Supplemental Information
Molecular Mechanisms Involved in the Side Effects of Fatty Acid Amide Hydrolase Inhibitors: A Structural Phenomics Approach to Proteome-wide Cellular Off-target Deconvolution and Disease Association
Short title: Cellular Off-target Binding and Drug Adverse Reaction
Shihab Dider1, Jiadong Ji2,3, Zheng Zhao4, Lei Xie3,5,*

1Department of Chemical Sciences, Hunter College, The City University of New York, New York, New York, United States of America

2Department of Biostatistics, School of Public Heath, Shandong University, Jinan, P. R. China

3Department of Computer Science, Hunter College, The City University of New York, New York, New York, United States of America

4National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health , Bethesda, Maryland, United States of America

5Ph.D. Program in Computer Science, Biology, and Biochemistry, The Graduate Center, The City University of New York, New York, New York, United States of America

*To whom correspondence should be addressed:

Figure S1.SMAP alignment score distribution for 40,491 non-redundant biological assemblies against FAAH inhibitor binding site. The histogram is fitted using Gaussian kernel density function.

RAT MSTMHLLTFALLFSCSFARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL 60

HUMAN MSTMRLLTLALLFSCSVARAACDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL 60

****:***:*******.*******************************************

RAT NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG 120

HUMAN NATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG 120

************************************************************

RAT LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRL 180

HUMAN LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYSWNHIILLVSDDHEGRAAQKRL 180

**************************************.*********************

RAT ETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLNM 240

HUMAN ETLLEERESKAEKVLQFDPGTKNVTALLMEAKELEARVIILSASEDDAATVYRAAAMLNM 240

*******************************:****************************

RAT TGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKEN 300

HUMAN TGSGYVWLVGEREISGNALRYAPDGILGLQLINGKNESAHISDAVGVVAQAVHELLEKEN 300

**************************:*********************************

RAT ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK 360

HUMAN ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFANYSIMNLQNRK 360

************************************************************

RAT LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTC 420

HUMAN LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTLSDGTC 420

******************************************************:*****

RAT KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA 480

HUMAN KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMNFTYEVHLVA 480

************************************************************

RAT DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI 540

HUMAN DGKFGTQERVNNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI 540

************************************************************

RAT LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA 600

HUMAN LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA 600

************************************************************

RAT LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP 660

HUMAN LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP 660

************************************************************

RAT EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA 720

HUMAN EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA 720

************************************************************

Figure S2. Sequence alignment of rat and human GluN1A subunit of NMDA receptor (Continue).

RAT VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH 780

HUMAN VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQNVSLSILKSH 780

************************************************************

RAT ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH 840

HUMAN ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH 840

************************************************************

RAT KDARRKQMQLAFAAVNVWRKNLQDRKSGRAEPDPKKKATFRAITSTLASSFKRRRSSKDT 900

HUMAN KDARRKQMQLAFAAVNVWRKNLQDRKSGRAEPDPKKKATFRAITSTLASSFKRRRSSKDT 900

************************************************************

RAT STGGGRGALQNQKDTVLPRRAIEREEGQLQLCSRHRES 938

HUMAN STGGGRGALQNQKDTVLPRRAIEREEGQLQLCSRHRES 938

**************************************

Figure S2. Sequence alignment of rat and human GluN1A subunit of NMDA receptor.

RAT MKPSAECCSPKFWLVLAVLAVSGSKARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFH 60

HUMAN MKPRAECCSPKFWLVLAVLAVSGSRARSQKSPPSIGIAVILVGTSDEVAIKDAHEKDDFH 60

*** ********************:***********************************

RAT HLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTL 120

HUMAN HLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQILDFISAQTL 120

************************************************************

RAT TPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQ 180

HUMAN TPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQ 180

************************************************************

RAT DFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYI 240

HUMAN DFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILLYCTKEEATYI 240

************************************************************

RAT FEVANSVGLTGYGYTWIVPSLVAGDTDTVPSEFPTGLISVSYDEWDYGLPARVRDGIAII 300

HUMAN FEVANSVGLTGYGYTWIVPSLVAGDTDTVPAEFPTGLISVSYDEWDYGLPARVRDGIAII 300

******************************:*****************************

RAT TTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHP 360

HUMAN TTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLSFSEDGYQMHP 360

************************************************************

RAT KLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVE 420

RAT KLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVTLEEAPFVIVE 420

************************************************************

RAT SVDPLSGTCMRNTVPCQKRIISENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYL 480

HUMAN SVDPLSGTCMRNTVPCQKRIVTENKTDEEPGYIKKCCKGFCIDILKKISKSVKFTYDLYL 480

********************::**************************************

RAT VTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSR 540

HUMAN VTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSR 540

************************************************************

RAT SNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSF 600

HUMAN SNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLADGREPGGPSF 600

************************************************************

RAT TIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYV 660

HUMAN TIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQEEYV 660

************************************************************

RAT DQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLS 720

HUMAN DQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFNQRGVDDALLS 720

************************************************************

RAT LKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAI 780

HUMAN LKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDSGWKRQVDLAI 780

************************************************************

Figure S3. Sequence alignment of rat and human GluN2B subunit of NMDA receptor (Continue).

RAT LQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEH 840

HUMAN LQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMALSLITFICEH 840

************************************************************

RAT LFYWQFRHCFMGVCSGKPGMVFSISRGIYSCIHGVAIEERQSVMNSPTATMNNTHSNILR 900

HUMAN LFYWQFRHCFMGVCSGKPGMVFSISRGIYSCIHGVAIEERQSVMNSPTATMNNTHSNILR 900

************************************************************

RAT LLRTAKNMANLSGVNGSPQSALDFIRRESSVYDISEHRRSFTHSDCKSYNNPPCEENLFS 960

HUMAN LLRTAKNMANLSGVNGSPQSALDFIRRESSVYDISEHRRSFTHSDCKSYNNPPCEENLFS 960

************************************************************

RAT DYISEVERTFGNLQLKDSNVYQDHYHHHHRPHSIGSTSSIDGLYDCDNPPFTTQPRSISK 1020

HUMAN DYISEVERTFGNLQLKDSNVYQDHYHHHHRPHSIGSASSIDGLYDCDNPPFTTQSRSISK 1020

************************************:***************** *****

RAT KPLDIGLPSSKHSQLSDLYGKFSFKSDRYSGHDDLIRSDVSDISTHTVTYGNIEGNAAKR 1080

HUMAN KPLDIGLPSSKHSQLSDLYGKFSFKSDRYSGHDDLIRSDVSDISTHTVTYGNIEGNAAKR 1080

************************************************************

RAT RKQQYKDSLKKRPASAKSRREFDEIELAYRRRPPRSPDHKRYFRDKEGLRDFYLDQFRTK 1140

HUMAN RKQQYKDSLKKRPASAKSRREFDEIELAYRRRPPRSPDHKRYFRDKEGLRDFYLDQFRTK 1140

************************************************************

RAT ENSPHWEHVDLTDIYKERSDDFKRDSVSGGGPCTNRSHLKHGTGEKHGVVGGVPAPWEKN 1200

HUMAN ENSPHWEHVDLTDIYKERSDDFKRDSVSGGGPCTNRSHIKHGTGDKHGVVSGVPAPWEKN 1200

**************************************:*****:*****.*********

RAT LTNVDWEDRSGGNFCRSCPSKLHNYSSTVAGQNSGRQACIRCEACKKAGNLYDISEDNSL 1260

HUMAN LTNVEWEDRSGGNFCRSCPSKLHNYSTTVTGQNSGRQACIRCEACKKAGNLYDISEDNSL 1260

****:*********************:**:******************************

RAT QELDQPAAPVAVTSNASSTKYPQSPTNSKAQKKNRNKLRRQHSYDTFVDLQKEEAALAPR 1320

HUMAN QELDQPAAPVAVTSNASTTKYPQSPTNSKAQKKNRNKLRRQHSYDTFVDLQKEEAALAPR 1320

*****************:******************************************

RAT SVSLKDKGRFMDGSPYAHMFEMPAGESSFAN-KSSVPTAGH-HHNNPGSGYMLSKSLYPD 1378

HUMAN SVSLKDKGRFMDGSPYAHMFEMSAGESTFANNKSSVPTAGHHHHNNPGGGYMLSKSLYPD 1380

********************** ****:*** ********* ******.***********

RAT RVTQNPFIPTFGDDQCLLHGSKSYFFRQPTVAGASKTRPDFRALVTNKPVVVTLHGAVPG 1438

HUMAN RVTQNPFIPTFGDDQCLLHGSKSYFFRQPTVAGASKARPDFRALVTNKPVVSALHGAVPA 1440

************************************:************** :******.

RAT RFQKDICIGNQSNPCVPNNKNPRAFNGSSNGHVYEKLSSIESDV 1482

HUMAN RFQKDICIGNQSNPCVPNNKNPRAFNGSSNGHVYEKLSSIESDV 1484

********************************************

Figure S3. Sequence alignment of rat and human GluN2B subunit of NMDA receptor.

Figure S4. Protein-ligand docking score distributions of FAAH inhibitors and decoys in the primary FAAH binding pocket.

Figure S5. Protein-ligand docking score distributions of FAAH inhibitors and decoys in the dimerization interface of GluN1a/GluN2B NMDA receptor.


Figure S6. RMSD of conformational trajectory MD simulation of BIA 10-2474 bound NMDAR.

Figure S7. Docking score distribution of NMDAR antagonists and FAAH inhibitors when docked to the NMDAR antagonist binding site.

Figure S8. Quantile-Quantile plot of gene-disease similarity score distribution against fitted EVD model.

Table S1. Amino acids involves in the dimerization interface of GluN1A/GluN2B NMDA receptor.

GluN1A / GluN2B
ILE / 519 / ILE / 515
ASN / 520 / ASN / 516
ASN / 521 / GLU / 517
GLU / 522 / SER / 520
ALA / 524 / GLU / 521
GLN / 525 / VAL / 527
LYS / 531 / PRO / 528
PRO / 532 / GLU / 531
TYR / 535 / THR / 532
TRP / 611 / SER / 555
GLY / 612 / CYS / 557
LEU / 614 / VAL / 558
LEU / 615 / MET / 561
ASN / 616 / MET / 631
TYR / 647 / SER / 633
THR / 648 / VAL / 634
ALA / 649 / TRP / 635
LEU / 651 / ALA / 636
ALA / 652 / PHE / 637
LEU / 655 / PHE / 638
VAL / 656 / VAL / 640
TYR / 692 / ALA / 644
ARG / 695 / SER / 645
GLN / 696 / THR / 647
PHE / 754 / ALA / 648
ARG / 755 / ASN / 649
SER / 756 / ALA / 651
LEU / 774 / ALA / 652
LEU / 777 / ILE / 655
LYS / 778 / ARG / 693
HIS / 780 / ASN / 694
GLU / 781 / ASN / 697
ASN / 782 / ASN / 698
GLY / 783 / PHE / 757
MET / 785 / ALA / 758
GLU / 786 / SER / 759
THR / 809 / THR / 760
CYS / 810 / GLY / 761
MET / 813 / ASP / 777
VAL / 816 / LEU / 778
PHE / 817 / ALA / 779
VAL / 820 / LEU / 781
GLY / 823 / GLN / 782
ILE / 824 / PHE / 784
GLY / 827 / GLY / 785
ASP / 786
GLY / 787
MET / 789
Table S2. Top 12 ranked phenotype associations of NMDA Receptor and their experimental supports
Disease Phenotype
/
Cosine Similarity
/
E-value
/
Experimental support
Long-term potentiation (LTP) deficit
/
0.6378
/ 5.47E-04 / Nicoll RA &Malenka RC1
Plasticity deficit
/
0.6231
/ 9.88E-04 / Shipton OAPaulsen O2

Ischaemic neurodegeneration

/

0.6082

/ 1.79E-03 / Robert F,Bert LStoppini L3

Glutamatergic dysfunction

/

0.6042

/ 2.09E-03 / Coyle JT4

Hypoxia hypoglycemia

/

0.6033

/ 2.17E-03 / Perez-Velazquez JLZhang L5

Dendrite injury

/ 0.5953 / 2.96E-03 / Monnerie H,et al.6

Excitotoxic disorder

/ 0.5943 / 3.07E-03 / ForanE Trotti D7

Long-term depression (LTD) deficit

/ 0.5678 / 8.35E-03 / Liu X,et al. 8

Stroke ischemia

/ 0.5538 / 1.40E-02 / Yu G, et al.9

Synaptic homeostasis

/ 0.5535 / 1.41E-02 / Turrigiano G10

Hypoxia ischemia

/ 0.5584 / 1.57E-02 / Cereb J11

GABAergic deficit

/ 0.5448 / 1.93E-02 / Abekawa T,et al.12

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12.Abekawa T, Ito K, Nakato Y, Koyama T. Developmental GABAergic deficit enhances methamphetamine-induced apoptosis. Psychopharmacology. 2011;215(3):413-27.