NGHIDN CO'U THI^T K £ C H U 6

oc C6NG NGHE SINH Hpc TOAN QUOC 2013

NGHIDN CO'U THI^T K £ C H U 6 | POLYPEPTIDE OINH HUONG CTC CHg DOC TO THAN KINH a-Cbtx CUA NOC R A N Naja kauthia BANG P H A N M E M DISCOVERY STUDIO 2.5

Nguyen H&ng Thanh', T r i n Linh TIUFTC^, Tnrtmg Nan H4i'*

' Vien C^ig nghg sinh hgc, WSn Han ISm Khoa hgc va Cdng ngh^ t^t Nam

^ Tnrdng Dai hgc Khoa hgc Tg nhidn. Dai hgc Qudc gia Tp. Ho Chi Mnh

T6M TAT

Trong nhihig nam gan day, v j ^ n^ien cmi phat trien vic-xin va thudc bitag cic phSn mem Tin sinh hgc dang ngay c ^ g phat aika rong rai. Voi m ^ lieu n ^ e n cuu Ihiel ke chuoi polypeptide co kha ning gao ai luc cao voi dpc to tbiin kinh alpha-cotnatexin (a- Cbtx) cua OQC ran Ntga kauthia, chiing toi da sir dung iriiin mim Discovery Studio 2.S de n ^ e n curu xay dung md hinh cau true va mo hlnh tuong tac ciia cac peptide tiem ning voi dpc to tbin kinh a-Ctrtx. 03 diura polypqitide co at luc cao voi doc l6 ttiin kinh a- Cbtxdadugic mo hinh b6a dua tren cac d u true khumi: ilCC4, 1L4W, 2BG9, 2QC] voi dp tuong dong tiinh t^r axit amin la bon S0%. Cac chudi polypeptide sau do dugc mo bfaih boa lao pfauc b$ gin ai luc voi doc td thin kinh a-Cbtx bing chuong trinh Dock Protein (ZDock). Cac phuc he duoc Idem tra, danh gia r*»St hioi^ bing chuoDS tiiah Standard Dynamic Cascade nham thn ra jAuc b | cd muc nang lupng Idiiio nbat. Chuoi polypeptide modcl2_a7 coai luc gin c^i nhit (ning lu^ng tdngsd nhd nhat la 1127.26 kcal/mol) dugc Ii^ chon de tien hanh n ^ e n cuu thyc ngfaifra trong dii n ^ | m tfan n ^ & n bo^t tmh sinh bgc tiep theo.

TirUioa: npc ran, Naja kauthia, polypeptides, dgc Id than kinh a-Cbtx, modelmg, ENscovery Studio.

MdeAu

Nghign ci>u phdt trien vac-xin vk thuoc bang eke p h ^ mkm Tm sinh hpc bong nhinig nim g ^ day dang n g ^ cang dirac phdt triSn r$ng r i i . Cke ky thu$t md hinh hoa cSu true dga tren s^ tiKTog ddng vh binh tg va cau tnic ^ chuftg Id dirg'c tinh hiru dgng trong vi^ nghien cuoi thiSt tap nn$t ngSn hang cdc phan tv sinh tipc tiem nang sir dgng trong cac md hlnh nghiin ciru phat bi^n vic-xin vd thuoc. V i ^ si> dgng cac chircmg bir^ phSn mdm tin anh hgc d l rnd phong cdu true, mo phdng hrorng tdc phdn b> da gdp phan lam gidm tticn gian va chi phi cho nghien ciiu thire nghi§m. mdt khac. ky thudt ndy cdn gidp cho cac nhd nghi§n ci>u tien hdnh ddng thdi cdc p h ^ thir. k i ^ tra, ddnh gid va sdng Ipc ben mgt so lirong \dn cac m i u hem nang. Mpt trong cdc hircmg nghien ciru dang dirpc quan tdm la nghien cthi phdt trien cac phdn b> cd kich t h u ^ nhd. ddng vai bd nhir cac chit gdn (ligand hay antogonist) tham gia vdo qud trinh nhdn biet khang nguydn khdng the, ho^c tliam gia vda qud trinh xuc tdc krch hoat hodc i>c chl hoat ddng cua r n ^ kiai protem chuc ndng ndo dd. MOt so cdc ngdn hdng dir Wgu v l d u true cdc ptidn b> nhd nhir Cambridge Structural Database (CSD) hay 2^NG (Unhreristy of Califomia) cung d p md hinh cau bOc cua cdc potysaccharide. cac chuoi pdypepbde dirm dang file pdb, SDF, MOL2. .. thudn ti^n cho vigc tfiao tdc va xv ly t)ang cac phin mim tin sinh hpc. Cdc ngdn hang dir ligu ndy d i ngdy mdt thuc diy qud trinh nghidn ciru sang Igc cdc phdn b> nhd dung trong nghien ciru phat bien vdc-xin vd thuoc (Kumaretal., 2006).

Ngc ran dirge biit d i n nhv mgt nguon nguyen li#u qui dCng tmng dilu bj cdc bdnh hiim ngheo nhv ung thv. cac t>^h vetim m^ch. cdc tignh lien quan din tie than kinh,... Cdc^ianh phan ddc ^ cd trong noc ran con dvgc sir dgng de bao chl mgt s6 loai thuoc cd tdc dung dieu trj benh cao huylt dp. cac kiai thudc d m mdu, chdng chdy mau npi tang, khong cfti sg phdt triin cua t l tiao ung thv. lam (iidm sv di can cda cac t l tiao ung thv.... Tuy nhien. ngc ran cdn dvcrc t i i ^ den nhv td mgt thdnh phan cgt: dgc, cd kha ndng gdy tir vong rit cao sau khi xdm nhdp vdo co tfii ngvoi vd dgng vdt qua dvong mau do bj ran d$c d n . Thdnh phan dgc to than kkih a-Cbtx (^pha-cobratoxin) dvpc coi la dgc nhat vd chu yeu dirge lim thiy trong ngc r i n h i dat Na^ kaouthia tfiudc hg Eapkiae va Hydrophiidae. Cdc nghien cim da chi ra rang, ddc t6 nay ddng vai bd nhv nhirng antagonist gan di lgc cao voi cac thg the nicotinic acetyteholine (nAChR), tir dd Idm irc cfil qud binh truyin din thin kinh. gdy ra cdc hi€n tuong nhv co gigt, ndn mi>a. l i ^ b> cN, m i l cam giac. fndc gay fioai tir tgi vung bj ran d n (Wetland et al., 2000). Cac thi nghifm dd cho thiy cdc thu thi nicotinic acetyk:hQiifie lam tmng gian cho mQt so chirc nang ciJa nao bp nhv nhdn thurc vd tsi nho. cung nhv trong qud tnnh diln ra trang thai t>enh It ciia mgt s6 tidnh lien quan din than kmh nhv tienh tam than pfidn li$t, benh Alzheimer, bgnh Parkinson, hdi chvng Tourette vd mdt vdi dang ddng kinh (Dani, 2001; Steiniein and Berband, 2008). Cd tne ^ y tdc dung cung nhv tac hai vd cung Idn ciia npc dpc ran, do dd, n g d i vi|c nghien ciru sir dung npc ddc oQa rdn nhv mOt nguon nguyen ligu qui thi vigc nghien cim cdc lo^i thudc dung bong dieu bi r i n d n cOng rit quan bgng.

Theo nghign cvu cua d c ^ c gia Boume va cpng sv. thg tfie nAChR cua ngudn vd mpt sd dgng vdt dvpc xac djnh Id cdc protein lap t h i nim xuydn mdng. dvpc d u tao gim 5 tiiu don vi bao xung quanh mdt loi tmng tam va nvdc. Cdc tieu don vj dvp^ d u tgo tir 5 kilu chuli polypeptide ta a, p. 5, E va y- Vung binh tv tham gia vao qud binh g i n phli b> vdi ddc t l Ulan kinh a-Cbbc Oagc xac djnh ndm ben tieu don vi a7. Vj bi cac axil amin tfiam gia vao qud binh gin vdi ddc t l duoc xac iJinh gim Cys192 vd Cysig3, Tyr 93,152, 190.197 d di Ivc cao vdi chat chu van va chit dli khdng (Boume et al.. 2005). Nghign ci>u ciia Kalchalski va cdng sv da chi ra ring, dot biln diim d l i vdi mgt so cac axit amin dac hieu CO ttii tgo ndn sg^ thay doi ve di Ivc gin hr 5 - 100 tin (Katchaiski-Katzir et al., 2003). Cdc axit amin tai cac vi bi Trp-86.

Tyr-93; Trp-150, Gfy-153; Arg-186, Asp-199 ddng vai bd quylt djnh tnwig viec tham gia vao iien kit gdn vdi phdi tir. Mpt socdcaxitaminbaothukhacddngvaitrdquyltanhdutnJcWia thy tfli nAChR nhv Tyr-188,Tyr-195va Cys-192/193 (Fmchart-Gaillard et al., 2002).

Cho din nay. d u tide bgc 3 ciia tieu phan a7 d a thg the nAChR cua ngvdi chva dirgrc cdng bo, cd the do dvpc eau t^o tir 5 biu don vj vdi kich thvde Idn (-60 kOa/beu don vi) va dvpc bao (juanh t>di cdc vung kj nvdc (protein xuyen mdng). do vgy vigc tao d u true bnh bie ed the gap khd khdn. Do do, hau het cac nghien cvu deu tap tmng nghien cim

HQI NGHI KHOA HQC CONG NGHg SINH HQC Tr--.. ^ ^^^^miKi'^lj • _J,

t x^wB • . u-ni=.i nac d u tnic dvgc tim thiy b i n ngdn hdng dO ligu protem PDBJ d u buc khdng gian cua thy thi nAChR cua g ^ " ^ " ' ^ ' ; ' ^ ' L ' J ^ f S a gTHai phdn b> d u bde 1kl8 vd 1kc4 dvdc x^]

chu ylu Id cdc chu& peptide d v ^ xdy dg|a bdn ^nh h/ly m u ^ ^ ^ ^ ^ ^^ ^^ ,QL3_ I O L 4 . 10L8. 10L9 dvpc x # = dvng bdi phvong phdp cOog huong hr hgt nhdn (^MR) va 4 pna ^ ^ ^ 1 ^^ ^1 2001). So sanh v l ; di^ng bing phirong ohdp md phong md hmh ^ ^ ^ ^""^^f^ggida hai dogn trinh t^ Id 91 %. Mdt s6 diim khdc • binh tv giira hiu phin a7 cua ngvoi vd ga cho thdy dd ^l^"^y,g\.^gQ ^ n g u * d w c thay t h i bdi d c axit amin bigt giira 2 binh tif Oagc quan tam nghien cvu gom: Ser-i t». ^ • j ^ ^ ^ ^ ^ ^^^^ ^ j j - ^ p^^n a7 cua gd d l hrong vng Id Thr, Ser. lie ben tnnh l v or ga. Th^c 16 ^J'^^'^^-rT^^ nhiSn muc ti6u cua d l ldi Id nghidn ciru dogn ttiilt k l dogn peptide tilm nang d kha riang gin voi dgc ^ ° - e . ^ ^ 7 ^ i ' „ " 5 7 ^ ^ "ngvdi, ding thdi do d c quan nggi v | | peptide dgc higu cho ngvdi, hvdng tdi sv dgng ' ^ , ^ , ^ f ^ ^ , 5 ! , " i ^ ^ ^ co Z ngvdi Sing d n d nhiing nghignf Mnh d$c higu miln djch giira ngvd. vd gd. cung nhv j f ^ " ; ^ f j ^ ^ p tiiu phin a7 cfla ngvdi. kit hgp vdi v i ^ phdn"

cvu ddnh gid mang bnh thing ke. Do >^y. chun^ **L^>^A?ofa ad d l ftilt k l dogn peptide tilm ndng d khd ndng bit, lich trinh lv tvong ding vd phdn bch d u buc beu phan a7 cua ga ae tniei i^eou^ i^y

cdp vdi dOc t i ngc rin a-CMx.

NGUY£N LI?U VA PHUONG PHAP Nguyen li$u

Ngdn hdng di> ligu protein www.rcsb.orq

Hg thing mdy tinh Woricslation tgi Vign Cdng nghg sinh hoc, Vi§n Hdn Idm Khoa hpc vd Cdng nghg Vigt Nam.

Phin mim Discovery Shidio 2.5 cua Hdng Accelrys. My.

PhvoTig phdp

Phtrong phdp mi phdng ciu true polypeptide

Chuang trinh Homology Modeling dvgc s.> dgng d l md phdng d u tnic ly «^"y^« ^ ^ , ' ^ ? , t " ? ^ S ^ S T ' ^ thudt t d n CHARMM. Cdc bvdc thvdng dvgc tiln hdnh trong qui binh xdy dvng md hinh cau buc phdn t v g i m d .

Nhdn dgng d c tgp di> ligu d u biic dvgc sil dyng lam khudn cho qud frinh md hinh hda dva vda cdng cg BLAST Homokigy Search.

So sanh d u biic cua cde tgp dir ligu (dgng PDB) d l tim ra cac vimg d u friie ttrong ding vd friing Igp bing cdng Of 'Stmcture Alignment Methods".

So d n h frinh b^ d a md hinh peptide d n thiet ke vdi tgp dif ligu mang thdng tin da dvpc so sdnh ciJa d c d u buc khudn bing c&ig cy "Sequence Alignment Methods".

Sd dgng d n g cg MODELER d l xdy dg-ng md hinh hda d u biic.

Phaang phip md hinh hda ciu true phOv hg propeptide va a-Cbtx

Chuong frlnh Dock Protein (ZDOCK) nam frong thv myc "Pnatein Modeling' cOa phin mim Discovery Shidio 2.5 dugt sir dgng d l tiln hdnh xay Ogng md hinh phuc h# polypeptide LPC chl ngc rin va dgc to friln kinh a-Cbbt. Chvong fririi ndy cung d p cdc phvong phdp d l tiln hanh do dgc d c thdng s6 ve tinh ky nvdc, d | tTnh dign. Og dm dign ciia ck nhdm nguydn Kr trdn b l mdt d a 02 phdn tGp pnatein vdi nhau dya tren thu^t todn ZDOCK. Chvong frinh sir dgng phuong phdp dv d d n Miudn miu bo sung dvgc ggi Id Pairvinse Shape Complementary (PSC) d l tgo ra d c kilu gin khdc nhau ( d c pose khdc nhau) dgi dign cho d c kilu tvong tdc khdc nhau giCra hai thy the va phoi b>. Phvang phi"

ndy (PSC) dirge sv dgng tuy chgn d n g vdi d c chi s l nang Ivpng v l mirc do desolvalion (DE) vd ITnh dij (elecfrostatics) d l phdn logi va xip hang d c trudng hpp docking thdnh cdng.

Phircmg phap mi phong ding hgc phin tir

"Standard Dynamics Cascade* Id mdt chvong trinh con ndm trong gdi chvong frlnh "Simulation'. Chvong trinh ndy tii hdnh d c bvdc Knh todn va toi vu d u tnic nguin nhdm tim ra d u tnic tot vu nhll. Chvong trinh dvpc tiln hdnli ba gim cac bvdc nhv sau:

Minimization: Id bvdc dau tign cua qud trinh nghien ciru md phdng dgng hgc phan tir. dong thdi d n g Id qji binh tli vu h d mve nang lvpng lan thv nhit. Qud frinh ndy sir dung thugt todn ban diu Id Steepest Descfli (SD) d l xi> ly d c lidn kit bong todn bg hg thong ma khdng lam thay doi nhieu d u tnic.

Minimization2: Day Id bvdc toi vu hda mve nang Ivgng lan thv 2, sir dung phvong phap Adopted Baa Newton-Raphson (ABNR). Qua frinh nay dvpc SIP dyng d l ddm bao mirc ndng Ivpng nhd nhit sd Oirgc i(

dyng cho giai dogn nghidn cvu ddng hpe tilp theo cOa qui frlnh.

Heating: Giai doan tilp theo cua qud frinh nghien edu ddng hpc Id xv ly hg tiling d u fruc vdi mpt nhidt dd x*

^nh.

Dynamis (Equilibration): OSy Id qui trinh chuin diu tien ciia qua frinh md phdng ddng hgc phdn b> d ^ ^ bing t d n bd hg thong d nhigt d$ yeu d u . Qua frinh nay se tiln hanh phan bo ndng Ivpng dvgrc cung clf|£]

mgi phdn h> frong he thing, dam bao hg thong t i n tgi d trgng thai d n bang dgng d nhigt dg xdc djnh. j | Production: La giai dogn xv IJ cdc s l ligu thong ke bang thu^t t d n Leap-frog Veriet. Kit qua eiia qud frinh^

Id tgo ndn d c tgp dv lieu mang fridng tin d u friic va tog dg khdng gian eua cdc d u hlnh khdng gian I™

nhau.

_ ; PC CCNGNGHg SINH HOC T 0 A N Q U 6 C 2013

K&T QUA VA T H A O L U A N I-va ch9n do^n peptide thiet ke

Dva vdo cac nghidn cim d u tnic dvpc cdng bo. cimg vdi kit qua so sdnh sif khac bigt gida frinh ta nAChR cda ngvdi vd cua gd. chung tdi quylt djnh lifa chgn dogn frinh tg d chieu ddi khdng 30 axit amin bit diu hr Leu-176 din Arg-205 fren frlnh ty d a chu6i nAChR eiia ngvdi dio mgc dich md phong tgo cku bite ly ttiuylt Tren dogn trinh tg ndy. d c axit amin nim d i^ fri Cys -192/193 ciing vdi d c frinh tg bao thu khac gom Tyr-188, Tyr-195, Arg-186 vd Asp-197 dvpc giir nguygn trong frinh tg ciia chuli pcriypeptide tiem nang. Cac vj fri khdc dvgc nghien ctru va ttiay t h i bdi mdt s6 axit amin phu hgp vdi myc tidu tdng cvdng di lifc d a chuli polypeptide len ddc t l ttian kinh a-Cbb(. Trinh tg eke chuoi polypeptide vdi vj frf cde axit amin thay ttii dirge ttie hign mdu do nhv sau:

aljumaa, I Z l GIFSSSCnBVainFDVDHGaiCrGSISYGWSIJJLffllQEAIlISSnFBGaroLVSlPS fl7_GalllU, m GIFKSSaiOVJBFPrUVQKaHiCfSSltTYGGKSLIlLCMQEADISGYISNGEHDL'.'SlPS

s7_biDuii, a7_GAlZn9,

241 LGITVLLSLTVEMLLVlEIMiTSDSVPLIMYFSS3IIIVGLSVVV7VIVLQYHHHDP3 261 LGHVLLSLTVFMLLVMiHPWSDSVEtaiOYFaSTHIIveiSWVmVMIfflHaBFD

Hlnh 1: So sanh trinh ty thu thi nAChR ciia ngirdf va cda ga Bang 1: Trinh tg 5 chuli polypeptide dirge thiet k l

(Cdc axit amm mdu do Id cdc axit amin dugrc thay thi) TT

1 2 3 4 5

T6n Model 1 a7 Model2 a7 Models a7 ModeI4 a7 Models a7

Trinh t v a,a

LVGIPGKRSE RFYECCKEPY P D V m V T M R LVGIVGKRSE RFDNCCKDEP HGDVTFTVTMR LVGIVGFRSH RFYECCKDEP H G D V m V T M R LVGIVGFRSH WVYECCKDEP HGOVTRVTMR NKDIRGWRHH WVYTCCKDEP HGDVTFTVTMR

Ghi chu Trinh t l / g l c

Thilt k l chud) polypeptld drc c h l npc ran bing Build Homology Models

Ndm chuli polypeptide dvpc md hinh hda dya trdn chvong frinh phin mim "Build Homology Models' fren co sd tvong dong vdi d c cau tnic khuOTi. Bing d n g eg "BLAST search' chiing tdi tim dvpc 04 trinh ty cd dg tvong ding cao nhat Id 1KC4, 1L4W, 2BG9A. 2QC1B. Clu friic ciia d c phkn b> l^udn miu dvgc Sen hdnh sdp chudi (alignment) frvdc khi dirge sd dyng lam khudn cho chvong frinh 'Build Homology Models". Kit qua sip chuli cho thiy, dg Igch chuin (RMSD) dya frdn sy khdc bigt v l d u biic cda chuoi mgch cacbon gida cac phdn tCr ndy deu nhd hon 5 A", phd hgp eho vigc sd dyng Idm khudn d l md hinh hda d u tnie edc chuli polypeptide. Kit qua xdy dyng md hlnh d u fruc d a 05 chuoi polypeptide thanh d n g dvpc ttil hign bong Hinh 2:

Hlnh 2: M5 hlnh cau tniic chudi polypeptide dvgrc ching Ifin (superimpose) vdi cdu tnic khudn la2BG9Ava2QC1B Kit qud d u o i pol^eptide vdi kich thvde 30 axit amin dvpc md phdng dy^ fren d u tnic philn p cOa mgt dogn trinh b,r frSn c l u tnic eua thy t h i nAChR tiiu phin a7. Kit qud frdn Hinh 2. chuli polypeptide dvgc md hinh hda d mau vdng nam ching kbit (superimposition) len d u tnic philn jS ciia thg the a7. dilu ndy the hign d u friic ciia chuoi polypeptide v l eo bdn la tvong dli gilng vdi d u tnic cua Uig ttie a7. diing vdi tinh todn ly thuylt ban dau.

Kit qud md hlnh hda c l u trOc phdc h | polypeptide vdn dgc to than kinh a-Cbtx

Phan b> protein d u tnic ddc t l a-Cbbc (PDB ID" 1YI5) dvgc ehiing tdi sv dung nhv mgt tfig the (receptor), moi phan hr polypeptide da dvpc xdy dyng d u frCic thdnh d n g ddng vai trd nhv mot chat gin (ligand) d l ten hdnh qud frinh xay dyng d u bdc phirc hg polypeptide-dpe to thin kinh a-Cbbc tiing chvong frlnh Dock Protein (ZDock). Qud frinh ndy dvpc tiln hdnh tvong t^ doi vdi 05 md hinh d u tnic chu^ polypeptide da dvgc xay dyng thdnh cdng d bvdc fren vdi phdn td dgc t l 1yi5 d l cho ra mdt tdp hgp d c pose eho tdng tnrdng hpp rieng re.

HOI NGHI KHOA HQC C 0 N G N G H £ S I N H H P C J

BS aanh g i i chit linmg cic mO hinh iiSn f'-fl'^'i""^*''^ h m i c ^ o s l (k.4u gSn) c6 mm: de, gSn t6t nhSt cho dijng chucrng trlnh Process P?=^ l^DK*) nhSm tim ra mp^ * " m ' , ; , „ , „ j j ^ ^ g i j ,^ - R M S D cutofT, phi-c h$ polypepfide »a doc to a-Cbbi ^Sc thong s ° d i / 7 c t n « P ^^ ^.^^ _.^^ ^^^^p 1,^^ ^ ^ ^ ^^ ,^p ^^^

•Ligand/receptor binding ste resKjues trong bSng thong ^d para ^ , ^ ^ ^^ ^^^ .^^ ^.^^ ^ ^ , ^ j , cSo pose thda man cac dl4u kien sSng loc va loai ^ ' f ^ ^ ^ ^ „ „l^ <,ac pose thda man diiu ki»n nhim tim ra pose g,an thao tSc vdi pSc pose l « n g du ^ u M B r i ^ D o c U r o n T w Wnh "Relihe Docked Pn^tains (RDock)" cdc pos. , cd mirc dO g«n t6l .ru n h i i Ap dgng » " • ' ' ° * " ? ° ° * ™™ s» dung lam dir ll^u ngudn d * tiin hSnh sang loc lin hai duyc iva choh sau khi ch,y " P ' d ^ ' ^ P ° f f RD«k t'h.^ hSn hai g S doan chinh d i t i , iru hda v i nang lu'ong ttnh ai«„

nhim tim ra pose cd mtrc dd gin t i l mi nhit. R p « k t h « ; henna g , ^^^ ^^^ 1^. ^ ^ vi nang lirpng desolvate hoa. Tijna si^it hai giai doan ta ml hjia 9 ^ ^ ^

^ p T H h t X ^ ' d r S S ^ v l ^ l n X g l n r P h r h?cd cm s i ^ O O C K cao nhit I . oiu t ^ c gin vdi „ nhidn nhit frong tgp hpp d c phdc hg ttiu dvgc.

Hinh 4: Pose 546 (ModBl2_a7) vdi Rdock score cao nhSt

K i t qud ddnh gid chit Ivg^g cua mfl hinh phdx: hg polypeptide vd dgc to

Cdc chuli polypeptide dvpc tien hdnh tvong ty nham tim ra pose t l i vu nhat cho kilu tvong tac giira cdc diuS polypeptide vdi dgc t l Sau qud trinh Refine Docked Prciteins (RDock). hrong dng vdi moi phirc h | ta thu dvpc inSl pose vdi chi s6 RDOCK cao nhit. Cde pose ndy dvgc sd dung d l tiln hdnh md phdng dgng hoc phdn td bang chwang frInhStandardDynamiesCascade. 5 pose ttiu dygc la pose 112, pose 546, pose 1, pose 81^ pose 319 Idn Ivpt tuong dng vdi cdc phdc hg tgo hot polypeptide dd thtIt ke h> modeM a7 din model5__a7 vdi dpc to a-Cbbt. Kit qud^da qid frlnh md phdng dgng hpc phan td dvpc tdp hpp va so sanh nham tim ra phirc hg d mdc nang lvpng nhd nhat, tvcng dng vdi phdc hg cd d u tnic In djnh nhit.

Bdng 3: Kit qud Standard Dynamics Cascade

Name

Pose 112 IWodel 1 Pose 546 Model 2 1 P o s e l Model 3 : Pose 81 Model 4

; Pose 319 Model 5 , Forcefield

CHARMm 1 CHARMm CHARMm j CHARMm 1 CI^ARMm

Initial Potential Energy (kcal/mol) _ -201.53991 -134.18491 -188.11698 -169.86669 -44 23239

Total Energy (kcal/mol)

:• 1196.57335 ,1127.26047 1193.63415 1195.70098 1234 20487

Potential Energy (kcal/mol) 335 92924 282.25970 306.62756 351 95257 344.44492

"•m

Kinetic ^i Energy (kcal/mol) 860 64412 845.00076 S67.00659 843.74841 889.75995

Kit qud md phdng dgng hgc phdn td "Standard Dynamics Cascade" cho thay, sy khdc bigt v l mdc nang lvpng ting s cua d c phdc hg la khdng Idn. Dilu nay cd thi giai thich Id do cac chudi polypeptide d trtnh ty tvong <5oi ngin vddl tvong ding cao. Do dd, khdng anh hvdng nhieu tdi mve nang lypng ting so chung d a toan bg phdc h|. Ddy cungJ mgt nhvgc diim ciia viec nghien cvu thilt k l d c do^n peptide vdi kich thvde nhd, do sy khdc bigt Id khdng dit Idn a khing d|nh tinh w g t trgi v l mat tvong tdc ai lyc. Ngoai ra, mdt t^ do phai ke d i n Id gidi hgn cua eac phdp tinh todn dij"

trdn cdc mfl hlnh ly thuyet. Ttieo mgt nghien cdu ciia Plewczynski vd cgng sy, do chinh xdc cita cac phin mim in phdng d u friic, phin mim md phong tvong tac phdn tv cho dii Id tit nhit nhv eHiTs, Gold, Dock... trong vi§c ngWft cdu md phdng clu tnic cOng chi dat 60% (Plewczynski et al, 2011). Hon nva, vigc tinh loan d l tim ra cdc kilutir^

ldc tli vu diu chi dya tren cdc ham tinh diem vdi nhieu nhat hai tnang ba chi tieu ddnh gid dd Id. kha ndng phdn bigt i

logi lidn k i t d v) b i g i n , k h a n d n g d y d d n di l y c lign k i t c i i a cae phoi t v v d kha n a n g s a n g Igc b> m d t c o s d d d ligu I d n ( H u a n g et a l . . 2 0 1 0 ) . V I v d y , d n d s y k i t h p p gii>a nghidn c i r u ttiyc nghigm va n g h i d n ciru tinh t o d n ly t h u y l t K i t q u a t h u d v p c frong b a n g frgn v d i p h i r c h g cOa model2_a7 gan v d i d d c t o a - C b b d m i r e nang I v p n g t i n g s o n h d n h i t Id 1127.26^ kcal/mol. D o d d , c h u l i polypeptide m o d e l 2 _ a 7 d y p c l y a c h g n d l b i l u h i g n v a nghidn c v u ho9t b'nh s i n h hpc trong d i e u kign p h d n g t h i n g h i g m . K i t q u d nay b v d c d i u kharig d j n h vigc nghien c d u s v d y n g v a l a m c h u p t i i n m i m Discovery Studio 2.5 d o A c c e l r y s phat t r i i n d y a fren b d p h i n m i m noi tiing Insight-ll fren h g t h i n g workstation S G I . K£T LUAN

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DESIGN A POTENTIAL POLYPEPTIDE CHAIN FOR HIGH-AFFINITY BINDING TO ALPHA-COBRATOXIN USING DISCOVERY STUDIO 2.5

N g u y e n H o n g T h a n h \ I r a n L i n h T h u o c ^ T r v o n g N a m HaP*

^ Insbtute of Biotechnology - VAST

^ University of Sciences - Ho Chi Mmh National University SUMMARY

In recent years, using bio informatics techniques for research and development of vaccines and drugs have b ^ rapidly developed. In the current study, our objective is to develop a polypeptide chain which can specifically bind to the alphiM:obratoxin (a-Cbtx) of Naja kauthia venom. Five difTerent polypeptide chains have t>eea modeled using Discovery Studio 2.5%ased on the sequential similarity with the templates (1KC4, 1L4W, 2BG9, 2QCI). With more than 80% of similarities al the specific region, the homologous models were supposed to be structurally similar with the templates The polypeptide chains were then rigidly docked to a-Cbtx at the specific binding-site to form the polypepride-a-Cbtx affinity bindmg complexes. These complexes were simultaneously validated and energy miniimzed by dynamic modeling using programe Standard Dynamic Cascade integrated in Simulation module.

The best complex has been chosen from which their total energy was lowest The result shown that the complex of polypeptide chain named model2_a7 with a-Cbtx had lowest total energy at 1127,26 kcal/mol. The model2_a7 was then selected for further empirical research using biological testing methods.

Ke)'H'ords: snake venome, Naja kautlua, polypeptides, a-Cbtx, modeling. Discovery Studio.

' Conesponding Author. Tel" +84 4 37562790; Email tnhal@Jbt.ac vn.