Isopropyl (6-(5-((4S)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamido)hexyl) phosphorofluoridate
[CAS# 353754-93-5]

Identification

• Classification: Organic raw materials >> Organic fluorine compound
• Name: Isopropyl (6-(5-((4S)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanamido)hexyl) phosphorofluoridate
• Synonyms: N-[6-[fluoro(propan-2-yloxy)phosphoryl]oxyhexyl]-5-[(4S)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanamide
• Molecular Formula: C₁₉H₃₅FN₃O₅PS
• Molecular Weight: 467.54
• CAS Registry Number: 353754-93-5
• SMILES: CC(C)OP(=O)(OCCCCCCNC(=O)CCCC[C@H]1C2C(CS1)NC(=O)N2)F

Properties

• Density: 1.2±0.1 g/cm³ Calc.^*
• Boiling point: 698.2±50.0 ºC 760 mmHg (Calc.)^*
• Flash point: 376.1±30.1 ºC (Calc.)^*
• Index of refraction: 1.494 (Calc.)^*

^* Calculated using Advanced Chemistry Development (ACD/Labs) Software.

Discovory and Applicatios

Isopropyl (6‑(5‑((4S)‑2‑oxohexahydro‑1H‑thieno[3,4‑d]imidazol‑4‑yl)pentanamido)hexyl) phosphorofluoridate is an organophosphorus compound that incorporates a thienoimidazolone moiety structurally related to biotin and an organophosphorofluoridate group. Organophosphorofluoridates are a class of phosphorus(V) esters in which a fluorine atom is directly bonded to phosphorus, and they are historically known for their reactivity toward nucleophiles, especially the active site serine hydroxyl found in serine hydrolases such as esterases, lipases, and proteases. The thieno[3,4‑d]imidazol‑2‑one ring system found in this compound is a bicyclic heterocycle analogous to the bicyclic ureido ring in biotin; derivatives of this system have been widely used in biotinyl chemistry, enzyme inhibitors, and chemical biology probes because the ring can mimic part of the biotin binding motif in proteins.

The chemical structure consists of three principal domains: an isopropyl phosphorofluoridate group attached through a hexyl aliphatic linker, an amide bond joining the hexyl chain to a pentanamide fragment, and a 2‑oxohexahydrothienoimidazole ring with specified stereochemistry at the 4‑position (4S). The isopropyl phosphorofluoridate group is chemically reactive because the phosphorus–fluorine bond is polarized and the phosphorus center is electrophilic. Organophosphorofluoridates are prepared by reacting suitable alcohols with phosphoryl fluorides or by fluorination of phosphorochloridates under controlled conditions. In this compound, the hexyl chain terminating in the amide linking group is tethered to the heterocyclic ring via a five‑carbon spacer, conferring both flexibility and distance between the phosphoryl reactive center and the biologically relevant heterocycle.

The discovery of organophosphorofluoridates dates to early twentieth century research in organophosphorus chemistry when phosphorus halides were explored for reactivity and agricultural applications. The presence of fluorine on phosphorus yields compounds with increased stability compared with other halides, but still high reactivity toward nucleophilic substitution. While many simple organophosphorofluoridates have been studied extensively in the context of toxicology and pesticide development, the incorporation of a complex heterocycle such as the thienoimidazole derivative with a biologically active side chain reflects more modern synthetic applications in chemical biology and medicinal chemistry.

In applied science, compounds of this type are used as **mechanism‑based inhibitors** of serine hydrolases. The phosphorofluoridate moiety can phosphorylate a serine hydroxyl group in the active site of enzymes such as chymotrypsin, acetylcholinesterase, and other esterases, leading to covalent inhibition. This mode of action has been exploited to profile enzyme activity in biochemical assays, to design potential therapeutic agents targeting specific hydrolases, and to develop chemical probes for studying enzyme function. The addition of a biologically recognized heterocycle such as the thienoimidazolone can influence enzyme binding affinity and selectivity by mimicking a natural substrate or ligand motif. The hexyl spacer and amide linkage provide a flexible connection that allows the phosphorofluoridate group to reach into the enzyme active site while the heterocyclic moiety interacts with peripheral binding sites.

Such compounds are typically handled in specialized chemical biology laboratories under strict safety protocols because organophosphorus compounds with reactive phosphorus centers can be toxic if they interact with unintended biological targets. The design of these molecules requires careful consideration of reactivity, stability, and selectivity to ensure that they serve as useful tools rather than indiscriminate toxins. In research practice, analogues of biotin containing phosphorofluoridate functional groups have been used to label or inhibit biotin‑binding proteins or related hydrolases in proteomic studies.

The practical synthesis of phosphorofluoridates often involves multi‑step organic sequences beginning with protected amines or alcohols, formation of the heterocyclic core via cyclization, introduction of the amide linkage, and final phosphorylation or fluorination steps to install the phosphorofluoridate. Each step typically requires purification by chromatography and characterization by spectroscopic methods such as nuclear magnetic resonance and mass spectrometry.

Applications of compounds of this type are largely within basic research in enzymology, chemical biology, and medicinal chemistry. They are not established pharmaceutical agents themselves, but they inform the design of enzyme inhibitors and contribute to understanding of enzyme mechanisms. The specific compound in question, with its defined stereochemistry and functional groups, represents a tailored reagent where the organophosphorofluoridate moiety serves as the reactive warhead and the heterocyclic biotin analogue directs interaction with targeted proteins.