Анищенко Иван Владимирович, Тузиков Александр Васильевич, Андрианов Александр Михайлович
Компьютерный дизайн потенциальных лекарственных препаратов для терапии СПИДа: β-галактозилцерамид и петля V3 белка gp120 ВИЧ-1
Математическая биология и биоинформатика. 2011;6(2):161-172.
doi: 10.17537/2011.6.161.
Список литературы
- Andrianov AM. Human immunodeficiency virus-1 gp120 V3 loop for anti-acquired immune deficiency syndrome drug discovery: computer-aided approaches to the problem solving. Expert Opin. Drug. Discov. 2011;6(4):419-435. doi: 10.1517/17460441.2011.560603
- Sirois S, Sing T, Chou KC. HIV-1 gp120 V3 loop for structure-based drug design. Curr. Protein Pept. Sci. 2005;6:413-422.
- LaRosa GJ, Davide JP, Weinhold K, Waterbury JA, Profy AT, Lewis JA, Langlois AJ, Dressman GR, Boswell RN, Shadduk P, Holley LH, Karplus M, Bolognesi DP., Matthews TJ, Emini EA and Putney SD. Conserved sequence and structural elements in the HIV-1 principal neutralizing determinant. Science. 1990;249:932-935. doi: 10.1126/science.2392685
- Andrianov AM, Anishchenko IV. Computational model of the HIV-1 subtype A V3 loop: study on the conformational mobility for structure-based anti-AIDS drug design. J. Biomol. Struct. Dynam. 2009;27:179-194.
- Anishchenko IV, Andrianov AM. Conformational analysis of the HIV-1 variable V3 loops: modeling of 3D structures and determination of the patterns in their spatial organization. Doklady Natsionalnoi Akademii Nauk Belarusi (Doklady of the National Academy of Sciences of Belarus). 2010;54:84-91 (in Rus.).
- Jiang X, Burke V, Totrov M, Williams C, Cardozo T, Gorny MK, Zolla-Pazner S, Kong XP. Conserved structural elements in the V3 crown of HIV-1 gp120. Nat. Struct. Mol. Biol. 2010;17:955-61.
- Bhat S, Spitalnik SL, Gonzalez-Scarano F, Silberberg DH. Galactosyl ceramide or a derivative is an essential component of the neural receptor for human immunodeficiency virus type 1 envelope glycoprotein gp120. Proc. Natl. Acad. Sci. USA. 1991;88:7131-7134. doi: 10.1073/pnas.88.16.7131
- Bhat S, Mettus RV, Reddy EP, Ugen KE, Srikanthan V, Williams WV, Weiner DB. The galactosyl ceramide/sulfatide receptor binding region of HIV-1 gp120 maps to amino acids 206-275. AIDS Res. Hum. Retroviruses. 1993;9:175-181. doi: 10.1089/aid.1993.9.175
- Fantini J, Hammache D, Delézay O, Yahi N, André-Barrès C, Rico-Lattes I, Lattes A. Synthetic soluble analogs of galactosylceramide (GALCER) bind to the V3 domain of HIV-1 gp120 and inhibit HIV-1-induced fusion and entry. J Biol Chem. 1997;272:7245-7252. doi: 10.1074/jbc.272.11.7245
- Garg H, Francella N, Tony KA, Augustine LA, Barchi JJ Jr, Fantini J, Puri A, Mootoo DR, Blumenthal R. Glycoside analogs of beta-galactosylceramide, a novel class of small molecule antiviral agents that inhibit HIV-1 entry. Antiviral Res. 2008;80:54-61. doi: 10.1016/j.antiviral.2008.04.004
- Yahi N, Sabatier JM, Nickel P, Mabrouk K, Gonzalez-Scarano F, Fantini J. Suramin inhibits binding of the V3 region of HIV-1 envelope glycoprotein gp120 to galactosylceramide, the receptor for HIV-1 gp120 on human colon epithelial cells. J. Biol. Chem. 1994;269:24349-24353.
- Yahi N, Sabatier JM, Baghdiguian S, Gonzalez-Scarano F, Fantini J. Synthetic multimeric peptides derived from the principal neutralization domain (V3 loop) of human immunodeficiency virus type 1 (HIV-1) gp120 bind to galactosylceramide and block HIV-1 infection in a human CD4-negative mucosal epithelial cell line. J. Virol. 1995;69:320-325.
- Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Research. 2000;28:235-242. doi: 10.1093/nar/28.1.235
- Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA. General Atomic and Molecular Electronic Structure System (GAMESS). J. Comput. Chem. 1993;14:1347-1363.
- Gordon MS, Schmidt MW. In: Advances in electronic structure theory: GAMESS a decade later. Dykstra C.E., Frenking G., Kim K.S., Scuseria G.E., eds. Amsterdam: Elsevier, 2005:1167-1189.
- Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA. Development and testing of a general Amber force field. J. Comput. Chem. 2004;25:1157-1174. doi: 10.1016/j.chemosphere.2004.08.026
- Bayly CI, Cieplak P, Cornell W, Kollman PA. Well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: the RESP model. J. Phys. Chem. 1993;97:10269-10280.
- Cornell WD, Cieplak P, Bayly CI, Kollmann PA. Application of the RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. Soc. 1993;115:9620-9631.
- Case DA, Darden TA, Cheatham TE, III, Simmerling CL, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, Merz KM, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Mathews DH, Seetin MG, Sagui C, Babin V, Kollman PA. AMBER 10. San Francisco: University of California, 2008.
- Berendsen HJ, Postma JP, DiNola A, Haak JR. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 1984;81:3684-3690.
- Anishchenko IV, Andrianov AM. Comparative modeling for structure predictions of the HIV-1 V3 variable loops: application to the virus subtype A. Doklady Natsionalnoi Akademii Nauk Belarusi (Doklady of the National Academy of Sciences of Belarus). 2009;53(3):79-86 (in Rus.).
- Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC, Thomas V, Rizzo R, Case DA, James TL, Kuntz ID. DOCK 6: Combining techniques to model RNA-small molecule complexes. RNA. 2009;15:1219-1230. doi: 10.1261/rna.1563609
- Massova I, Kollman PA. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 1999;121:8133-8143.
- Ablameyko SV, Abramov SM, Anishchanka UV, Medvedev SV, Paramonov NN, Tchij OP. SKIF supercomputer configurations. Minsk: United Institute of Informatics Problems, 2005.
- Kumar RM, Elango M, Subramanian V. Carbohydrate-aromatic interactions: the role of curvature on XH·π interactions. J. Phys. Chem. 2010;114:4313-4324.
- Fantini J, Yahi N. Molecular insights into amyloid regulation by membrane cholesterol and sphingolipids: common mechanisms in neurodegenerative diseases. Expert Rev. Mol. Med. 2010;12(e27):1-22.
- Tian H, Lan C, Chen Y-H. Sequence variation and consensus sequence of V3 loop on HIV-1 gp120. Immunology Letters. 2002;83:231-233. doi: 10.1016/S0165-2478(02)00101-3
- Fernández-Alonso MC, Cañada FJ, Jiménez-Barbero J, Cuevas G. Molecular recognition of saccharides by proteins. Insights on the origin of the carbohydrate−aromatic interactions. J. Amer. Chem. Soc. 2005;127:7379-7386.
- Díaz MD, Fernández-Alonso MC, Cuevas G, Cañada FJ, Jiménez-Barbero J. On the role of aromatic-sugar interactions in the molecular recognition of carbohydrates: A 3D view by using NMR. Pure Appl. Chem. 2008;80:1827-1835.
- Harouse JM, Bhat S, Spitalnik SI, Laughlin M, Stefano K, Silberberg DH, Gonzalez-Scarano F. Inhibition of entry of HIV-1 in neural cell lines by antibodies against galactosyl ceramide. Science. 1991;253:320-323. doi: 10.1126/science.1857969
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