KHAO S A T V A I TRO CUA LIEN KET HYDRO TRONG HOAT TINH
•
XUC TAC CD38 VA MOT SO THE DOT BIEN
HOANG THj HOA, DANG IJ^NG VAN Trung tim Lfng dpng tin hpc trong hda hpc, Dai hpc Khoa hpc tp nhien, Dai hpc Qude gia Hi Npi
SUMMARY
Using the docking softwares integrated molecular mechanics and quantum mechanics the hydrogen bonds map (HDM) ofligands in CD38 and E226- and El46- mutants have been calculated. There is an evidence to prove the existence of relationship between HDM and catalytic activities. The calculation also shown that the docking calculation could give useful information to studying protein-ligand com- plexes.
I. Md DAU Trong nhQng nghign cQu trudc day [1,2], blng vigc
Qng dpng cac phan mdm kdt hpp ed hpc lupng tQ va Cd hpc phan tQ, chung tfli da tfnh toan dp bao Inh hudng ciJa dflt bidn gen ddn tfnh ehlt xuc tac cua CD38 tu nhign va cac thd dflt bidn eua nfl. TQ dd da gia djnh rang lign kit hydro cd vai trd chi phfl'i dac tinh xuc tac cija cac enzym. Tuy vay, vigc khao sat lign kdt hydro mdi chl dQng d mflt sd nhflm chQc d$e trQng cua phfl'i
tQ nhQ nhdm OH eiJa ribosyl ma trong thpe te lign ke't hydro vln eo thd hinh thanh d cac nguygn td am dign khac nhQ N. Bai bao nay trlnh bay nhQng kdt qui khIo sat ky ludng hdn vd lign kg't hydro giQa CD38 va cae thd dflt bien vdi cac phfl'i tQ ed lign quan nhIm khIng djnh vai trd cua lign kg't hydro ddn hoat tfnh xuc tac cua CD38.
II. DOI TtfONG VA PHUONG P H A P N G H I E N CtfU NhQ da big't [3], CD38 la mflt protein, khflng chl la
khang thd ma efln cd hoat tfnh xuc tac cho phln Qng vdng hfla va thijy phan nicotinamit adenine dinueleotit (NAD). Trong qua trlnh xuc tac eua CD38 chl cd mflt phln tham gia trpc tidp vao phln Qng dd kdt hpp vdi Cd chit gpi la "tam hoat dflng". Clu tao dac bigt eiJa tam hoat dflng quyg't djnh tinh dae higu va hoat tfnh xuc tac cua CD38. Tam hoat dflng cua CD38 tp nhign va cac thd dflt bidn gdm cfl 10 axitamin sau; Arg127, Asp155, Glu146, Glu226, Lys129, Ser126, Ser193, Thr221, Trp125 va Trp 189. Vigc thay thd mflt vai axi- tamin trong tam hoat dflng cija CD38 nhu Glu146 va Glu226 bdi cac axitamin khac lam thay dfl'i vd cd bin
hoat tfnh xuc tac eua CD38 [4,5].
PhUdng phap nghign cQu gdm cac budc nhQ sau:
- xay dpng cae thd dflt bien blng each thay thd Glut46 va Glu226 trong tam hoat dflng eua CD38 va tfl'i QU hinh hpc sin phlm thu dupe trgn phln mdm Hyper- chem 7.5 [6], What if [7] va Svifiss-PDB Viewer [8].
- SQ dpng phln mdm Quantum 3.3 |9] dd gin kg't CD38 va cac thd dflt bidn vdi cac phfli tQ thfch hpp, tQ dfl xac djnh bin dd lign kdt hydro cija cac phfl'i tQ khac nhau tham gia vao phln Qng xuc tac eua CD38 vdi cac axitamin trong tam hoat dflng cija CD38 va cac thd dflt bidn.
III. K E T QUA VA THAO L U ^ N
1. Dflt bien gen CD38 va to'i lAi h i n h hpc. cija tdng blnh phQdng sai khac trung blnh tpa dfl eua Khi so sanh clu true dflt bidn thu dQpc tQ ba phln ^^c nguygn tQ cua thd dflt bidn va 1yh3 la r l t nhfl, mdm Hyperchem 7.5, What if va Sw/iss-PDB View/er chQng td khflng cfl sp sai khac nhidu giQa clu true 1yh3 vdi cau true CD38 gfl'c (ma trong ngan hang dQ ligu gfl'e vdi cae clu true dflt bidn. Kg't qui gia trj RMSD protein PDB la 1yh3) ddu cho gia trj RMSD (A") tQc can dQpc trinh bay trong bing 1.
H6a hpc & tfng d u n g
5 ^ 2 4 (ioS)/20og
<m
Bing 1: So sanh cS'u true i()\ biS'n gen bang ba ph^n m^m vdi 1yh3 Th^
dot bie'n E146A E146D E146F E146G E146K E146L E146N E146Q E226D E226G E226Q
RMSD (A°) Hyperchem
0.0004 0.0002 0.0014 0.0002 0.0003 0.0004 0.0007 0.0014 0.0017 0.0005 0.0006
What if 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
Swiss-PDB Viewer 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340
Gia trj RMSD khi so sanh c l u true dflt bidn bdi cac phln mdm vdi clu true 1yh3 gdc cung dQdc tfnh toan trgn What if. What if khflng so sanh sai khac tpa dfl 6 vj trf dflt big'n ma lai so sanh tpa dfl eua cac nguygn tQ cac axitamin khflng thay thd. Vi v l y each thQc sd sanh nay chQa lam ro dQpe vai tro eua dflt bidn ddi vdi hoat tfnh xuc tac cua protein. Dd cd thd Ipa chpn dQpc phln mem tfl'i Qu, chung tfli da thQ g i n kdt nicotinamit ribozd monophotphat (NMN) Ign 3 clu hinh dflt bidn eua CD38 nhan dQpc tQ 3 phln mdm trgn va so sanh clu true thu dQpc vdi thpe nghigm.
Bing 2: NSng lU^ng gS'n kS't NMN vdi cac t h l dgt bie'n E226G
Ph^n m^m
Egin k{t
Hyperchem 7.5 -34.5400
What if -35.6012
Swiss-PDB Viewer -36.1286
^^m
Hyperchem What if Swiss-PDB Viewer
Luih 1: So sanh cau hinh NMN thi/c nghiem vdri cac ca'u hinh thu difcjfc khi gin ke't NMN vdri cac the dpt bien thu difcjfc tuf ba phan m^m
Cac ke't qua tfnh toan cho thay cau true dflt bidn thu dupc tQ Swiss-PDB Viewer cho nSng IQpng g i n ke't phQc phfl'i tQ - protein am nhat va RMSD la nho nhat.
Do do, trong cac tfnh toan gin ke't blng Quantum nen sQ dgng cau true dflt bien thu dQpc tQ Swiss-PDB Viewer.
2. Gdn ke't pho'i tu" len protein
SQ dpng phan mem Quantum [9] da thu dQpe ket qua kha phu hpp vdi thpe nghigm. Tuy vay, kdt qua tinh lai php thufle kha nhieu vao vigc chpn tam hflp gin ke't gidi han khflng gian djnh vi phfl'i tQ trong vung tam hoat dflng cija enzym (dQdi day gpi t i t la tam iQdi).
De khao sat ky hfln ve dfl chfnh xac eija Quantum 3.3, nhQng tinh toan gin ke't dQpe thpe hign vdi cac hg phQe pho'i tQ - protein: 2hct, 2o3q, 2o3r, 2o3s, 2o3t va 2o3u.
Cac tfnh toan nay cho ddng thdi n5ng lupng gin kdt phfl'i tQ - protein va gia trj RMSD so vdi toa dfl nguygn tQ cua cae phQc tQdng Qng dQpe xac djnh tQ thpe nghigm dung de xac dinh dfl tin cay cua phln mdm.
Chung tfli da tinh nang lupng gin kgt eua phQc phfl'i tQ - protein vdi cae each chpn tam iQdi khac nhau. Kdt qui dupe trlnh bay trong bing 3.
Bing 3: NSng \\Ji)ng gin kg't va RMSD cua mgt s8' phijfc phfi'i tiy - protein vofi cac cich chpn tam lifi}i khac nhau
PhiJc 2hct 2o3q 2o3r 2o3s 2o3t 2o3u
PhJ'l til NMN CXR 1 CXR CXR CGR NGD
Slf nguyen tiir trong ph(S'l tiir
36 54 54 54 56 45
Etiii<
-43.2520 -37.1946 -31.4087 -36.9169 -37.0485 -32.1207 -37.5022 -40.8993
•37.8531 -39.5759 -50.9927 -42.9607
RMSD 0,6842 1.0825 2.5935 1.8834 0.3198 1.8041 0.4260 2.7533 7.4275 1.7534 1.3438 4.9116
ram \\s6\
T3m hlnh hgc 0 vbnji 5 c?nh
T3m hlnh hoc N vong 6 cjnh T3m hlnh hoc 0 giiJa 2 P Tam hinh hgc N vbng 6 canh
TSm hinh hoc 0 ciia nh(5m OH
T3m hlnh hoc N vong 6 canh
Tam hlnh hpc la didm ed toa dfl la trung binh toa dfl eua cac nguygn tQ protein trong vung tam hoat dflng (active site). TQ blng trfln chung tfli nh|n thly ndu chpn tam IQdi la tam hinh hpc thi RMSD thQdng la nhfl
m Hoa h p c & tfng d u n g
Si 2 4 (ioS)/20og
nhlt efln nang IQpng gin kdt khflng phli trong trQdng hpp nao cung am nhlt. Vfli 2o3t, chpn tam IQdi la 0 cua nhdm OH cho RMSD nhd hdn va nang IQpng gin kg't am hdn khi chpn tam IQdi la tam hinh hpc. Ngoai 2o3q, cac phQc cdn lai deu thfla man ndu chpn tam ludi la tam hinh hpc thi sai sd tpa dfl cua phfl'i tQ vdi thpe nghigm la it nhlt va nang IQpng g i n kdt eua phQc phdi tQ - protein cung la nhd nhlt. Do dd khi tinh toan gin ket diing Quantum, vdi nhQng protein chQa CO sd ligu thpe nghigm de so sanh, ngn chpn nhieu tam IQdi khac nhau de tim ra diem thfla man nang lupng gin kdt cua phQc phfl'i tQ - protein am nhlt va RMSD nhfl nhlt.
NhQvgy, sau khi thpe hign phep tfnh toan vdi phln mdm Quantum cho nhidu hg khac nhau da cho phep chung tfli cfl mflt sfl nhan xet sau:
NSng IQpng gin kdt phdi tQ - protein va RMSD php thufle rlt Idn vao vigc chpn tam iQdi dae bigt la vdi cac phfl'i tQ cfl chuoi dai va linh hoat. Ng'u chpn tam IQdi tfl't thl kdt qui cho nang IQpng vQa nhd va sai sd so vdi thpe nghigm cung khflng dang kd.
Khi tinh toan gin kg't phfl'i tQ - protein cln cfl dQ ligu thpe nghigm dd kidm chQng, ndu khflng, ngn ed cac
phln mem tfnh toan khac ed cung chQc nang dd so sanh kg't qui thu dupe.
3. CoT che hoat tinh xuc tac cua CD38 va cac the dot bid'n va vai tro cua lien kg't hydro
De khIo sat ed chd hoat tfnh xuc tac cija CD38 va cac thd dflt bidn, chung tfli da tidn hanh phep tinh toan theo ba budc sau:
Budc 1: Thpe hign qua trlnh gin ket NAD vao tam hoat dflng de tao phQc Miehaelis trong CD38 tp nhign va cae the dflt bien eua no.
Budc 2: SQ dpng ky thuat gin ke't minh blng each tach rfli dufli NA va gin ket phln ion trung gian ADPRI cdn lai vao protein tao ra phQc ehlt trung gian-enzym.
Budc 3: xay dpng "bin dd" lign ket hydro giQa cae phfl'i tQ va CD38 cung cae the dflt bien. TQ dd phan tfch vai trfl cua lign kdt hydro trong hoat tinh xuc tac cua CD38.
Rigng vfli cae phQc cija thd dflt bien El46, do chQa cfl cae dQ ligu clu true tinh thd trong nggn hang dQ ligu protein (Protein Data Bank) ngn trudc khi thpe hign bQdc 1 cln dflt bien blng cac phln mem What if ho$e Swiss PDB Viewer.
Bing 4: Bin dS lien k^t hyflro giiTa NAD vdi cac axitamin trong tam hoat HQng cua CD38 va t h l HQt biCTn E226Q
Thd dot bie'n E226Q
CD38
Nguygn tijr cija NAD
OvongS 0 0.i.P).
NvongS OvflngS
0 0..(P) NvongS
DO dai li£n kg't hydro ( A' )*
Glu^"^
(0) 3.66
2.89 Glu^^*
(0)
3.25 Gln"^
(0) 2.20
Trp^2=
(0)
3.01 Ser^^^
(0)
3.19
3.08 Arg'^'
(N)
3.47
2.95 Lys'^'
(N)
3.31
3.12 Asp'^'
(0)
3.53
3.13 Thr^^^
(N)
3.06 3.16
3.26 3.42 Khoing cich giOa liai nguySn tit im di$n.
Hoa hpc & tfng d u n g
Si 2 4 (ioS)/20og
m
Bang 5: Bin dd llSn kS't hydro gliTa ADPRI vdi cdc axitamin tam ho^t dOng cua CD38 va cic t h l dQt blln Thl
dgt bie'n CD38 E226Q E146A E146D
E146F
E146G E146L
E146N
Nguygn tiir cua ADPRI OH_ribosyl OH ribosyl
0 ( P ) OH_ribosyl
0 ( P ) Ov6ng5 OH_ribosyl
0 ( P ) 0 ( P ) OH_ribosyl
0 ( P ) OH.ribosyl
0 ( P )
DO dai lien ke't hydro Glu'^'
(0) Glu"^
(0) 3.57 3.04
3.03 3.06
2.69 3.11
2.69 2.89
2.86 3.10
Gln^^^
(0)
2.73 Trp'^^
(0) 1.42 3.09
2.87
2.62 3.15(N)
3.38
3.04 3.18(N)i
Ser'^' (0)
3.13 3.41
3.21 A r g ' "
(N)
3.30 3.18
2.89 3.03
3.12 3.47 2.87
2.87 3.16
A ' ) * Lys'^
(N)
3.08 3.38
A s p ' "
(0)
3.52 3.57
Thr^^' (N)
3.35:3.11/
3.47
3.12(0)
3.54 3.05:3.19;
3.46/3.26
3.15:3.20 (0) + Khoing cich giOa hai nguySn tCf im di$n.
NAD-CD38 NAD-E226Q
3.25: d(3 dai IkHydro 3'-0H-0 (Glu226) 2.20: di5 dai IkHydro 3'-0H-0 (Gln226) 2.89: d(5 dai IkHydro 2'-0H-0 (Glu146) 3.66: dd djli IkHydro 2'-0H-0 (Glu146)
Hlnh 2: NAD va tSm hoat dOng trong phtfc cua NAD vdi CD38 t\f nhign va E226Q
O)) Hoa hpc & tfng dung
Si 2 4 (ioS)/2oog
Dd danh gia Inh hQdng cua sp thay thd Glu226 bdi Gln226, Chung tfli da so sanh cac khoing each ngIn nhlt ciJa cae nguygn tQ trong phQc phfl'i tQ - protein giQa NAD vdi CD38 tp nhign va phQc E226Q. Cd the thly ring NAD ed thd tien gin hdn tdi Gln226 eua E226Q so vdi Glu226 cua CD38 tp nhign {Hlnh 2).
Vi khflng cfl mflt lign kdt hydro nao giOa 2'-3' OH ribosyl vdi Gln226 ngn du NAD ed thd tien sau vao vung tam boat dflng cua the dflt bien E226Q thl nfl cung ft bj gin chat vao tam^hoat dflng do dd loai trQ cac hoat tinh xuc tac cua the dflt bidn.
Khi gin ket ADPRI vao CD38 va E226Q thl kieu gin ket ciJa ADPRI trong CD38 tp nhign hoan toan khac so vfli kieu gin ket eua nfl trong E226Q. VI vay cac thd dflt bien cija Glu226 lam mlt hoan toan hoat tinh xuc tac [4].
Graeff va cac ddng nghigp [5] da ehl ra ring mflt sd thd dflt bidn Glut 46 lam tang hoat tinh vong hoa va Qc chd hoat tfnh thuy phan. Kdt qua tfnh toan ap dpng cho cae phQc^vdi cac thd dfl,t bien El46 cho thly eo nhQng thay ddi ed bin vd kieu gin ke't cija chat trung gian do co sp thay the Glu146 blng nhQng axit amin khac. Trong CD38 tp nhign, ADPRI dQpe lam ben bdi 4 lign kg't hydro giQa nhdm ribosyl 2'- OH va 3'- OH vdi Glu146 va Glu226. Tuy nhign vdi^E146A, khflng ed mflt lign kg't hydro nao. TQ dd ed the nhgn^thly ndu nhflm ribosyl cang bi giQ ch§t bdi cae lien kdt hydro thi hoat tfnh thuy phan NAD cang Idn va hoat tinh vdng hfla cang nhfl.
NhQ vay, nhQng tfnh toan gin ke't da cunp elp cae thflng tin hfju feh dfl'i vfli vigc dp bao mQc dfl anh hudng cua lign kg't hydro va dflt bien gen den cic hoat tfnh xuc tac eua CD38 tp nhign.
TAI LI5;U THAM KHAO
1. Oang ling Vgn, Tap chf Hoa hpc, T46 N2 (2008) 188-194.
2. Dang Ung Van, Nguyen Hoa My, Hidemi Nagao.
Joint Symposium on Computational Chemistry. Abstract.
Hanoi 21-22 December 2007. p 24.
3. Ferrero E., Malavasi F. (1999). J. Leukocyte Biol.
65 151-161.
4. Lee, H.C. (2006) Mol. Med. 12 (11-12) 317-323.
5. Graeff, R., Liu, Q., Kriksunov, I.A, Hao, Q. and Lee H.C. (2006) J. Biol. Chem. 281 28951-28957.
6. HYPERCHEM7.5TM Release 7.5 for Windows Molecular Modeling System Copyright @20Q2 Hyper- eube,lnc.
7. http://swift.embi.ru.nl/servers/html/index.html.
8. http://swissmodel.expasy.0rg//SWISS-MODEL.html.
9. QUANTUM 3.3 Docking/Library Screening Soft- ware 2007. ©
NgiMphdn bifn: GS, TS LAM NGQC THIEM cac tac gil elm dn BQ Khoa hgc va COng nghg da tai trp cho cOng trlnh
thflng qua fld tai khoa hgc ctf bin 507206.
NGHIEN cufu T H A N H PHAN HOA HOC...
(Tiip theo trang 48)
IV. KET LU4N
TQ djch chig't rd cay hQdng bai mpc hoang b HQdng ehlt nay la p-sitosterol va p-Sitosterol-3-O-p-D- Sdn - Ha Tinh blng phQdng phap sic ky da tach dope olucoovranosit CAc hon rh^t nAv l^n Aiu tign rtirnr hai hpp chit. Blng phQdng phap phd UV, IR, MS va Q'^jcopyranosit. Lac npp enat nay lan dau tign dupe NMR da xac djnh dQpc clu true hda hpc cua hai hpp phan lap tQ rg egy hodng bai {Dianella ensifolia L).
TAI L i e u THAIVI KHAO
1. Vign Khoa hpc va Cflng nghg Vigt Nam, Danh ipc Hat Yai, Thailand.
cic loii thuc vit Vi§t Nam, Nha xult bin Nflng nghigp Ha Nfli, 2005.
2. D5 Tit Lpi, NhQng ciy thud'c vi vj thud'c Vi$t Nam, Nha xult bin Y hpc. Ha Nfli, 2001.
3. V. Lojanapiwatna, K. Chaneharoen, K. Sakarin and P. Wiriyachitra, Chemical constituents of Dianella en- sifolia Redoute., (1982), Prince of Songkia University,
4. Dictionary of Natural product on CD-Rom, Chap- man and Hall-CRC (2005).
5. Kojima H., Sato N., Hatano A., Ogura H. (1990), Sterol glucosides from Prunella vulgaris, Phytochemistry, 29, pp. 2351-2355. ©
NgiMphdn bifn: PGS, TS NGUYEN D A N G QUANG
Hoa hpc & tfng d u n g
Si 2 4 (ioS)/20og
