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by: Emily Braun II


Emily Braun II
GPA 3.82

Patrick Stayton

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Patrick Stayton
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This 22 page Class Notes was uploaded by Emily Braun II on Wednesday September 9, 2015. The Class Notes belongs to BIOEN 457 at University of Washington taught by Patrick Stayton in Fall. Since its upload, it has received 27 views. For similar materials see /class/191999/bioen-457-university-of-washington in Bioengineering at University of Washington.


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Date Created: 09/09/15
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mammary shape m m gemnlwe have m salve ma equanan numzncally me Dx enme Mz mds mma mm m enme maum wa discmm space 1 wa chnpnllp mm dissing chunks o mm is m mama ma elzchustzoc pmennal may a masa ympmms 1 Nu wa wam m mw ma elzcuvstanc pmammmma palm betweenydpmms wa simply magma mmthz valuzsauhz male 5n pam Wa mast ma eqvaunns mm mmaammmwmpaaa m langexhemgcan mmus aaa is m faxmuf n mm m enme sahmanu hz Palsmnequanan KL1th 41712kyxk W 41712kyxk 4 12yxk 7 ALL 12 whaaa 1 ma spacing naawaan gm palms Assignmg charges an ha Gm Mas11 gm palm wa med m mw ma charge dzmty d a maxhyamms Haw an anon mmmms pmhahly wamcamndz manna pasmam ama y dpmms Sn wa spmma charge up amasmgnpans an m ma 5 malest gm palms mug a mutant weighung schzmz O1CIO1a1b1C where a b c are the fractional coordinates of a grid point from the charge qo e g Imagine an atom of charge 1e near the corner of a square ie on a 2 D grid Most of the charge perhaps 07e will get put on the closest corner grid point Perhaps 012e will go on each of the two next nearest corners Finally 006e will go on the corner furthest away The total charge remains the same ie 1e Assigning Dielectric Values to the Grid We also need to know what the value of is in between the grid points Generally we39ll say it is 2 4 inside the molecule and 78 outside the molecule There39s a couple of different ways of deciding what inside the molecule actually means Van der Waals surface definition Any grid point lying inside the van der Waals surface of any atom is given a dielectric of 2 4 Molecular surface definition Any grid point accessible to a solvent probe molecule is assigned a dielectric of 78 all others are assigned 2 4 This typically uses what39s known as a Connolly surface Boundary Conditions Now that we39ve defined how and are distributed across the grid we have to specify boundary conditions In the present case this involves specifying the value of the electrostatic potential at some point in space once we know this we can start to calculate the potential at neighbouring grid points using our finite difference equation But how can we do this surely the whole point of what we re doing is to calculate the potential True but we do know one thing about the potential We know that at an infinite distance from the molecule the electrostatic potential will be zero So if we re using a large grid we say that the electrostatic potential at the edges of the box is zero Once this value is set we can solve the PB equation to find out what the potential is throughout the rest of the box Focusing The accuracy of the finite difference method depends on the grid spacing and how much the potential varies Generally speaking the smaller the grid spacing we use the more accurate the potential will be Note however that for a cubic grid containing N grid points along each side the total number of grid points is NNN Solving the PB equation using a grid of 100 pointsside takes 8 times longer than with a grid of 50 pointsside If we want to accurately calculate the potential at the center of a very large molecule we may find that the number of grid points required is too large to cope with e g Suppose we have a molecule that s about 100A long To calculate the potential for the entire molecule with a grid spacing of 05A we will have to use a 200200200 grid this will take ages to calculate We can get around this problem by using a technique called focusing First we calculate the potential using a grid with fewer grid points but a bigger spacing eg a 505050 grid of spacing 2A Second we focus in on the molecule using a finer grid say of spacing 1A with dimensions 505050 We obtain the boundary conditions for this grid from the first grid 39 Third we focus in again using a still finer grid of 05A again with dimensions 505050 We obtain the boundary conditions for this grid from the second grid HIV Lifecycle ll1 lyniipliixytt Prer ifil39iibilun39 site ill armn Two World Views 0 Illttr39usmtn theCI39H Coll 7 men more quot inlettiouei 139 lrlUl39l 1 Molecular Mechanics a All enzyme caller protease turnips ihc lbiw rim JIM II V mature Fi ii39il t l Tim DNA timers Ilii mu Inn ilHi inurlts EliHt inln the hays cell s httpcmminf nihg Vm delingguideid cumentsm lecularimechanicsid cumenthtml iii Ill 39 H i w with 39iii It Iii iilt 39 2 Structural Thermodynamlcs 31 from mw n H into my cLli wmpunvnis Rm arse Imnwcripmw NNR TISquot iiIE arclion RH r n mlm w Nut lmsidri nmhtgi39 cnn39i wis single strand me a dim RN iriiii almiqu llIilli DNA it httpwwwgeorgetownedugumcedmediaimagescd4jpg Role of HIV protease Cleavage of Peptide Bond C 93 95 Cleaves TyrPro or PhePro Viral Polyprotein W Inactive Mammalian peptidase do not cleave amide bonds of prolines 4 Proleas e I70 IlePro Poiypmiein Inactivation of protease leads to is cut by protease inioindividual production of immature noninfectious we particles Active proteins How HIV Protease Inhibitors Inhibit Viral Replication HIV protease recognizes a complementary shape on polyprotein and cuts protein i7oii ProPh SPL U 54 i fits like quotLock and Keyquot Protease is a homodimer V Asp and lie residues form HiV WOW856 u HO I r U important interactions With Inhibitor mimics cutting site Hydm39ys s 4 peptide or peptidomimetic Ergxzsg c eby Phe ASP Leu IM inhibitor inactivating protease 1 s Inhibitor Drug 74 Speci city pockets cleavage site 32 3 1 H I L H CDNH CDNH CO NH In HIV pockets prefer large hydrophobic side chains Phe Pro P239 CO Competi ive Inhibitor 1 Bind active site 2 Unable to be cleaved by protease 3 Mimic the transition state Mechanism for Protease Uncatalyzed C TR Hydrolysis C OH Water Attack HN cR Catalyzed Act LR oclt OH Extent of Reaction L V 5 C 1 a E39J IL 4844 Pup 7 fj Lr H5 Ll F Ft H H H R K 1 0 n H 1 1 H r r NH 5 llfr I aw 1 rirA39 my y my r r r 39 j NH Ruhr J u 1 I 339 j i39 Le 0 r3 I 939 h In 395 pH rlli39v t fla yfjf Allquot 13quot WIFE I quot Enlistam Lrvuliallial39 Ectuil FIGURE 4 Ernestine reaction mechanism OIHW protests tit1 substrate transition Mate Biopolymers 19995115968 Strategy for Protease Inhibitors C R D39 OH Trans39t39on State lmer 0 C 0H l l Interface 0 Is Tlghtest Binding HN Transition State Mimic That Can t Be Cleaved Dimer Interface g o StructureFunction View 39 39 F F39 1d Ratlonal Based D651gn one 16 S 0 Lead nding M lecular mechanics meLh dsarebased nmef 11 wing prin iples 39 39 39 Nuclei and electr nsarelumpedint at m7like particles Fmdjmg any compound that Shows the bIOIOglcal ElemHy that you are A m7like particles are spherical radii bminedfr mmeasurements nhe ry and havean charge looklng for 39 bmmedfr mLhe ry 1m mcli m are based n springsandclassical p tendals 7 Sldeeffects of eXlstmg drugs screemng natural compounds structure Int mod nsmustbepreassignedt spe ificsets f at ms Immen 39 quot39L39nra quot based demgn o 39 39 39 The bject fm lecularmechanicsist predicttheenergyass ciabedwithagivenc nf rmali n fam lecule Lead Optlmlzatlon H waver m lecular mechanics energies have n meaning as abs 1me quantities Only differences inenergy b nf39hav 39A39llul h39 quot39b 7 Improve blologlcal act1V1ty spem mty bloavallabllty solub111ty WWW quot m quotmquot quot5 9mmquot mp 9 am mm gyeqm 53 y Enefgy 7 Computatlonal techmques to predlct 1nh1b1tor blndlng af mty Screw ng Ene gw Bending Energy T m n Energy N n7B nded Inbemui nEnergy These squad m getherwith the dataparamet rsrequiredt describe the behavi r fdifferent kinds fat ms andb nds iscalledaf me7 eld NIany different kinds ff mefnelds have been devel pea venhe years 5 me include addiu39 nalenergy terms that describe the kinds fdef rmali m s mef rcefieldsacc untf rc pun betweenbending and stretching in adjacent ndsin den imp vetheaccumcy fthemechanicalm del The mathematical f m fthe energy terms wries f mf mefneldt f me7 eld Them re 0 mm nf rms will be described PEFR 2KbbRbeq2 2K eReeq2 2 gm cosn R Y dihedral A i j B i j qi q j 5sz rng SEER 1 atom pairs u 39 39 We called the functi n a quotp tentialquot nergyfuncti nasitd esn tc ntain c ntnhuti nsmadet thet tal energy made hythem ti ns fthe at ms inv lved1tisp ssihlet calculatetheseusingm lecular dynamics meth ds The functi n aimst give reas nahlevaluesf rthe difference in quotmicr statequot energies betweentw different c nf rmati ns The ahs lute value f rthe energy given d es n tmean anything ceitainly NOT the free energy ff rmati n only differences have meaning Th 39 examinati n fany pr cess which inv lves the change in chemicalh nding eg ne cann tsimulate chemical reacti ns in an enzyme active site with it T heahlet calculatethep tential energy fapr teinusingtheah veequati ninv lvesalargenumher fparametersequilihnumh ndl ngthsheq b nd stretching c nstants Kb The r cess ffinding these is ardu us and in there are nlyar undf urp tential energy functi ns inc mm nusa pr teins CHARMm AMBER GROMOS and ECEPP th ugh results htained with cunentp tential energy functi ns are nlyappr ximate they have ne great advantage rthey arec mputati nally heap This all ws the intr ducti n frealisticrepresentati n fenvir nmentr such as having large numbers fexplicitlym delled waterm le ules surr undi pr t in1tals all ws the calculati n fthep tential energyf rmany diff rentc nf rmati ns fthe same m lecule This facilitates the use techniques such asm lecular dynamics which all ws the thermal m ti ns fasystemt be x l redThiscan bec ntmstedwith quantum chemicalmeth dswhich even f rsmall systems are s expensive that nly alimited numb r fcalculati ns can be made but pr duce very accumte energies Molecular Mechanics Energy 2 Bond Stretching Energy stretclnng39 Bending Energy Torsion Energy NonBonded Interaction Energy 4 Non Bonded Interactions Stretching Energy The stretching energy equati nishased nH keslaw The quotkbquotpammeterc ntr lsthe stiffness fthe b nd spring while defines its equilihnum length Unique quotth and paiameters are assignedt each pair fb nded at ms based ntheirtypes eg CC on oec etc This equati n stimatesthe energy ass ciated with vihiati n ah ut the equilihnumh nd length This is the equati n can be seen in the f 11 wing pl t f a parah la as Bending Energy Thehending energy equati nisals hased nH keslaw The quoththetaquot paiameterc ntr lsthe stiffness fthe angle spring whiletheta defines its equilibrium angle This equati nestimates the nergy ngle ass ciated with vibrati n ab ut the equilibnum b nd a Bending Energy 2 Z a 990 or kb I o Umque paramaersf r angle bending are ass gned L ach b nded anleL fat ms based n Lhelr Lypes e g ccc ceoec CeCeH em The effect the kb and lkLheLal pammeErslsL br aden r sLeepen e sl pe the pamb la The larger Lhe value em re energylsrequlredt def nnanangle rb nd n hall wp l L 10 The H kaanp Lenual lssh wnm tth ll wing pl if three values f k Torsion Energy 4 Z A 1 cosn torsions Torsion Energy TheL SI n nergy mm O ne LhanL representaphyslmlpr cess The L 31 nal energyr presents Lhe am unL fen rgy LhaLmusLbe added L r subuacLed n m Lhe sueL hing Energy Bendng En rgy N neB nded InEmcu n Energy n nmenL mg r L lmsL ma e L p m del dihedral angle aLhane f r example mgane used a a m delf r any HeCeCeHb nd The A parameterc nLr ls Lhe amphde the curve Lhen paramaer c ntr ls lLs pen dmLy and lphll shlfts Lhe EnLlre curve al ng Lhe r Lau n angle axis tau The paramaers are d Lermmed n m curve mun Umqueparamaersf rt 31 nal r Lau nareasslgnedL eachb nded quarLeL fat ms based nLheuLypes eg CVCCC CVOVCVN HCCVH as T SI np Lenualswuh Lhraac mbmaLl ns HAM and ph are sh wnm Lhef ll wlngpl L g Nonbonded Energies van der Waals tenn Electrostatic term Van der VVaals attraction regime The an Patametetsc nu lthe depth andp siu39 nintetat mic distance fthep tendal energ wellf ragiven Pait fn neb ndedintetacting at ms eg CC ocoHetc1neffect A determi the de detennines the dame fquothanlnessquot f gree f quotstickinessquot fthevan derWaals am the at ms eg marshmall wrlike billiard ballrlilte etc n a E a The quotAquot parameter canbe btainedfr mat mic p larimbility measut ments t it can be calculated mechanically The quotBquot pammeteris typically rivede mctystall graphic datas ast rep duce fvari ul s q bserved average c ntact distances between diffexent kinds f at ms in crystals us m lec e Molecular Dynamics Newt nseqmu39 nis usedinthem lecular dynamicsf lmalismt simulate at micm ti n and ditecu39 n m u39 nvel cityareg vemed by thef tces that the at ms fthe system exert n ach thet as described by Newt ns equau39 n Inptacu39ce the at ms ate assignediniu39al vel cities thatc nf tmt the t tal kinetic e f the system which in tutn is dictated by the desired simulau39 n temperature This 39s inf nnati nthe stu39 n feachat mthr ugh utaspecifiedperi d fu39me typically nthe ier fpic sec nds 10mm sec nds Thef tce nanat mcanbe calculatedh mthe change in enetgy between its currentp siu39 nanditsp siu39 nasmall distanceawayThiscanbetec 39 39 39 quot 39 H y quot 39 39 39 39 ms sitin The basic ingredients rm lecular dynamicsatethe calculati n fthef tce netch at m and h mthat inf nnau39 n they sin39 n reach at leTr ugh utaspecified peri d fu39me typically ndte tdet fpic sec nds 10mm sec nds Th f e at mcan be calculatedfr mthe change in enetgy between itsc mmp siu39 nanditsp siu39 nasmal dismnceawayTlnscanberec 39 39 A quot 39 H y quot 39 39 394 ms squot un Energies can be alculated using either m lecular mechanics t qmntum mechanics meth ds M lecular mechanics energiesarelirnitedt applicaii nsthatd n tinv lve drastic changes in elem nic sttuctute su hasb nd 39tgbteald tum mechanical enelgies can be used t study dynamic pt cesses inv lving hemical changes veland 39 39 39 quot 39 fsucha pt gtam wledge ftheat min tcesandmassescanth nbeusedt s lvef tdnep siu39 ns feachat mal ngaseties f exuemely small time steps nthe tdet ffemt sec nds 1er ssec nds The resulting series fmapsh ts f slrucmral changes vet time is calledamject ry The use fthism th dt c mpule uaject riescanbe m teeasily seenwhenNewt nsequau39 nisexptessedinthef ll Wing tm utt39 n First the at mic acc mu ns ate c mpuledfr mthe f tces and masses The vel ciu39es ate next calculatedfr mthe acceletau39 ns based n the f 11 wing telau39 nship Inptacu39cemaject tiesaten tditectly btainedft mNewt nsequatt39 nduet lack fananal 39 als l l A uaject ry between tw eg1 femt sec ml u r ndelmln The initial at mic 9 sin39 ns at tim t predict the at micp siu39 ns at time quott delta tquot Thep siu39 ns at quott delta tquot are used t predict the p s n us at quott 2d lta quotand s The quotleapfr gquot meth dis a c m nnurnerical appr acht calculating traject ries based n Newt ns equati n The steps can be summarized as f 11 ws solve for ai at t using update vi at t Atf2 using 39 39T vit A1212 At update ri at t At usingquot 1 11 At rit 1 393 39 At The meth d derives its name fr m the fact that the vel city andp siti n inf rrnati n successively alternate at 12 time step intervals M lecular dynamics has n defined p int f terrninati n ther than the am unt f time that can be practically c vered Unf rtunately the urrent pic sec nd rder fmagnitude limit is ftenn tl ng en ught f 11 Wmany kinds fstate t state transf nnati ns such aslarge c nf rrnati naltransiti ns in pr teins M lecular dynamics calculati ns can be perf rrned using AMBER CHARMM CHARMMGAMESS Disc ver QUANTACHARMm and SYBYL The Design Process 0 Database Searching and Docking Methods de novo Design Methods 0 Combination Docking and Design Ith Lend Duslyned mug mu Doslt r Imm m Sllualul on lead Eiomm o aneplol lair 3 S vlc1ulc Donor blue Acceptor red Hydrophobic Green 1 Define Shape and gt 2 Chemical Databases gt3 Score Ligands Contacts at Binding Site Concord estimates 3D Conformations PEFR 2KbbRbeq2 2K eReeq2 2 get cosn R Y dihedral A Bi quIJ 850W 1 atom pairs u DOCK by Kuntz at UCSF Step 1 Start with crystal coordinates of target receptor Step 2 Generate molecular surface for receptor Solvent Accessible Surface My day Waals swiace aucmsl HE Suvlace what scme am 315 call me am vmtremlunad vulume by emmpe Wm Flmhmund m m 1964 JMEIarhclE http WWW victorchangunsw edu aupublicbrechunetsci html Contact Surface 7 Green ReiEntry Surface 7 Blue Step 3 Generate spheres m ml the active site Side View of spheres Matching and Scoring Step 4 Matching gt Real Molecules Step 5 Scoring Each ciicntcd molecule is then scored for t There are cuncntiy 3 scoring schemes Shape scoring which uses a loose approximation to the LennardJones potential mm i Force eld scoring which uses the AMBER potential Final Evaluation Tms is the l prsc nng enehtstieih re the meieeiiie thinketzi m the HlVlrprutaseacnie site using Amba39 fnreee eld scunng Comparison of Docked Orientation to Structure Ligand Scoring Based on Force Field Analysis Fragment Positioning Methods de novo design Thisimage shuwsan Mcssinieieik result mm Sarchmg an setive site re With4 runetiehsi mugs Tms runetiehsi site hep is curnputed re the sehve site erhemaggiuhhih er th Nemethyl acetami Withs sunsee shewmg h pesitivened reguns ufele m zucpulmual Link Best Pieces Together hnpwww netsci orgScienceCompchemfeature04 htrnl Combinatorial Libraries 200 000 Drug Like Compounds Screening Libraries 7 39 Target Proteins p tram Genomics 77 25 Billion momatea Parallel ii quotiquot j if Syntheticalty Accessible Drug lee libraries L Compounds rillIi 4 7 Prototype 39 NCE Biological Model HighThroughput StructureActivity Screening Data knalySis HIV Lifecycle E IN lymplimyti WW3 iy bilunquot site ill action I ll inert tn ithDt Cell 7 membrane infectious a n lrlUl39l fut enzyme called protease tulips the lh i v slim puma In mourn proteine Tim DNA timers II iL mull111 l d intIrma Elsiquot inllJ Ilie host cell39s mm Tite will l39iegina Vital RNA Eu Ilia ie rrlrm curiae5 ul Hll39t39 into the CitIll mmmnents Rowme quot lml39liuiii39i39ipm 39 NNR TIEquot tile action EMUquot quot nF T39il mquot Nut l msidt nmlogs39 commie ingin strand gm 9quot ads RNMritu tkILibhh flr39lli UN Witt1391 r httpwwwgeorgetowned ugumcedmediaimagescd4jpg quotquot Cutting Sites Role of HIV protease W Cleaves TyrPro or PhePro Viral Polyproteiri Inactive Mammalian peptidase do not cleave amide bonds of prolines 4 Proleas e tf Protease is a homodimer Asp and lie residues form important interactions with peptide or peptidomimetic inhibitor Polyprotein Inactivation of protease leads to is cut by protease inloindividual production of immature noninfectious we particles Active proteins How HIV Protease Inhibitors Inhibit Viral Replication HIV protease recognizes a complementary shape on polyprolein and cuts protein i fits like quotLock and Keyquot 1 I I I Inhibitor mimics cutting site and binds to protease u but cannot be cut thereby inactivating protease it 7 Inhibitor Drug 7 Cleavage of Peptide Bond 170 IIe Pro i70IIe ProPhe A5pLeu 164 HIV Protease HO quotHydrolysisquot Phe Asp Leuiazi 10 Speci city pockets cleavage site 32 31 2 P1 P139 HL CONH JK CONII A In HIV pockets prefer large hydrophobic side chains Phe Pro Competi ive Inhibitor F39239 CONH CO 1 Bind active site 2 Unable to be cleaved by protease 3 Mimic the transition state Strategy for Protease Inhibitors C R Dimer OH Transition State Interface 3939393939393939 OC OH Is Tightest Binding CO HN R C0 Dimer Transition State Mimic Interface Cg That Can t Be Cleaved o Rational Based Design 0 Lead nding 7 Finding any compound that shows the biological activity that you are looking for 7 Sideeffects of existing drugs screening natural compounds structure based design 0 Lead optimization 7 Improve biological activity speci city bioavailablity solubility 7 Computational techniques to predict inhibitor binding af nity Annu Rev Biophys Biomol Struct 1998 27 24984 HIV Protease Saquinavir 11 HIV Protease Inhibitors 1e residues Hg 5 Only 1 Ofthe Asp nserved water rnolecule for many protease Inhitors reSldues ls protonated Water molecule bridges polyprotein and Iles o protease indmavrnntenmons With Hiv protease aetwe ste Blue lmpnnanthydmgm band lnta39actmns Red intermons M39h speci city sites ormepmtease Saqumavir mta39actmns W h Hiv pmtease same site Blue lmpnnanthydmgm band mta39actmns Red intenmons With speu uty sites omie protease Saqu1nav1r A 1 First inhibitor ofHIVl protease Created using peptide derivatives to tran 39 39 n state Minimum length ofthe inhibitor started changing moieties changing P1 to DIQ led to most Saqulnavm no 318559 improvement DecahydroisoquinolineScarbonyl DIQ maintained water molecule n N N N H 0 v0 Ro 313533 Bulklxn39a uurenm s tr FIGURE 4 Enzyme l enutiun mechanism 0139 HIV protease H Via substrate transition state N N N H Biopolymas 1999 11 5963 Intermediates for Ritonavir Great in vitro inhibition lC 04 uM Poor Aqueous solubility o H on H o o Oquot Q 6 U 639 quot A74704 Pyridyl groups to improve solubility Asymmetric inhibitors work Diol inhibitors affected porcine pepsin enzymes A77003 a 0 e o 0 Q Norvlr Flltonavl r g 39 it of lndinavir Crixivan Lead Compound 9 150 other cited compounds Very poor aqueous solubility poor pharmacokinetics L682679 Molecular modeling and crystal structures as aids L685434 I 7 0H KN t N Ki 052 nM for HIV1 33 nM for HIV2 0AM Highly selective for retroviral proteases UMP323 N H o NJIN ko H SD146 o N MN SD152 0 water molecule Attempts to eliminate the role of the UMP450 Using DOCK 6 membered ring with para 0 could interact to replace water and bind to Asp Ki 7 uM wi hout moi ies filling 82 and 82 Du Pont Merck 7 membered cyclic urea ring DMP323 has subnanomolar inhibi ion constant poor bioavailability SD146 and SD152 have larger groups capable of interacting with enzyme but have poor water solubility HIV has subtypes high mutation rate Primary mutations associated with Protease subtype variability 510 resistance to protease inhibitors Polymorphism map for HIV in North America Mutations lower affinity for inhibitor I more than the affinity for substrate Red most variable J Cellular Biochem Suppl 2001 37828 l3 Inhibitor binding is dominated by entropy term 2 H Su bstrate Black AG White AH Hatched TAS H OH H 0 H H H H H 395 Drug w N NJYNH YN N NJ NH E Inhibitor 0 H O H 0 2 o N M o N 8 Large effect of solvatlon Asn82 Velez Wme 0 WW 4 entropy due to hydrophoblc Original Drug Original Drug inhibitors YE OH 3 ONIJYEH Mggggdoug Preshape the inhibitor to o 0 Z N H 0 reduce the loss of NH A 82 Hero Indiiiawr Ncltmaiiir Saqumamr Ritonawr conformatlonal entropy upon binding Second Generation HIV protease 1nh1b1tors p Effect of Double mutant srGinAsn4yr x Pru Iiu VIIuim p171 24mgion S rrrrrrrrrrrrrrrrrrrr quotAsia s 7777 a iisnmm minim v PraGln llunmu YFF raglnn i ASK a are HSaerhe AsnPhu Pm llmVaLNH is A lilVpmlmw l 4 o oo N HgtSerNH co NZLcongE NQ f KNIga Ww 0H CONH coVaINn O U E g E a U Huipmiam E A NI 0 EN o Kva272 l on KNI577 KNI764 Siibaugg lgvd lyi mwrt 345 K N l 5 i 7 K N 64 quot rigs i g i i Although AAG term is positive it is By designing inhibitors with favorable much smaller than for 1st generation en halplc termS YOU can ntr0duce some inhibitors due to flexibility KNl 764 o o N Njhg man eXIbility into the inhibitor structure binds the double mutant tighter than 1St genera ion inhibitors bind the wildtype i L Jl lll fi l39 i 1134133 L illl1 3 llli i i i l liifc fiiZ KFLTE II Biopolymers 1999511 5968 Take Home Points Using computational techniques to predict inhibitor binding af nity companies have developed potent HIV protease inhibitors HIV protease prefers large bulky hydrophobic groups Nonscissile group ofthe protease inhibitor is placed between the 2 Asp groups Buried Water molecule bridges the carbonyl groups ofthe inhibitor and 2 He s ofthe protease 1st generation inhibitor binding is driven by entropic term 2quotquot1 generation inhibitor has favorable enthalpic term allowing greater overall exibility


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