Abstract
The relationship between penta-coordinate phosphorus compounds and biochemistry is briefly reviewed. Some interesting phenomena such as peptide formation, ester formation, ester exchange on phosphorus and N to O migration occur at room temperature when the amino group of amino acid is associated with phosphoryl group. Serine or threonine in conjugate of nucleo-side-amino acid could recognize different nucleobases. N-phosphoryl Histine and Ser-His dipeptide could cleavage nucleic acid, protein and ester in neutral medium. It is found that the above phenomena all undergo penta-coordinate intermediate of phosphorus atom, which is proposed as the key factor to determine their activities.
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Joyce, G. F., RNA evolution and origins of life, Nature, 1989, 338: 217–224.
Dickerson, R. E., Chemical evolution and the origin of life, Sci. Amer., 1978, 239(3): 70–86.
Orgel, L. E., The origin of life on the Earth, Sci. Amer., 1994, 271(4): 76–83.
Westheimer, F. H., Why nature chose phosphates, Science, 1987, 235(4793): 1173–1178.
Todd, L., Where there’s life, there’s phosphorus, in Science and Scientists (eds. Makoto, K., Keiko, N., Tairo, O.), Tokyo: Japan Sci. Soc. Press, 1981, 275–279.
Weckwerth, G., Schidlowski, M., Phosphorus as a potential guide in the search for extinct life on Mars, Adv. Space Res., 1995, 15(3): 185–191.
Nelson, L. D., Cox, M. M., Lehninger Principles of Biochemistry, 2nd ed., New York: Worth Publishers, Inc., 1993, 652–658.
van Ool, P. J. J. M., Buck, H. M., A quantum-chemical model description for the function of cyclic AMP, Its degradation and activation of protein kinase, Recl. Tranv. Chim. Pays-Bas, 1981, 100: 79–80.
van Ool, P. J. J. M., Buck, H. M., The mechanisms of action of cAMP: A quantum chemical study, Eur. J. Biochem., 1981, 121(2): 329–334.
Blatter, W. A., Knowles, J. R., Stereochemical course of glycerol kinase, pyruvate kinase, and hexokinase: phosphoryl transfer from chiral[γ(s)-16 O,17 O,18O]ATP, J. Am. Chem. Soc., 1979, 101: 510–511.
Kin, E. E., Wyckoff, H. W., Reaction mechanism of alkaline phosphatase based on crystal structures, J. Mol. Biol., 1991, 218: 449–464.
Anslyn, E., Breslow, R., On the mechanism of catalysis by ribonuclease: cleavage and isomerization of the dinucleotide UpU catalyzed by imidazole buffers, J. Am. Chem. Soc., 1989, 111(12): 4473–4482.
McGuigan, G., Cahard, D., Sheeka, H. M. et al., Aryl phosphoramidate derivatives of d4T have improved anti-HIV efficiency in tissue culture and may act by the generation of a novel intercellular metabolite, J. Med. Chem., 1996, 39(8): 1748–1753.
Wagner, C. R., McIntee, E. J., Schinazi, R. F. et al., Aromatic amino-acid phosphoramidate diesters and trimesters of 3′-azido-3′-deoxythymidine(AZT) are nontoxic inhibitors of HIV-1 replication, Bioorg. Med. Chem. Lett., 1995, 5(16): 1819–1824.
Balzarini, J., Egberink, H., Hartmann, K. et al., Antiretrovirus specificity and intracellular metabolism of 2′,3′-didehydro- 2′,3′-dideoxythymidine (stavudine) and its 5′-monophosphate triester prodrug So324, Mol. Pharmacol., 1996, 50(5): 1207–1213.
Valette, G., Pompon, A., Girardet, J. L. et al., Decomposition pathways andin vitro HIV inhibitory effects of IsoddA pronucleotides: Toward a rational approach for intracellular delivery of nucleoside 5′-monophosphates, J. Med. Chem., 1996, 39(10): 1981–1990.
Fu, H., Zhao, Y. F., Penta-coordinate phosphorus compounds of amino acid and nucleoside, Acta Chimica Sincia (in Chinese), 2000, 58(1): 6–12.
Zhang, B. Z., Zhang, G. T., Zhao, Y. F., The reactiviy study of N-(O,O-dialkyl)phosphoryl alanine with alcohol, Journal of Chinese Science and Technology University (in Chinese), 1994, 24: 496–499.
Li, Y. M., Yin, Y. W., Zhao, Y. F., Phosphoryl group participation leads to peptide formation from N-phosphorylamino acids, Int. J. Peptide Protein Res., 1992, 39: 375–381.
Ma, X. B., Zhao, Y. F., Phosphoryl group participation in the reactions of N-phosphoryldipeptide acids, Phosphorus, Sulfur and Silicon, 1992, 66: 107–114.
Li, Y. C., Tan, B., Zhao, Y. F., Phosphoryl transfer reaction of phosphohistidine, Heteroatom Chemistry, 1993, 4(4): 415–419.
Ma, X. B., Zhao, Y. F., Synthesis and novel properties of N-phosphoryl peptides, J. Org. Chem., 1989, 54(16): 4005–4008.
Yang, H. J., Liu, L., Liu, C. Y. et al., N-S phosphoryl migration in phosphoryl glutation, Int. J. Peptide Protein Res., 1993, 42: 39–43.
Zhao, Y. F., Yan, Q. J., Wang, Q. et al., Phosphoryl transfer reaction regulation by amino acid side chains: a model for phosphoproteins, Int. J. Peptide Protein Res., 1996, 46: 276–281.
Xue, C. B., Yin, Y. W., Zhao, Y. F., Studies on phosphoserine and phosphothreonine derivatives, Tetrahedron Lett., 1988, 29: 1145–1148.
Zhou, W. H., Ju, Y., Zhao, Y. F. et al., Simultaneous formation of peptides and nucleotides from N-phosphothreonine, Origins Life Evol. B, 1996, 26(6): 547–560.
Fu, H., Li, Z. L., Zhao, F. F. et al., Oligomerization of N, O-bis(trimethylsilyl)-alpha-amino acids into peptides mediated byo-phenylene phosphorochloridate, J. Am. Chem. Soc., 1999, 121(2): 291–295.
Chen, X., Zhao, Y. F., Ester exchange reaction of oxyphosphorane with thymidine, Synthetic Commun., 1995, 25(22): 3691–3694.
Li, Y. S., Zhao, Y. F., Hatfield, S. et al., Dipeptide seryl-histidine and related oligopeptides cleave DNA, protein, and a carboxyl ester, Bioorg. Med. Chem., 2000, 8(12): 2675–2680.
Li, Y. F., Sha, Y. W., Ma, Y. et al., Cleavage of DNA by N-phosphoryl histidine, Biochem. Biophy. Res. Commun., 1995, 213(3): 875–880.
Zhao, Y. F., Cao, P. S., Phosphoryl amino-acids common origin for nucleic-acids and protein, J. Biol. Phys., 1994, 20: 283–287.
Zhou, W. H., Ju Y., Zhao, Y. F. et al., Stimultaneous formation of peptides from N-phosphothreonine, Origins Life Evol. B, 1996, 26: 547–556.
Zhao, Y. F., Cao, P. S., Why nature chose alpha-amino acids, Pure Appl. Chem., 1999, 71(6): 1163–1166.
Landweber, L. F., Testing ancient RNA-protein interactions, Proc. Natl. Acad. Sci. USA, 1999, 96(20): 11067–11068.
Holmes, R. R., Hexacoordinate phosphorus via donor interaction, Implications regarding enzymatic reaction intermediates, Acc. Chem. Res., 1998, 31(9): 535–542.
Messmore, J. M., Raines, R. T., Pentavalent organo-vanadates as transition state analogues for phosphoryl transfer reactions, J. Am. Chem. Soc., 2000, 122(41): 9911–9916.
Parang, K., Till, J. H., Ablooglu, A. J. et al., Mechanism-based design of a protein kinase inhibitor, Nat. Struct. Biol., 2001, 8(1): 37–41.
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Lin, C., Li, Y., Cheng, C. et al. Penta-coordinate phosphorous compounds and biochemistry. Sc. China Ser. B-Chem. 45, 337–348 (2002). https://doi.org/10.1007/BF02879344
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DOI: https://doi.org/10.1007/BF02879344