Short Title: Cellular Off-Target Binding and Drug Adverse Reaction

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.

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

Plasticity deficit

0.6231

Ischaemic neurodegeneration

0.6082

Glutamatergic dysfunction

0.6042

Hypoxia hypoglycemia

0.6033

Dendrite injury

Excitotoxic disorder

Long-term depression (LTD) deficit

Stroke ischemia

Synaptic homeostasis

Hypoxia ischemia

GABAergic deficit

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