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Trabedersen

Trabedersen

Synopsis, Chemistry

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Also known as: Trabedersen [inn:ban], Unii-98oyr854ny, 98oyr854ny, Ap-2-09, Dna, d(p-thio)(c-g-g-c-a-t-g-t-c-t-a-t-t-t-t-g-t-a), 925681-61-4

Molecular Formula

C₁₇₇H₂₂₆N₆₀O₉₄P₁₇S₁₇+

Molecular Weight

5770 g/mol

InChI Key

HSWLVDBGZCETRH-UHFFFAOYSA-O

Trabedersen is a transforming growth factor (TGF)-beta2 specific phosphorothioate antisense oligodeoxynucleotide with the sequence 5'-CGGCATGTCTATTTTGTA-3', with potential antineoplastic activity. Trebedersen binds to TGF-beta2 mRNA causing inhibition of protein translation, thereby decreasing TGF-beta2 protein levels; decreasing intratumoral TGF-beta2 levels may result in the inhibition of tumor cell growth and migration, and tumor angiogenesis. TGF-beta2, a cytokine often over-expressed in various malignancies, may play an important role in promoting the growth, progression, and migration of tumor cells.

1 2D Structure

Trabedersen

2 Identification

2.1 Computed Descriptors

2.1.1 IUPAC Name

1-[5-[[[2-[[[2-[[[2-[[[2-[[[2-[[[2-[[[5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[2-[[[2-[[[2-[[[5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[5-(2-amino-6-oxo-1H-purin-9-yl)-2-[[[5-(4-amino-2-oxopyrimidin-1-yl)-2-(hydroxymethyl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(6-aminopurin-9-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(6-aminopurin-9-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-hydroxyphosphinothioyl]oxymethyl]-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-3-yl]oxy-sulfanylphosphoryl]oxymethyl]-4-hydroxyoxolan-2-yl]-5-methylpyrimidine-2,4-dione;[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[5-(6-aminopurin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphinothioyl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphinothioyl]oxyoxolan-2-yl]methoxy-hydroxyphosphinothioyl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-oxo-sulfanylphosphanium

2.1.2 InChI

InChI=1S/C137H175N46O73P13S13.C40H50N14O21P4S4/c1-54-27-173(132(198)164-117(54)186)91-13-60(185)75(231-91)34-217-257(204,270)247-64-17-95(174-28-55(2)118(187)165-133(174)199)234-78(64)37-222-262(209,275)249-66-19-97(176-30-57(4)120(189)167-135(176)201)236-80(66)39-223-267(214,280)253-70-23-101(180-50-151-106-111(142)147-48-149-113(106)180)240-84(70)43-227-263(210,276)250-67-20-98(177-31-58(5)121(190)168-136(177)202)235-79(67)38-221-259(206,272)245-62-15-93(171-11-8-89(139)156-130(171)196)232-76(62)35-219-261(208,274)248-65-18-96(175-29-56(3)119(188)166-134(175)200)238-82(65)41-225-268(215,281)255-73-26-104(183-53-154-109-116(183)160-128(145)163-125(109)194)242-86(73)45-228-264(211,277)251-68-21-99(178-32-59(6)122(191)169-137(178)203)237-81(68)40-224-266(213,279)252-69-22-100(179-49-150-105-110(141)146-47-148-112(105)179)239-83(69)42-226-260(207,273)246-63-16-94(172-12-9-90(140)157-131(172)197)233-77(63)36-220-265(212,278)254-72-25-103(182-52-153-108-115(182)159-127(144)162-124(108)193)243-87(72)46-229-269(216,282)256-71-24-102(181-51-152-107-114(181)158-126(143)161-123(107)192)241-85(71)44-218-258(205,271)244-61-14-92(230-74(61)33-184)170-10-7-88(138)155-129(170)195;1-16-7-51(39(59)49-35(16)56)27-4-19(23(70-27)9-65-76(61)80)73-78(63,82)68-12-25-21(6-29(72-25)54-15-46-31-34(54)47-38(42)48-37(31)58)75-79(64,83)67-11-24-20(5-28(71-24)52-8-17(2)36(57)50-40(52)60)74-77(62,81)66-10-22-18(55)3-26(69-22)53-14-45-30-32(41)43-13-44-33(30)53/h7-12,27-32,47-53,60-87,91-104,184-185H,13-26,33-46H2,1-6H3,(H,204,270)(H,205,271)(H,206,272)(H,207,273)(H,208,274)(H,209,275)(H,210,276)(H,211,277)(H,212,278)(H,213,279)(H,214,280)(H,215,281)(H,216,282)(H2,138,155,195)(H2,139,156,196)(H2,140,157,197)(H2,141,146,148)(H2,142,147,149)(H,164,186,198)(H,165,187,199)(H,166,188,200)(H,167,189,201)(H,168,190,202)(H,169,191,203)(H3,143,158,161,192)(H3,144,159,162,193)(H3,145,160,163,194);7-8,13-15,18-29,55H,3-6,9-12H2,1-2H3,(H10-,41,42,43,44,47,48,49,50,56,57,58,59,60,61,62,63,64,80,81,82,83)/p+1

2.1.3 InChI Key

HSWLVDBGZCETRH-UHFFFAOYSA-O

2.1.4 Canonical SMILES

CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(OC3CC(OC3COP(=S)(O)OC4CC(OC4COP(=S)(O)OC5CC(OC5COP(=S)(O)OC6CC(OC6COP(=S)(O)OC7CC(OC7COP(=S)(O)OC8CC(OC8COP(=S)(O)OC9CC(OC9COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1COP(=S)(O)OC1CC(OC1CO)N1C=CC(=NC1=O)N)N1C=NC2=C1N=C(NC2=O)N)N1C=NC2=C1N=C(NC2=O)N)N1C=CC(=NC1=O)N)N1C=NC2=C(N=CN=C21)N)N1C=C(C(=O)NC1=O)C)N1C=NC2=C1N=C(NC2=O)N)N1C=C(C(=O)NC1=O)C)N1C=CC(=NC1=O)N)N1C=C(C(=O)NC1=O)C)N1C=NC2=C(N=CN=C21)N)N1C=C(C(=O)NC1=O)C)N1C=C(C(=O)NC1=O)C)S)O.CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO[P+](=O)S)OP(=S)(O)OCC3C(CC(O3)N4C=NC5=C4N=C(NC5=O)N)OP(=S)(O)OCC6C(CC(O6)N7C=C(C(=O)NC7=O)C)OP(=S)(O)OCC8C(CC(O8)N9C=NC1=C(N=CN=C19)N)O

2.2 Synonyms

2.2.1 MeSH Synonyms

1. Ap 12009

2. Ap-2-09

3. Dna, D(p-thio)(c-g-g-c-a-t-g-t-c-t-a-t-t-t-t-g-t-a)

2.2.2 Depositor-Supplied Synonyms

1. Trabedersen [inn:ban]

2. Unii-98oyr854ny

3. 98oyr854ny

4. Ap-2-09

5. Dna, D(p-thio)(c-g-g-c-a-t-g-t-c-t-a-t-t-t-t-g-t-a)

6. 925681-61-4

2.3 Create Date

2018-03-25

3 Chemical and Physical Properties

Molecular Formula	C₁₇₇H₂₂₆N₆₀O₉₄P₁₇S₁₇+
Molecular Weight	5770 g/mol
Hydrogen Bond Donor Count	42
Hydrogen Bond Acceptor Count	131
Rotatable Bond Count	102
Exact Mass	5766.5573904 g/mol
Monoisotopic Mass	5765.5540356 g/mol
Topological Polar Surface Area	2470 Å²
Heavy Atom Count	365
Formal Charge	1
Complexity	15200
Isotope Atom Count	0
Defined Atom Stereocenter Count	0
Undefined Atom Stereocenter Count	54
Defined Bond Stereocenter Count	0
Undefined Bond Stereocenter Count	0
Covalently Bonded Unit Count	2

4 Drug and Medication Information

4.1 Drug Indication

Investigated for use/treatment in brain cancer, colorectal cancer, melanoma, and pancreatic cancer.

5 Pharmacology and Biochemistry

5.1 MeSH Pharmacological Classification

Antineoplastic Agents

Substances that inhibit or prevent the proliferation of NEOPLASMS. (See all compounds classified as Antineoplastic Agents.)

5.2 Mechanism of Action

AP 12009 is an antisense oligodeoxynucleotide that specifically inhibits TGF-beta2. TGF-beta overexpression is a hallmark of various malignant tumors. This is due to the pivotal role of TGF-beta as it regulates key mechanisms of tumor development, namely immunosuppression, metastasis, angiogenesis, and proliferation.