Docking and molecular dynamics simulation study of inhibitor 2-Fluoroaristeromycin with anti-malarial drug target PfSAHH
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Andersen HC (1983) Rattle: a “velocity” version of the shake algorithm for molecular dynamics calculations. J Comput Phys 52(1):24–34
Ando T, Iwata M, Zulfiqar F, Miyamoto T, Nakanishi M, Kitade Y (2008a) Synthesis of 2-modified aristeromycins and their analogs as potent inhibitors against Plasmodium falciparum S-adenosyl-l-homocysteine hydrolase. Bioorg Med Chem 16(7):3809–3815
Ando T, Kojima K, Chahota P, Kozaki A, Milind ND, Kitade Y (2008b) Synthesis of 4′-modified noraristeromycins to clarify the effect of the 4′-hydroxyl groups for inhibitory activity against S-adenosyl-l-homocysteine hydrolase. Bioorg Med Chem Lett 18(8):2615–2618
Bowers KJ, Chow E, Xu H, Dror R O, Eastwood M P, Gregerson BA, Klepeis JL, Kolossvary I, Moraes M A, Sacerdoti FD, Salmon JK, Shan Y, Shaw D E (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proc. ACM/IEEE conf. on supercomputing (Tampa, FL, 2006)
Bujnicki JM, Prigge ST, Caridha D, Chiang PK (2003) Structure, evolution, and inhibitor interaction of S-adenosyl-l-homocysteine hydrolase from Plasmodium falciparum. Proteins 52(4):624–632
Cai S, Li QS, Borchardt RT, Kuczera K, Schowen RL (2007) The antiviral drug ribavirin is a selective inhibitor of S-adenosyl-l-homocysteine hydrolase from Trypanosoma cruzi. Bioorg Med Chem 15(23):7281–7287
Carugo O (2007) Statistical validation of the root-mean-square-distance, a measure of protein structural proximity. Protein Eng Des Sel 20(1):33–37
Carugo O, Pongor S (2001) A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci 10(7):1470–1473
Chiang PK (1998) Biological effects of inhibitors of S-adenosylhomocysteine hydrolase. Pharmacol Ther 77(2):115–134
Das SR, Schneller SW, Balzarini J, De Clercq E (2002) A mercapto analogue of 5′-noraristeromycin. Bioorg Med Chem 10(2):457–460
Hudec R, Hamada K, Mikoshiba K (2013) A fluorescence-based assay for the measurement of S-adenosylhomocysteine hydrolase activity in biological samples. Anal Biochem 433(2):95–101
Ito M, Hamano T, Komatsu T, Asamitsu K, Yamakawa T, Okamoto T (2014) A novel IKKα inhibitor, noraristeromycin, blocks the chronic inflammation associated with collagen-induced arthritis in mice. Mod Rheumatol 24(5):775–780
Kaminski GA, Friesner RA (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem 105:6474–6487
Kitade Y, Kozaki A, Miwa T, Nakanishi M (2002) Synthesis of base-modified noraristeromycin derivatives and their inhibitory activity against human and Plasmodium falciparum recombinant S-adenosyl-l-homocysteine hydrolase. Tetrahedron 58:1271–1277
Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16):2785–2791
Nakanishi M (2007) S-adenosyl-l-homocysteine hydrolase as an attractive target for antimicrobial drugs. Yakugaku Zasshi 127(6):977–982
Seley KL, Schneller SW, Rattendi D, Bacchi CJ (1997) (+)-7-Deaza-5′-noraristeromycin as an anti-trypanosomal agent. J Med Chem 40(4):622–624
Shaw DE (2008) Research desmond molecular dynamics system, version 3.1. New York
Singh DB, Gupta MK, Singh DV, Singh SK, Misra K (2013) Docking and in silico ADMET studies of noraristeromycin, curcumin and its derivatives with Plasmodium falciparum SAH hydrolase: a molecular drug target against malaria. Interdiscip Sci 5(1):1–12
Tanaka N, Umeda T, Kusakabe Y, Nakanishi M, Kitade Y, Nakamura KT (2013) Structural biology for developing antimalarial compounds. Yakugaku Zasshi 133(5):527–537
Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49:3315–3321