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 / GluN2BILE / 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 RC1Plasticity deficit
/0.6231
/ 9.88E-04 / Shipton OAPaulsen O2Ischaemic neurodegeneration
/0.6082
/ 1.79E-03 / Robert F,Bert LStoppini L3Glutamatergic dysfunction
/0.6042
/ 2.09E-03 / Coyle JT4Hypoxia hypoglycemia
/0.6033
/ 2.17E-03 / Perez-Velazquez JLZhang L5Dendrite injury
/ 0.5953 / 2.96E-03 / Monnerie H,et al.6Excitotoxic disorder
/ 0.5943 / 3.07E-03 / ForanE Trotti D7Long-term depression (LTD) deficit
/ 0.5678 / 8.35E-03 / Liu X,et al. 8Stroke ischemia
/ 0.5538 / 1.40E-02 / Yu G, et al.9Synaptic homeostasis
/ 0.5535 / 1.41E-02 / Turrigiano G10Hypoxia ischemia
/ 0.5584 / 1.57E-02 / Cereb J11GABAergic deficit
/ 0.5448 / 1.93E-02 / Abekawa T,et al.121.Nicoll RA, Malenka RC. Contrasting properties of two forms of long-term potentiation in the hippocampus. 1995.
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