Design and Synthesis of Substrates for Model Ribosomal Reactions

Abstract

2'/3'-O-[Bz(NO(2))-Orn(Boc)]-5'-O-Piv-Ado (1) and its deoxy analog: 3'-O-[Bz(NO(2))-Orn(Boc)]-5'-O-Piv-2'-dAdo (2) were designed and synthesized as substrates for the model ribosome reaction we used to demonstrate the crucial role of A76 2'-OH of peptidyl-tRNA in the rate acceleration of peptide bond formation during protein biosynthesis.

Successful Application of the Lipase as a Catalyst in the Combinative Approach, Using an Efficient and Selective Iterative Procedure for the Chemo-Enzymatic Alpha-Amino Group Protection in the Natural Amino Acids, Representing the Ornithyl Model System as a Starting Research Pattern: Homogeneous and Heterogeneous Synthesis

“…Moreover in the water Ϫ -alcohol (MeOH, ethylene glycol, 1,2-propylene glycol etc.) combined solvents system (media), the aminolysis reaction is accelerated by the alcohol and water assisted catalysis, due to the homogeneous or mixed (water : alcohol) cluster creation and proton shuttling mechanism, accelerating of the tetrahedral intermediate formation [26]. Due to the presence of a stronger nucleophile (amino group) than the alcohol or water components in the reaction media, the hydrolysis reaction does not proceed, and the obtained product (amide) is more thermodynamically stable.…”

“…Different conditions were selected, depending on the combinative approach (a different solvent system, free or immobilized lipase, a carboxy-free, or a carboxy-protected amino-component.) When a carboxy-protected L-Orn was used as an amino-component, the reaction rate was slowly higher in some extent, probably due to the better enzyme affinity towards the protected L-Orn as its methyl ester [30].…”

“…╥ A variety of acyclic aliphatic esters of Fmoc-, Z-and Bz(NO 2 )-protective groups: n-butyl, n-pentyl, n-hexyl, n-heptyl, n-octyl, n-nonyl, n-decyl, n-undecyl, n-dodecyl, as well as their isomers with a branched carbon chain were synthesized, and their activity in the lipase catalyzed aminolysis reaction (protection of the alpha-amino group) were studied [30]. Matos et.…”

“…revealed [31], that esters of longer, straight chain alcohols, were better substrates than those of shorter chain alcohols, probably due to the unity properties of this long-chain alcohols as better leaving groups (nucleophuges). The results will be published elsewhere [30]. Also it is forwarded, that the synthesis of cyclic aliphatic, aromatic as well as aliphatic-aromatic esters (alcohol synthons) of the above noted protective groups (acyl synthons) as synthetic equivalents and the study of their reactive ability will be realized.…”

“…In the presence of at least two functional groups in the amino acids, their selective protection is necessary and is required, with goal -to avoid (protect) the process from the unwanted side reactions, as well as the carrying out of the synthesis in the desired direction. Utilization of the 9-fluorenylmethyloxycarbonyl moiety (Fmoc) as a protecting group for the amino function of the amino acids in the solid-phase peptide synthesis [1] of the benzyloxycarbonyl protection (Z) -also as N-protective group -in the realization of the peptide synthesis in solution (solution-phase peptide synthesis) [2][3][4][5] as well as the permanent р-nitro benzoyl protecting group (Bz(NO 2 ) -for increasing of the sensitivity in the UV-area during the peptide analysis [3], and also for synthesis of model compounds [6,7], as well as for protection of nucleosides and nucleotides, and finally -for increasing of the sensitivity and selectivity in the nucleoside, nucleotide and oligonucleotide synthesis and analysis [8], enforce the using of protected biomonomer derivatives, and particularly in this case -of the protected amino acids. Fmoc-group is labile in basic media, but it is stable in acidic conditions, respectivelyit deprotects in the principle of the basic elimination (pyridine, or 10% diethylamine in DMF) [9].…”