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Handout 2 - Non-covalent Interactions

by: Evan Roberts

Handout 2 - Non-covalent Interactions CH 405/505

Marketplace > University of Alabama - Tuscaloosa > Chemistry > CH 405/505 > Handout 2 Non covalent Interactions
Evan Roberts
GPA 3.57
Medicinal Chemistry
Timothy Snowden

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About this Document

This is the filled-in 2nd handout (Days 2-3) and an additional page of notes.
Medicinal Chemistry
Timothy Snowden
One Day of Notes
25 ?




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This 11 page One Day of Notes was uploaded by Evan Roberts on Friday January 23, 2015. The One Day of Notes belongs to CH 405/505 at University of Alabama - Tuscaloosa taught by Timothy Snowden in Spring2015. Since its upload, it has received 207 views. For similar materials see Medicinal Chemistry in Chemistry at University of Alabama - Tuscaloosa.

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Date Created: 01/23/15
Egg7 1 quotr Ef n a jk Ea Ema L4 Cw V11 CYWOSP quot 96ch CMI5kL Ck Fri y 39 ch l but Wan lll n W Fmi r 777 I DEEJ 47 murmmm quot 5 0 Binding sites are typically g i rf c j Oi 7 hollows or clefts on or near the surface of biomacromolecules 0 Most drugs are in equilibrium between being bound and unbound to their target 0 Functional groups on the drug are involved in binding interactions and are called quotomb m qrovP i J J Speci c regions within the binding site that are involved in binding interactions are called 19er 5430 J J Binding 1 regions Jinding groups im n EH55 lnlermolecular bonds ung site willi up in it V Binding i H I rlirn Unbound drug Bound drug Binding interactions usually result in an madam W F WJCM analakawi change where the binding site changes shape to accommodate the drug The induced t may also alter the overall shape and Qumri m of the drug target 0 Binding energies are weaker in solvent exposed regions of the target eg protein surface and stronger when buried within a hydrophobic pocket w heal mol 0 Strongest of the intermolecular bonds The strength of the ionic interaction is inversely proportional to the distance between the two charged groups 1r Stronger interactions occur in hydrophobic regions interactions are weak in polar environments Ionic bonds are the most as a onemmk abqnme t imcfi drug enters the bmdmg s1te 9 www Drug NH3 gt5 Intermolecular handing forcw 32 Eondipole interactions 550 kcal mol39l Occurs when the charge on one molecule interacts with the dipole moment of another Much stronger than a dipoledipole interaction M p lm I39 a r 7 7 0 Much stronger in low dielectric regionsweak in polar regions Strength of interaction falls off less rapidly with distance than dipoledipole interactions mol l Takes place between an electron de cient hydrogen and an electron rich heteroatom ex acceptors R3N R20 R3Pz The electron deficient H is usually attached to a heteroatom donors 0H NH or SH DHA distance is typically 2 ng A Hydrogen bond strength is dependent upon of the microenvironment gym 112 7 and PM of the donor and accept ea 7 r 539 8 I I blf m xHI I I Drug HBD 1 quotBA 39 I 33 The interaction is highly directional donoracceptor orbitals that are mmlic quota 7 maximize H bonding interactions 1 Optimum orientation is where the X H bond points directly to the lone pair on Y such that the angle between X H and Y is 1800 by gt Hybridised ls Hybridised orbital orbital orbital H BD HBA Intermolecular bonding forces 33 Hydrogen bonds R c I R tf RC RO JL J X tn 9 W o J OH 7 R j Strong HBAs IR R 395 RF RCl Weak HBAs a a lt39 I 7 c Wan H Cn r R R H NH Tertlary aminequotgood HBA Amide N acts as poor HBA Anillne N acts as poor HBA Examples of good hydrogen bond donors ammonium ions carboxylic acids phenols thiols ie pKII 10 a Responsible for much of the shape of proteins and double helical DNA Vls39I J39 34 15 kcal mol39l Dipoles align with each other as the drug enters the binding site 0 Dipole alignment orients the molecule in the binding site Orientation is detrimental if the binding groups are not positioned correctly The strength of the interaction dramatically decreases with increasing microenvironment polarity and distance 1r3 Localised dipole moment IntermoleeHUar bonding fom 11 Stacking Cation It interactions HES 12 keal mol Most often occurs between e39 rich and e39 poor aromatics slip slack offset Hilli n s f Pnl r Intermolecular bonding 35 1c Stacking interactions 0 DNA intercalation is an example of 11 stacking interactions Ammonium salts can coordinate e39 rich aromatics by cation7 interactions G R NR3 Eihdi llju ng w i tile 4 keel mini Occur when a full or partial charge on one molecule induces a dipole on a proximal polarizable group Very strong distance and microenvironment polarity dependence 1r6 approaching carbonyl dipole induces dipole in polarizable CH3 group Intermolecular bonding fnm van tiler Waals interactions 4 139 km nulll Electron motion creates transient areas of high and low electron densities creating weak transient dipoles net nondirectional Interactions drop off rapidly with distance 1r6 Chance charge soparatlon ielron quot i 39 rl rficlanor gt 7 U Fluctuating g hi pom A second molecule Charged separation a Induced by i EV quot E I rst molecule Van dor Wanlu39 toms Van dor Waals quot interaction 4 Ni Drug must be within binding region for interactions to occur The overall contribution of van der Waals interactions can be crucial to binding Important for 0 me U with small l li r lOC was 2 I Hydrophobic regions 5 5 Transienl dipole on drug 39 6 8 van der Waals interaction W l l 5 DESQLVE EF pealties 0 Polar regions of a drug and its target especially surface binding regions are 7 prior to interaction an 1 3g is necessary and requires energy energy penalty 0 The energy change resulting from desolvated drugtarget interactions must be greater than the energy required for desolvation of the resting state MEI i n Recall A60 AHO TAS0 H x WE mil 0 o u I H C quot C R R u R R o n at A Solvnled Guilcslr and Binding Site I 839 Desalvrlio 39 Ei39 rgiquoti quot lquot C GM Hamming Squot390 313 With Sysleln is less stable than in A Binding Site Residues G0 510 kcalmol G0 505 kcalmol G0 39521 kcalmOI AGObindmg 11 kcaIrriol 3n vv Hydrophobic regions of a drug and a drug target are not solvated however they are sheathed in highly ordered innerouter sphere solvent shells m gallium f entropy Fwd 1 39 Interactions between the hydrophobic regions of a drug and its target free the ordered water molecules p93 i4 ve entropy 0 Association of hydrophobic solutes allows i39or Van der Waals contacts S lt 0 S gt 0 aa39a A i g9 I a e in via any a st 5 Ea 3 go a a a a n o e a we 39 mm 3 r a e e as aw e mi a 6 a g an em a a at a e Interactions between the hydrophobic regions of a drug and its target free the ordered water molecules Results in dramatic increase in femAvior x4 7 and possible increase in enthalpy depends upon extent of Van der Waals interactions AGbinding 03 kcalmolA2 of nonpolar contact surface area due to hydrophobic effect a 1 Binding ydphobic r i VAVAV regions Highly structured wayers u Unstructured water around hydrophobic regions Increase in entropy


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