1. Mechanism of Curcumin Inhibiting Amyloid-  Peptides Aggregation by Molecular Dynamics Simulations Zhenyu Qian, and Guanghong Wei State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, P. R. China I. INTRODUCTION Increasing evidence shows that small oligomers, rather than monomers and mature fibrils, play a crucial role in cytotoxicity to trigger pathological processes. Curcumin, as indigenous medicine and natural spice, is reported to inhibit the formation of Ab oligomers and fibrils in vivo, and disaggregate preformed Ab fibrils [1]. Non-toxicity and capability of crossing the blood-brain barrier make curcumin more competitive than other inhibitors [2]. II. METHODS All of the MD simulations have been performed in the isothermal-isobaric (NPT) ensemble using the GROMACS 4.5.3 software package. The initial topology and force field parameters of curcumin was generated in the PRODRG2 Server. The protein and curcumin are represented by the GROMOS96 53a6 force field. III. RESULTS AND DISCUSSION Our simulations show that curcumin has a preference to bind to the hydrophobic 16-22 and 30-36 regions of preformed A  protofibrils. The N-terminal residues are not the amyloidogenic segments which leads to fibrillization. The A  16-22 peptides mainly adopt a  -barrel conformation in the absence of curcumin, which exhibit great cytotoxicity based on experimental observation. Interacting with curcumin, A  16-22  -barrel is much reduced in probability. Detailed structure analysis shows that the intermolecular H-bonds between peptides are much reduced because curcumin will also form H-bonds with A  16-22 peptides. Besides, the  -  stacking interaction between the aromatic ring of curcumin and Phe is stronger than that between the Phe aromatic rings, which makes curcumin- peptide interaction more competitive than the peptide-peptide interaction. However, curcumin inhibit the aggregation of A  30-36 not so efficiently as that of A  16-22. V. CONCLUSIONS We have investigated the binding site of curcumin at A  1-42 protofibril and the mechanism of curcumin inhabiting A  peptide aggregation. The hydrophobic and  stacking interacion plays an important role in A  -curcumin interaction. In addition, curcumin reduces the formation of  -sheet- rich oligomers of Ab16-22 more effectively than that of Ab30-36. REFERENCES 1. Yang, F. et al. J. Biol. Chem. 2005, 280, 5892-5901. 2. Garcia-Alloza, M. et al. J. Neurochem. 2007, 102, 1095-1104. The aggregation of amyloid-  peptides is associated with the pathogenesis of Alzheimer’s disease, and the atomic-level A  -curcumin interaction and the inhibition mechanism remain elusive. In this study, we have investigated the binding dynamics of curcumin to A  1-42 protofibrils and the curcumin-inhibited mechanism of A  -fragment aggregation using molecular dynamics (MD) simulations. Our simulations show that curcumin has a preference to bind to the hydrophobic 16- 22 and 30-36 regions of preformed A  protofibrils. Further replica-exchange MD simulations initiated from a disordered mixture of A  segments (A  16-22 and A  30-36) and curcumins show that curcumin has different influence on the aggregation of these two segments. Curcumin takes strong restrictive effect on the inter-molecular interactions of A  16-22 and thus reduces the formation of b-sheet-rich oligomers of A  16-22 more effectively than that of A  30-36. This study provides structural insight into the inhibition mechanism of A  aggregation by curcumin, which is helpful for novel design of A  inhibitor. ABSTRACT A  1-42 Sequence: DAEFRHDSGY 10 EVHHQKLVFF 20 AEDVGSNKGA 30 IIGLMVGGVVIA 42 Fig. 1 Contact number per chain of A  1-42 hexamer with curcumin. The sequence of A  -42 and the chemical structure of curcumin are also showed. The inset snapshot is the initial setup of system. Cluster-1 (17.2%) A  16-22-CurcuminA  16-22 Cluster-2 (9.9%) Cluster-3 (8.8%)Cluster-4 (6.9%) Cluster-5 (2.9%)Cluster-6 (2.7%) Cluster-1 (6.0%)Cluster-2 (5.7%) Cluster-3 (4.8%)Cluster-4 (4.4%) Cluster-5 (4.0%)Cluster-6 (3.7%) Fig. 2 Free energy surface (in kcal/mol) of A  16-22 peptides as a function of number of H-bonds and radius of gyration without (left) or with (right) curcumin at 310K. Fig. 3 Representative structures for the first six most- populated clusters of A  16-22 hexamer without (left) or with (right) curcumin. Fig. 4 Analysis of  -stacking interactions between aromatic ring of the Phe and Phe residues (left) or the Phe residue and curcumin (right). Fig. 5 Contact probability map of the A  16-22 residues without curcumin (left) or with curcumin (right). Fig. 5 Contact probability map of the A  30-36 residues without curcumin (left) or with curcumin (right).