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Non MedChem-Friendly SMARTS

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Structural alerts or "toxicophores" are substructures found in chemicals that are highly correlated with undesirable properties typically associated with human or environmental toxicity. A number of studies over the past 20 years have provided descriptions of individual chemical substructures associated with particular pharmacological endpoints, typically in the format of a Daylight SMARTS description. Moreover when such substructures are used to filter medicinally unfriendly compounds out of the drug discovery pipeline, a significant reduction in compound failure rates in the clinic has been observed. For a comprehensive and freely accessible source of structural alerts please go to the OCHEM toxalerts database.

Below are the SMARTS descriptions used by SureChEMBL that would indicate whether a compound would match one or more structural alerts and hence considered to have a MedChem unfriendly status.  

Chemical_GroupSMARTS
2,2-dimethyl-4,5-dicarboxy-dithiole C1(C)(C)SC(C(=O)O)=C(C(=O)O)S1
2,3,4_trihydroxyphenyl c([OH])c([OH])c([OH])
2,3,5_trihydroxyphenyl c([OH])c([OH])cc([OH])
acid_anhydrides C(=O)OC(=O)
acid_halides [S,C](=[O,S])[F,Br,Cl,I]
Acridine c1c2cc4ccccc4nc2ccc1
Active_Phosphate P(=S)([OH1,O$(O[#6])])([OH1,O$(O[#6])])[S,O]
acyl_cyanide C(=O)-C#N
Adjacent_Ring_Double_Bonds [*;R]=[*;R]=[*;R]
Aldehyde [#6][C!H0]=O
Aliphatic_Triflate COS(=O)(=O)C(F)(F)F
AlkylEnamine [C;H1$(C([#6;!$(C=O)])),H0$(C([#6;!$(C=O)])[#6;!$(C=O)])]=[CH1]!@N([#6;!$(C(=O))])[#6;!$(C(=O))]
Allene *=C=*
Alpha_Halo_Carbonyl [C;!$(C[N])](=O)!@[C;h1,h2;H1,H2][F,Cl,Br,I]
amidotetrazole c1nnnn1C=O
Amino_Naphtalimide c1(N)ccc(C(=O)NC3(=O))c(c3ccc2)c21
Aminonitrile NC#N
Anhydride [#6]C(=O)OC(=O)[#6]
Any_Carbazide O=*N=[N+]=[N-]
aromatic_azides cN=N=N
Azanitrone N=[N+]([O-])C
azoalkanals [N;R0]=[N;R0]CC=O
Azobenzene c1ccccc1[N!r]=[N!r]c2ccccc2
Azocyanamide [N;R0]=[N;R0]C#N
b-Carbonyl_Quaternary_Nitrogen C(=O)CC[N+,n+]
benzylic_quaternary_nitrogen cC[N+,NX4]
beta-carbonyl_quaternary_nitrogen C(=O)C[N+,n+,NX4,nX4]
Beta-Fluoro-ethyl-ON [C;H2$(CF),H1$(C(F)F)]!@[CH2][N,O]
biotin_analogue C12C(NC(N1)=O)CSC2
carbazides C(=O)N=N=N
carbodiimides N=C=N
CCl3-CHO_releasing C(Cl)(Cl)(Cl)C([O,S])[NX3]
Chloramidine [Cl]C([C&R0])=N
Conjugated_Dithioether SC(=[!r])S
Crown_Ether_12CRO4 O1CCOCCOCCOCC1
Crown_Ether_15CRO5 O1CCOCCOCCOCCOCC1
Crown_Ether_16CRO6 O1CCOCCOCCOCCOCCOCC1
crown_ethers [O;R1][C;R1][C;R1][O;R1][C;R1][C;R1][O;R1]
cyanamide N[CH2]C#N
Cyanophosphonate P(OCC)(OCC)(=O)C#N
Cyanohydrin N#CC[OH1]
di_and_triphosphates P(=O)([OH])OP(=O)[OH]
Diacetylene C#CC#C
Diazoalkane C=[N+]=[N-]
Diazonium_Salt [N+]#N
Diene C!@=[CH1]-C!@=[CH1]-[CX3](=O)
Dinitrobenzene_1 c1c([N+](=O)[O-])c([N+](=O)[O-])ccc1
Dinitrobenzene_2 c1c([N+](=O)[O-])ccc([N+](=O)[O-])c1
Dinitrobenzene_3 c1c([N+](=O)[O-])cc([N+](=O)[O-])cc1
disulfides [SX2][SX2]
Dithiocarbamate NC(=S)S
Dithiole-2-thione S1SC=CC1=S
Dithiole-3-thione S1C=CSC1=C
Dithiomethylene_acetal S[C;!$(C=*)]S
Enyne C=!@CC#C
epoxides,_thioepoxides,_aziridines C1[O,S,N]C1
ester_of_HOBT C(=O)Onnn
Flavin c1cccc(NC(=NC(=[N,S,O])NC(=O)3)C3=N2)c12
Fluorescein c1cc(O)cc(OC(=CC(=O)C=C3)C3=C2)c12
Fluorinated_Carbon_1 C(C(CF)F)F
Fluorinated_Carbon_2 C(C(F)F)(F)F
four_member_lactones C1(=O)OCC1
geminal_amines [NH1;!r][CX4][NH1;!r]
geminal_dinitriles N#CCC#N
halo-pyridine,_-diazoles_and_-triazoles [Cl,Br,I]c1[c,n][c,n][c,n][c,n]n1
hydrazothiourea N=NC(S)N
Imidazolium c1[n+]([#6])ccn1([#6])
Imine2 [#6,#8,#16]-[CH1]=[NH1]
imines_(not_ring) [#6][C;R0](=[N;R0,O0])[#6]
isocyanates_&_isothiocyanates N=C=[S,O]
isonitrile [N+]#[C-]
ketene C=C=O
Lawesson_Reagent_Derivatives P(=S)(S)S
methylidene-1,3-dithiole S1C=CSC1=S
Michael_Phenyl_Ketone c1ccccc1C(=O)C=!@CC(=O)!@*
N-halo [NX3,NX4][F,Cl,Br,I]
Nitrobenz-azadiazole_1 c1ccc(n[o,s]n2)c2c1[N+](=O)[O-]
Nitrobenz-azadiazole_2 c1c([N+](=O)[O-])cc(n[o,s]n2)c2c1
nitrosamine N-[N;X2](=O)
nitroso [N&D2](=O)
noname N1=C[S,NH1]C(=[C,N,P][C,N,O,P])C1(=O)
N-Oxide_aliphatic [N+!$(N=O)][O-X1]
N-S_(not_sulfonamides) [#6][S;O0][N;H0]
Orthoester C(O)(O)[OH]
o-tertbutylphenol c1c([OH1])c(C(C)(C)C)ccc1
Oxobenzothiepine C1(=O)C=CCSC=C1
P_or_S_Halides [P,S][Cl,Br,F,I]
p-Aminoaryl_diazo Nc1aaa(N!@=N)aa1
PCP PCP
paranitrophenyl_esters C(=O)Oc1ccc(N(=O)=O)cc1
pentahalophenyl c1c([F,Cl])c([F,Cl])c([F,Cl])c([F,Cl])c1([F,Cl])
pentafluorophenyl_esters C(=O)Oc1c(F)c(F)c(F)c(F)c1(F)
peroxide [#8]~[#8]
Phenanthrene c12cccc3c1c4c(cc3)cccc4cc2
phosphonate_esters [#6]P(=O)(~O)O[#6]
phosphoramides NP(=O)(N)N
phosphorane C=P
Phosphorus_Halide [S,P][F,Cl,Br,I]
Polyene C=!@CC=!@C
polyenes C=CC=CC=CC=C
polyene_chain_between_aromatics cC=CC=CC=Cc
polyines CC#CC#CC
Polynuclear_Aromatic_1 c1cccc(cc(cccc2)c2c3)c13
Polynuclear_Aromatic_2 c1cccc(c(cccc2)c2cc3)c13
Polysulfide *[SX2][SX2][SX2]*
Sulphur_Halide [#16][F,Cl,Br,I]
pyrene_fragments c1c2cccc3c2c4c(cc3)cccc4c1
Pyrylium c1ccc[o+]c1
reactive_carbonyls [C;!r](=[O,S])[S;!r]
reactive_carbonyls [C;!r](=[O,S])[CX2;!r][F,Br,Cl]
Ring_Triple_Bond [C,c;R]#[C,c;R]
S=N_(not_ring) [S;R0]=[N;R0]
Sulfonate_Ester O=[SX4](=O)OC
sulfonyl_cyanide S(=O)(=O)C#N
Sulphate_Ester COS(=O)O[C,c]
sulphonates COS(=O)(=O)[C,c]
Sulphur_Nitrogen_single_bond [SX2H0]!@[N]
Tetraazinane C1NNC=NN1
Thiocyanate SC#N
thioesters C[O,S;R0][C;R0](=S)
thioles_(not_aromatic) [!a][SX2;H1]
Thiophosphothionate P(=S)(-[S;H1,H0$(S(P)C)])(-[O;H1,H0$(O(P)C)])(-N(C)C)
thiourea [N;!r][C;!r](=S)[N;!r]
Three_Membered_Heterocycle *1[O,S]*1
Tri_Pentavalent_S [#16v3,#16v5]
Triacyloxime C(=O)N(C(=O))OC(=O)
Triazole c1cnnn1!@C!@[NH1][#6]
triflate OS(=O)(=O)(C(F)(F)(F))
Triphenyl_Boranyl B(c1ccccc1)(c2ccccc2)c3ccccc3
triphenylphosphines P(c1aaaaa1)(c1aaaaa1)(c1aaaaa1)
Triphenyl_Silyl [Si](c1ccccc1)(c2ccccc2)(c3ccccc3)
Vinyl_Halide [Cl,Br,I]C=[!O!R]
Vinyl_Sulphone [#6][CH1]!@=[CH1][S;H1,H0$(S(C)C)](=O)(=O)
sulphates [#6]S(=O)(=O)O
tropone C1C(=O)C=CC=CC=1
Oxime [#6]C(=!@N[$(OC),$([OH])])[#6]
hydrazone [#6]C(=!@NNa)[#6]
Nitrosone_not_nitro [$(N(~!@[#6])!@O);!$([N+]([O-])=O)]
Thiocarbonyl_group C=S
acid_anhydrides_2 [#6]C(=O)!@OC(=!@[N,O])[#6]
trifluroacetate_amide FC(F)(F)C(=O)N
triple_bond [#6]C#[CH]
Allene C=C=C
thiatetrazolidine [$(Sc1nnn[nH,n-]1),$(Sc1nn[nH,n-]n1)]
oxy-amide [#6]C(=O)!@C!@C(=O)N
formate_formide O=[CH][O,N][#6]
pyranone O=C1C=COC=C1
Coumarin c1cc2C=CC(=O)Oc2cc1
aminothiazole s1ccnc1[N!H0]
Thiazolidinone O=C1CSCN1
Thiomorpholinedione N1C(=O)CSCC1=O
oxepine O1C=CC=CC=C1
cyclobutene C1CC=C1
poly_sub_atomatic *!@c1c(!@*)c(!@*)c(!@*)c(!@*)c1
Isotopes [2H,3H,11C,11c,14C,14c,125I,32P,33P,35S]
Undesirable_Elements_Salts [Ac,Ag,Am,Ar,As,At,Au,Ba,Be,Bi,Bk,Cd,Ce,Cf,Cm,Cr,Cs,Dy,Er,
Eu,Fr,Ga,Gd,Ge,He,Hf,Ho,In,Ir,Kr,La,Lu,Mo,Nb,Nd,Ne,Ni,
Np,Os,Pa,Pb,Pd,Pm,Po,Pr,Pt,Pu,Ra,Rb,Re,Rh,Rn,Ru,Sb,Sc,
Se,Sm,Sr,Ta,Tb,Tc,Te,Th,Ti,Tl,Tm,U,V,W,Xe,Y,Yb,Zr]
Metal_Carbon_bond [#6;$([#6]~[#3,#11,#12,#13,#19,#20,#26,#27,#28,#29,#30])]
Aromatic_N-Oxide_more_than_one [n+][O-X1].[n+][O-X1]
Nitro_more_than_one [N+](=O)[O-].[N+](=O)[O-]
Cyano_gte_2 [C]-[CH0]#[NH0].[C]-[CH0]#[NH0].[C]-[CH0]#[NH0]
Chlor_or_Fluor_gte_5 [Br,Cl,F].[Br,Cl,F].[Br,Cl,F].[Br,Cl,F].[Br,Cl,F].[Br,Cl,F]
Phosphorus_More_Than_1 P.P
gte_2_N_quats [N,n;H0;+;!$(N~O);!$(n~O)].[N,n;H0;+;!$(N~O);!$(n~O)].[N,n;H0;+;!$(N~O);!$(n~O)]
gte_2_sulfonic_acid [C,c]S(=O)(=O)[O;D1].[C,c]S(=O)(=O)[O;D1].[C,c]S(=O)(=O)[O;D1]

Details presented within this documentation reproduced from:

ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions
Iurii Sushko, Elena Salmina, Vladimir A. Potemkin, Gennadiy Poda, and Igor V. Tetko
Journal of Chemical Information and Modeling 2012 52 (8), 2310-2316

 

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