aloga: Molekulsko sidranje liganda v aktivno mesto encima OBVEZOSTI ŠTUDETA: - PRISOTOST A SEMIARJU - IZPOLJE SEMIARSKI LIST I MAPA Z DATOTEKAMI - 50 % SMISELO PRAVILIH REZULTATOV SEMIARSKIH ALOG
4 PRIMER SEMIARSKIH ALOG IZ FARMACEVTSKE KEMIJE III SKUPIA 8 Datum: Seminar iz molekulskega modeliranja pri farmacevtski kemiji III Ime in priimek: 1. aloga [Izgradnja tridimenzionalnega modela molekule in izračun nekaterih lastnosti] 1.1. arišite tridimenzionalni model molekule 1 in ga geometrijsko optimizirajte z uporabo polja sil MM2. ato izračunajte oz. na optimizirani konformaciji določite: Cl O H 2 * * * * H 2 H 2 H 2 # Molekula 1 - potencialno energijo dobljene konformacije = kcal/mol - prispevek deformacij vezi (»stretch term«) k celotni potencialni energiji = kcal/mol - torzijski kot definiran z * pri tej energiji: * = - razdaljo med klorom in dušikom (#) gvanidinske skupine v dobljeni konformaciji = nm - s programom ChemDraw izračunajte porazdelitveni koeficient (ClogP) = Optimizirano strukturo molekule 1 v obliki modela kroglic in paličic shranite z imenom: aloga1.c3xml 1.2. Optimizirano konformacijo molekule 1 prikažite z molekulsko površino, ki je dostopna topilu (solvent-accessible surface area). Strukturo molekule 1 s prikazano površino dostopno topilu shranite z imenom: aloga11.c3xml 1.3. Izračunajte delne naboje optimizirane konformacije molekule 1 s semiempirično metodo Extended Hückel dostopno v programu ChemBio3D in izpišite vrednost nabojev za vse težke atome (vsi atomi razen vodika) in komentirajte, kje v molekuli se nahajajo kemijsko reaktivni centri. Vrednosti delnih nabojev težkih atomov: 1.4. Izvedite 10 ps simulacije molekulske dinamike za molekulo 1. Posamezni korak molekulske dinamike naj bo dolg 1 fs. Oglejte si gibanje molekule med MD simulacijo in opišite vaša opažanja upoštevaje strukturne značilnosti le-te. Število korakov MD simulacije = Opažanja: Energijo struktur generiranih tekom simulacije molekulske dinamike shranite tako, da z desnim klikom miške v področju Output prikličete meni in v njem izberete Export. Kot tip datoteke izberite končnico txt. Ime datoteke naj bo: MDenergija.txt 2. aloga [Torzijski potencial] arišite tridimenzionalni model molekule 2 in ga geometrijsko optimizirajte z uporabo polja sil MM2. HOOC H O O Molekula 2 * * * * H 2 - potencialna energija dobljene konformacije = kcal/mol - vrednost torzijskega kota * = Optimizirano strukturo v obliki modela paličic shranite z imenom: aloga2.c3xml ato optimizirano konformacijo molekule 2 togo zavrtite za 360 okoli označenega torzijskega kota * z uporabo funkcije dihedral driver (single energy plot), dostopne v programu ChemBio3D in si oglejte izračunan torzijski potencial. Izmerite razdaljo med poljubnim karboksilnim kisikom in obročnim aminskim dušikom in s premikanjem po torzijskem potencialu določite tisto vrednost torzijskega kota *, pri katerem je razdalja najdaljša? Kako ugodna je ta lega z energijskega stališča glede na preostale lege? Vrednost torzijskega kota * = Razdalja med atomoma = nm Strukturo v konformaciji, kjer je razdalja med atomoma najkrajša, shranite z imenom: aloga21. c3xml 3. aloga [Tridimenzionalno prileganje dveh sorodnih biološko aktivnih molekul] Komentar: Vse izračunane delne naboje shranite v obliki Excelove tabele z imenom aboji Ločeno narišite tridimenzionalna modela molekul histamina in ciklizina, ki obe delujeta v histaminskem sistemu in ju geometrijsko optimizirajte z uporabo polja sil MM2. apišite, kakšno je njuno farmakološko/fiziološko delovanje ter določite potencialno energijo dobljenih optimiziranih konformacij. Farmakološko/fiziološko delovanje histamina in ciklizina: SEMIARSKE ALOGE DOSTOPE A SPLETU
5 PREDSTAVITEV PROGRAMOV ZA DELO A SEMIARJU Predstavitev programa za risanje kemijskih struktur: ChemDraw Predstavitev programa za molekulsko modeliranje: ChemBio3D Predstavitev programa za molekulsko sidranje: Arguslab Prikaz uporabe programov na seminarskih primerih
6 TIPI SEMIARSKIH ALOG 1. aloga: 3D modeli molekul in računanje osnovnih lastnosti 2. aloga: Torzijski potencial in lastnosti konformacij 3. aloga: Prileganje dveh molekul s primerljivo biološko aktivnostjo 4. aloga: Molekulsko sidranje liganda v aktivno mesto encima
7 1. PROGRAM ChemDraw Risanje struktur in kemijskih reakcij Računaje MR spektrov apovedovanje fizikalno-kemijskih lastnosti Osnovni podatki o spojinah HO O H H HO
8 2. PROGRAM ChemBio3D Molekulska grafika Molekulske površine Molekulska mehanika Molekulska dinamika Konformacijska analiza Superpozicija molekul
9 MODELIRAJE A SEMIARJU ZA ALOGE 1-3 POTEKA PREKO GRAFIČEGA UMESIKA PROGRAMA CHEMBIO3D
10 1. aloga: 3D modeli molekul in računanje osnovnih lastnosti 1. Gradnja molekul in vizualizacija (molekulski model + molekulske površine) 2. Meritev geometrijskih parametrov (razdalj, valenčnih kotov, torzijskih torzijskih kotov) 3. Analiza energijskih vrednosti in izračunanih parametrov (delnih nabojev) 1. Graditev modela O
11 MERJEJE GEOMETRIJSKIH PARAMETROV Valenčni kot Torzijski kot Razdalja med atomoma MOLEKULSKA POVRŠIA
12 PODATKI O POTEKU EERGIJSKE MIIMIZACIJE Uporabljeno polje sil Iteracija število korakov MM2 Minimization Iteration 94: Minimization terminated normally because the gradient norm is less than the minimum gradient norm Stretch: Bend: Stretch-Bend: Torsion: on-1,4 VDW: ,4 VDW: Dipole/Dipole: Total Energy: kcal/mol Calculation completed Uspešna konvergenca minimizacijskega algoritma Vezni členi evezni členi
13 IZRAČU DELIH ABOJEV (Extended Hücklova metoda) C(1) C Alkene C(2) C Alkene C(3) C Alkene C(4) C Alkene C(5) C Alkene C(6) C Alkene C(7) C Alkane C(8) C Alkane O(9) O Enol C(10) C Alkane H(11) H H(12) H H(13) H H(14) H H(15) H H(16) H H(17) H H(18) H H(19) H H(20) H H(21) H H(22) H ajbolj polarizirana kovalentna vez v molekuli
14 PRIPRAVA SISTEMA ZA SIMULACIJO MOLEKULSKE DIAMIKE Časovni korak Interval shranjevanja podatkov Rezultati MM2 Dynamics Iteration Time Total Energy Potential Energy Temperature ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± ± Število korakov = Simulacijski čas
15 2. aloga: Torzijski potencial in lastnosti konformacij C d1 O OH OS ROTACIJE C C 1. Preiskovanje razdalj med atomi pri različnih torzijskih kotih d2 d3 Primer: ISKAJE AJKRAJŠE I ADLJŠE RAZDALJE ROTACIJO OKROG TORZIJE IZVEDEMO S FUKCIJO DIHEADRAL DRIVER
16 OMEJEA ROTACIJA H Energija (kcal/mol) OS ROTACIJE Območji, kjer rotacija zaradi steričnih ovir ni možna Torzijski kot Območje proste rotacije 1 Območje proste rotacije 2
17 3. aloga: PRIMERJAVA KOFORMACIJI DVEH MOLEKUL d1 d2 RSMD RMSD vrednost je odvisna od relativnega položaja obeh molekul Iskanje optimalnega RMSD pred Prileganje PRILEGAJE MOLEKULE A DRUGO KOT TOGO TELO = RSMD d i i, j= 1 d 2 i, j = 0 RSMD prileg. = i, j= 1 d 2 i, j
18 PRIMER ALOGE Histamin evrotransmiter RMSD= 5.5 Å d1 d2 DODATI LIPOFILI PODROČJI Difenhidramin Antagonist na Histaminskih H1 receptorjih RMSD= 0.1 Å PRILEGAJE IZVEDEMO S FUKCIJO OVERLAY
19 MODELIRAJE A SEMIARJU ZA ALOGO 4 POTEKA PREKO GRAFIČEGA UMESIKA PROGRAMA ARGUSLAB Prosto dostopen na spletu: Brezplačni program za kvantnokemijsko računanje in molekulsko sidranje
20 VALIDACIJA PROGRAMA ZA MOLEKULSKO SIDRAJE VALIDACIJA SIDRAJA: Sposobnost reprodukcije vezavne konformacije liganda v makromolekuli določene eksperimentalno npr. z rentgensko difrakcijo (RMSD < 2.5Å med eskperimentalno in izračunano konformacijo). Izračunana konformacija Eksperimentalna konformacija
21 ALOGA IZ MOLEKULSKEGA SIDRAJA UPORABA AVODIL Molecular docking tutorial Sulfonamide-type D-Glu inhibitor docked into the MurD active site using ArgusLab In this tutorial [1] you will learn how to prepare and run a molecular docking calculations. You will first extract an experimentally determined binding conformation of a D-Glu sulfonamide inhibitor of the bacterial enzyme MurD and subsequently dock it into its binding site. Finally, we will compare the docked structure with the x-ray structure to see how well they match. This type of calculations is often used when validating docking programs before performing large-scale virtual screening. Before you can dock a molecule, you first need to define the atoms that make up the Ligand (drug, inhibitor, etc.) and the Binding Site on the protein where the drug binds. The protein 2JFF.pdb crystal structure used in this exercise can be freely accessed and downloaded from the Brookhaven Protein Databank. This structure represents an important result of a collaborative antibacterial research project where several Slovenian researchers were involved.[2] 1. Download and open the PDB structure 2JFF. 2. Create "Ligand and Binding Site groups". Left-click on "1440 LK2" in the Tree View to select the sulfonamide inhibitor. It should appear yellow. Select the Edit/Hide Unselected menu option to hide all atoms that are not selected. The only atoms showing on the screen should be the D-Glu sulfonamide inhibitor. Center the sulfonamide inhibitor in the window by selecting the View/Center Molecule In Window menu or pressing the button on the toolbar. While the inhibitor is selected, add hydrogens by and pressing the You should see something like this: button on the toolbar. Open the web browser and type in the Brookhaven Protein Databank ( web address and in the search field type 2JFF. Download the structure as a.pdb file preferably to Desktop. Open the 2JFF.pdb located in the folder you designated during download in ArgusLab. This is a PDB file so make sure you select the correct file type in the file open dialog (pdb type). Make sure the Molecule Tree View tool is visible. Either select Tools/Molecule Tree View menu option or click the button on the toolbar to toggle the Tree View. Expand the tree view of 2JFF and open up the Residues/Misc folder to show the sulfonamide inhibitor (LK2). You should see something like this: Right-click on "1440 LK2" in the Tree View and select the "Make a Ligand Group from this Residue" option. ArgusLab will construct a group underneath the Groups folder with the same name "1 LK2" that is of type = Ligand. Left-click on either the "1440 LK2" residue in the Residues/Misc folder. This action will again select the atoms of the Ligand on the screen. Copy and Paste the selected residue. Look in the Residues/Misc folder in the Tree View tool and you will see a new highlighted residue with a name like "2480 LK2". (different number is also possible).
22 4. ALOGA: VALIDACIJA PROGRAMA ZA MOLEKULSKO SIDRAJE Kvantitativno ovrednotenje RSMD = i, j = 1 d 2 i, j Le med pari atomov, ki jih primerjamo!
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