Structural transitions in the prion protein from the cellular form, PrPC, into the pathological isoform, PrPSc, are regarded as the main cause of the transmissible spongiform encephalopathies, also known as prion diseases. Hence, discovering and designing effective antiprion drugs that can inhibit PrPC to PrPSc conversion is regarded as a promising way to cure prion disease. Among several strategies to inhibit PrPC to PrPSc conversion, stabilizing the native PrPC via specific binding is believed to be one of the valuable approaches and many antiprion compounds have been reported based on this strategy. However, the detailed mechanism to stabilize the native PrPC is still unknown. As such, to unravel the stabilizing mechanism of these compounds to PrPC is valuable for the further design and discovery of antiprion compounds. In this study, by molecular dynamics simulation method, we investigated the stabilizing mechanism of several antiprion compounds on PrPC that were previously reported to have specific binding to the “hot spot” region of PrPC. Our simulation results reveal that the stabilization mechanism of specific binding compounds can be summarized as (I) to stabilize both the flexible C-terminal of α2 and the hydrophobic core, such as BMD42-29 and GN8; (II) to stabilize the hydrophobic core, such as J1 and GJP49; (III) to stabilize the overall structure of PrPC by high binding affinity, as NPR-056. In addition, as indicated by the H-bond analysis and decomposition analysis of binding free energy, the residues N159 and Q160 play an important role in the specific binding of the studied compounds and all these compounds interact with PrPC in a similar way with the key interacting residues L130 in the β1 strand, P158, N159, Q160, etc. in the α1-β2 loop, and H187, T190, T191, etc. in the α2 C-terminus although the compounds have large structural difference. As a whole, our obtained results can provide some insights into the specific binding mechanism of main antiprion compounds to the “hot spot” region of PrPC at the molecular level and also provide guidance for effective antiprion drug design in the future.Keywords: antiprion compound; molecular dynamics simulation; Prion disease; specific binding;

Resveratrol and its derivatives have been shown to display beneficial effects to neurodegenerative diseases. However, the molecular mechanism of resveratrol and its derivatives on prion conformational conversion is poorly understood. In this work, the interaction mechanism between prion and resveratrol as well as its derivatives was investigated using steady-state fluorescence quenching, Thioflavin T binding assay, Western blotting, and molecular dynamics simulation. Protein fluorescence quenching method and Thioflavin T assay revealed that resveratrol and its derivatives could interact with prion and interrupt prion fibril formation. Molecular dynamics simulation results indicated that resveratrol can stabilize the PrP127–147 peptide mainly through π–π stacking interactions between resveratrol and Tyr128. The hydrogen bonds interactions between resveratrol and the PrP127–147 peptide could further reduce the flexibility and the propensity to aggregate. The results of this study not only can provide useful information about the interaction mechanism between resveratrol and prion, but also can provide useful clues for further design of new inhibitors inhibiting prion aggregation.Keywords: aggregation; molecular dynamics simulations; Prion; resveratrol; ThT;

The structural transition of prion proteins from a native α-helix (PrPC) to a misfolded β-sheet-rich conformation (PrPSc) is believed to be the main cause of a number of prion diseases in humans and animals. Understanding the molecular basis of misfolding and aggregation of prion proteins will be valuable for unveiling the etiology of prion diseases. However, due to the limitation of conventional experimental techniques and the heterogeneous property of oligomers, little is known about the molecular architecture of misfolded PrPSc and the mechanism of structural transition from PrPC to PrPSc. The prion fragment 127–147 (PrP127–147) has been reported to be a critical region for PrPSc formation in Gerstmann–Straussler–Scheinker (GSS) syndrome and thus has been used as a model for the study of prion aggregation. In the present study, we employ molecular dynamics (MD) simulation techniques to study the conformational change of this fragment that could be relevant to the PrPC–PrPSc transition. Employing extensive replica exchange molecular dynamics (REMD) and conventional MD simulations, we sample a huge number of conformations of PrP127–147. Using the Markov state model (MSM), we identify the metastable conformational states of this fragment and the kinetic network of transitions between the states. The resulting MSM reveals that disordered random-coiled conformations are the dominant structures. A key metastable folded state with typical extended β-sheet structures is identified with Pro137 being located in a turn region, consistent with a previous experimental report. Conformational analysis reveals that intrapeptide hydrophobic interaction and two key residue interactions, including Arg136–His140 and Pro137–His140, contribute a lot to the formation of ordered extended β-sheet states. However, network pathway analysis from the most populated disordered state indicates that the formation of extended β-sheet states is quite slow (at the millisecond level), as large structural rearrangement is needed from disordered states. We speculate that the formation process of the extended β-sheet folded states may represent an important event during the early formation of prion oligomers and the results of our study provide insights into the molecular details of the early stage of prion aggregation.

•20(S)-Sulfonylamidine CPT-derivatives were prepared and tested for cytotoxicity.•Several analogs showed superior cytotoxic activity compared to irinotecan.•Key structural features related to cytotoxicity were identified by SAR analysis.•Compounds 9 and 15c interacted with Topo I-DNA by a different binding mode from CPT.•These compounds are new generation CPT-derived antitumor agents.In an ongoing investigation of 20-sulfonylamidine derivatives (9, YQL-9a) of camptothecin (1) as potential anticancer agents directly and selectively inhibiting topoisomerase (Topo) I, the sulfonylamidine pharmacophore was held constant, and a camptothecin derivatives with various substitution patterns were synthesized. The new compounds were evaluated for antiproliferative activity against three human tumor cell lines, A-549, KB, and multidrug resistant (MDR) KB subline (KBvin). Several analogs showed comparable or superior antiproliferative activity compared to the clinically prescribed 1 and irinotecan (3). Significantly, the 20-sulfonylamidine derivatives exhibited comparable cytotoxicity against KBvin, while 1 and 3 were less active against this cell line. Among them, compound 15c displayed much better cytotoxic activity than the controls 1, 3, and 9. Novel key structural features related to the antiproliferative activities were identified by structure–activity relationship (SAR) analysis. In a molecular docking model, compounds 9 and 15c interacted with Topo I-DNA through a different binding mode from 1 and 3. The sulfonylamidine side chains of 9 and 15c could likely form direct hydrogen bonds with Topo I, while hydrophobic interaction with Topo I and π–π stacking with double strand DNA were also confirmed as binding driving forces. The results from docking models were consistent with the SAR conclusions. The introduction of bulky substituents at the 20-position contributed to the altered binding mode of the compound by allowing them to form new interactions with Topo I residues. The information obtained in this study will be helpful for the design of new derivatives of 1 with most promising anticancer activity.CPT (green), 9 (magenta), and 15c (blue) in the binding site of DNA-Topo-I.

•The competitive mechanism between GS-461203 and UTP to NS5B was studied.•The resistance mechanism to GS-461203 conferred by S282T mutant was explored.•The unbinding pathway of GS-461203 to NS5B was studied using random acceleration molecular dynamics simulation•The potential of mean force profile of GS-461203 to NS5B was calculated based on steered molecular dynamics simulation.The active metabolite GS-461203 of hepatitis C virus (HCV) non-structural protein 5B (NS5B) inhibitor sofosbuvir can stall RNA synthesis or replication by competitively inhibiting the natural substrate nucleoside triphosphate like UTP. Unfortunately, S282T mutant can lead to the resistance to sofosbuvir. Here, the detailed binding mechanism and unbinding process of GS-461203 and UTP to HCV NS5B were unraveled by using conventional molecular dynamics (MD) simulation and steered molecular dynamics (SMD) simulation. Our simulation results demonstrate that both polar and nonpolar interactions are favorable for GS-461203 and UTP binding. Meanwhile, we also identified the key residues responsible for GS-461203 and UTP binding in NS5B-RNA together with the three unbinding process steps including translation, reversal of base and ribose and complete divorce. The 2′-fluoro-2′-C-methyl ribose of GS-461203 can form stronger polar and nonpolar interactions with residues S282 and I160 than UTP. The results can also explain the reason why GS-461203 can effectively be incorporated into RNA synthesis or replication. In the S282T mutant system, the binding affinity attenuation of UTP relative to wild type HCV NS5B is less than that of GS-461203. The obtained binding and unbinding mechanism of HCV NS5B with the inhibitor GS-461203 and substrate in our work will provide useful guidance for the development of new and effective HCV NS5B inhibitors with low resistance.

The aggregation of human islet amyloid polypeptide (hIAPP) is closely related with the occurrence of type 2 diabetes (T2D). Natural flavonoid morin was confirmed to not only inhibit the amyloid formation of hIAPP, but disaggregate its preformed amyloid fibrils. In this study, with the goal of elucidating the molecular mechanism of inhibition and destabilization of morin on the full-length hIAPP1–37 oligomer, molecular dynamics simulations were performed for hIAPP1–37 pentamer in the presence and absence of morin. The obtained results show that during the protein–inhibitor interaction, morin can notably alter the structural properties of hIAPP1–37 pentamer, such as morphology, solvent accessible surface area and secondary structure. Moreover, we identified three possible binding sites of morin on hIAPP, all of which located near the amyloidogenic region of this protein. From the binding free energy calculations, we found that Site II was the most possible one. Further conformational analysis together with energy decomposition showed that the residues His18, Phe23 and Ile26 play a key role in the binding with morin by hydrogen bond, π–π and hydrophobic interactions. The proposal of the theoretical mechanism of morin against hIAPP aggregation will provide valuable information for the development of new drugs to inhibit hIAPP aggregation.

The palindromic region AGAAAAGA (PrP113–120) in prion is highly amyloidogenic and very critical in the structural conversion of cellular prion protein to its pathogenetic form. In this region, there is an important point mutation A117V, which is closely related to the occurrence of Gerstmann–Straussler–Scheinker Syndrome. However, the detailed knowledge about the effects of the A117V mutation on the folding and aggregation of the palindromic sequences is still lacking. To investigate the impacts of A117V mutation on the earliest steps along the PrP113–120 aggregation pathway, replica exchange molecular dynamics simulations of the monomer, 2- and 4-peptide systems of PrP113–120 and its A117V mutant were carried out. The simulations of monomers indicate that both WT and the A117V mutated PrP113–120 are mostly random coils with helical structures transiently populated. Differently, the A117V mutation enhances the intrinsic disorder of PrP113–120. The simulations of 2- and 4-peptide systems of the two species show that the A117V mutation increases the sheet contents and the populations of oligomers, which may be attributed to the enhancement of inter-peptide backbone hydrogen bonding interactions and side chain hydrophobic interactions. Overall, the study provides structural insights into the impacts of the A117V mutation on the folding and assembly of the palindromic sequences, which might be helpful to elucidate the mechanism underlying prion disease and the origin of the Gerstmann–Straussler–Scheinker Syndrome.

Natural polyphenols are one of the most actively investigated categories of amyloid inhibitors, and resveratrol has recently been reported to inhibit and remodel the human islet amyloid polypeptide (hIAPP) oligomers and fibrils. However, the exact mechanism of its action is still unknown, especially for the full-length hIAPP1–37. To this end, we performed all-atom molecular dynamics simulations for hIAPP1–37 pentamer with and without resveratrol. The obtained results show that the binding of resveratrol is able to cause remarkable conformational changes of hIAPP1–37 pentamer, in terms of secondary structures, order degree, and morphology. By clustering analysis, two possible binding sites of resveratrol on the hIAPP1–37 pentamer were found, located at the grooves of the top and bottom surfaces of β-sheet layer, respectively. After the binding free energy calculation and residue energy decomposition, it can be concluded that the bottom site is the more possible one, and that the nonpolar interactions act as the driving force for the binding of hIAPP1–37 to resveratrol. In addition, Arg11 is the most important residue for the binding of resveratrol. The full understanding of inhibitory mechanism of resveratrol on the hIAPP1–37 oligomer, and the identification of its binding sites on this protein are helpful for the future design and discovery of new amyloid inhibitors.

NS5B, a hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) that plays a key role in viral replication, is an important target in the discovery of antiviral agents. PF-00868554 is a potent non-nucleoside inhibitor (NNI) that binds to the Thumb II allosteric pocket of NS5B polymerase and has shown significant promise in phase II clinical trials. Unfortunately, several PF-00868554 resistant mutants have been identified. M423 variants were the most common NS5B mutations that occurred after PF-00868554 monotherapy. In this study, we used molecular dynamics (MD) simulations, binding free energy calculations and free energy decomposition to explore the drug resistance mechanism of HCV to PF-00868554 resulting from three representative mutations (M423T/V/I) in NS5B polymerase. Free energy decomposition analysis reveals that the loss of binding affinity mainly comes from the reduction of both van der Waals (ΔEvdw) and electrostatic interaction contributions in the gas phase (ΔEele). Further structural analysis indicates that the location of PF-00868554 and the binding mode changed due to mutation of the residue at the 423 site of NS5B polymerase from methionine to threonine, isoleucine or valine, which further resulted in the loss of binding ability of PF-00868554 to NS5B polymerase. The obtained computational results will have important value for the rational design of novel non-nucleoside inhibitors targeting HCV NS5B polymerase.

Nanomaterials (NMs) have been widely used in the biomedical field. To explore the biological effects of graphene as one of the most widely used NMs, we studied the adsorption behavior and induced conformational changes of proteins representing different secondary structures on graphene: β-strands (WW domain), mixed α/β structure (BBA protein), and α-helices (λ-repressor). Our results indicate these model proteins were adsorbed onto the graphene surface quickly and tightly, however, varied degrees of conformational changes were observed. During the adsorption process, we found the β motif is a stiffer structural unit than the α-helix. Moreover, the level of conformational changes of the proteins is related not only to their sequence and structural properties but also to their orientation. Overall, from the different levels of intermolecular interaction, the protein adsorption was driven by van der Waals, hydrophobic and π–π stacking interactions. Our work suggests that classical molecular dynamics simulations and MM-GBSA calculations can provide useful information about the dynamics and energetics of the adsorption of proteins onto graphene. We believe that these findings will help us to further understand the adsorption of proteins on hydrophobic carbon nanomaterials at the atomic level.

Three novel series of N3-substituted imidacloprid derivatives were designed and synthesized, and their structures were identified on the basis of satisfactory analytical and spectral (1H NMR, 13C NMR, MS, elemental analysis, and X-ray) data. Preliminary bioassays indicated that all of the derivatives exhibited significant insecticidal activities against Aphis craccivora, with LC50 values ranging from 0.00895 to 0.49947 mmol/L, and the insecticidal activities of some of them were comparable to those of the control imidacloprid. Some key structural features related to their insecticidal activities were identified, and the binding modes between target compounds and nAChR model were also further explored by molecular docking. By comparing the interaction features of imidacloprid and compound 26 with highest insecticidal activity, the origin of the high insecticidal activity of compound 26 was identified. On the basis of the conformations generated by molecular docking, a satisfactory 2D-QSAR model with six selected descriptors was built using genetic algorithm–multiple linear regression (GA-MLR) method. The analysis of the built model showed the molecular size, shape, and the ability to form hydrogen bond were important for insecticidal potency. The information obtained in the study will be very helpful for the design of new derivatives with high insecticidal activities.

As one of the most important antiviral drugs against 2009 influenza A (H1N1), will zanamivir be effective for the possible drug resistant mutants? To answer this question, we combined multiple molecular dynamics simulations and molecular mechanics generalized Born surface area (MM-GBSA) calculations to study the efficiency of zanamivir over the most frequent drug-resistant strains of neuraminidase including R293K, R152K, E119A/D and H275Y mutants. The calculated results indicate that the modeled mutants of the 2009-H1N1 strains except H275Y will be significantly resistant to zanamivir. The resistance to zanamivir is mainly caused by the loss of polar interactions. The identified potential resistance sites in this study will be useful for the development of new effective anti-influenza drugs and to avoid the occurrence of the state without effective drugs to new mutant influenza strains.

The outbreak and high speed global spread of the new strain of influenza A (H1N1) virus in 2009 poses a serious threat to the general population and governments. At present, the most effective drugs for the treatment of 2009 influenza A (H1N1) virus are neuraminidase inhibitors: mainly oseltamivir and zanamivir. The use of these two inhibitors will undoubtedly increase, and therefore it is more likely that drug-resistant influenza strains will arise. The identification of the potential resistance sites for these drugs in advance and the understanding of corresponding molecular basis to cause drug resistance are no doubt very important to fight against the new resistant influenza strains. In this study, first, the complexes of neuraminidase with the substrate sialic acid and two inhibitors oseltamivir and zanamivir were obtained by fitting them to the 3D structure of 2009 influenza A (H1N1) neuraminidase obtained by homology modeling. By using these complexes as the initial structures, molecular dynamics simulation and molecular mechanics generalized Born surface area (MM-GBSA) calculations were performed to identify the residues with significant contribution to the binding of substrate and inhibitors. By analyzing the difference of interaction profiles of substrate and inhibitors, the potential drug resistance sites for two inhibitors were identified. Parts of the identified sites have been verified to confer resistance to oseltamivir and zanamivir for influenza virus of the past flu epidemic. The identified potential resistance sites in this study will be useful for the development of new effective drugs against the drug resistance and avoid the situation of having no effective drugs to treat new mutant influenza strains.Keywords: 2009 H1N1 influenza A virus; drug resistance; molecular dynamics simulation; molecular mechanics generalized Born surface area (MM-GBSA); neuraminidase inhibitors;

The emergence of the extremely aggressive influenza recently has highlighted the urgent need for new effective treatments. The influenza RNA-dependent RNA polymerase (RdRp) heterotrimer including PA, PB1 and PB2 has crucial roles in viral RNA replication and transcription. The highly conserved PB1 binding site on PA can be considered as a novel potential drug target site. The interaction between PB1 binding site and PA is crucial to many functions of the virus. In this study, to understand the detailed interaction profile and to characterize the binding hot spots in the interactions of the PA−PB1 complex, an 8 ns molecular dynamics simulation of the subunit PA−PB1 combined with MM-PBSA (molecular mechanics Poisson−Boltzmann surface area), MM-GBSA (molecular mechanics generalized Born surface area) computations and virtual alanine scanning were performed. The results from the free energy decomposition indicate that the intermolecular van der Waals interaction and the nonpolar solvation term provide the driving force for binding process. Through the pair interaction analysis and virtual alanine scanning, we identified the binding hot spots of PA and the basic binding motif of PB1. This information can provide some insights for the structure-based RNA-dependent RNA polymerase inhibitors design. The identified binding motif can be used as the starting point for the rational design of small molecules or peptide mimics. This study will also lead to new opportunities toward the development of new generation therapeutic agents exhibiting specificity and low resistance to influenza virus.Keywords: free energy calculation; Influenza virus RNA polymerase; molecular dynamics simulation; protein−protein interaction; structure-based drug design;

The central event in the pathogenesis of prion protein (PrP) is a profound conformational change from its α-helical (PrPC) to its β-sheet-rich isoform (PrPSc). Many single amino acid mutations of PrP are associated with familial prion diseases, such as D202N, E211Q, and Q217R mutations located at the third native α-helix of human PrP. In order to explore the underlying structural and dynamic effects of these mutations, we performed all-atom molecular dynamics (MD) simulations for the wild-type (WT) PrP and its mutants. The obtained results indicate that these amino acid substitutions have subtle effects on the protein structures, but show large changes of the overall electrostatic potential distributions. We can infer that the changes of PrP electrostatic surface due to the studied mutations may influence the intermolecular interactions during the aggregation process. In addition, the mutations also affect the thermodynamic stabilities of PrP.

The structural transition of prion proteins from a native α-helix (PrPC) to a misfolded β-sheet-rich conformation (PrPSc) is believed to be the main cause of a number of prion diseases in humans and animals. Understanding the molecular basis of misfolding and aggregation of prion proteins will be valuable for unveiling the etiology of prion diseases. However, due to the limitation of conventional experimental techniques and the heterogeneous property of oligomers, little is known about the molecular architecture of misfolded PrPSc and the mechanism of structural transition from PrPC to PrPSc. The prion fragment 127–147 (PrP127–147) has been reported to be a critical region for PrPSc formation in Gerstmann–Straussler–Scheinker (GSS) syndrome and thus has been used as a model for the study of prion aggregation. In the present study, we employ molecular dynamics (MD) simulation techniques to study the conformational change of this fragment that could be relevant to the PrPC–PrPSc transition. Employing extensive replica exchange molecular dynamics (REMD) and conventional MD simulations, we sample a huge number of conformations of PrP127–147. Using the Markov state model (MSM), we identify the metastable conformational states of this fragment and the kinetic network of transitions between the states. The resulting MSM reveals that disordered random-coiled conformations are the dominant structures. A key metastable folded state with typical extended β-sheet structures is identified with Pro137 being located in a turn region, consistent with a previous experimental report. Conformational analysis reveals that intrapeptide hydrophobic interaction and two key residue interactions, including Arg136–His140 and Pro137–His140, contribute a lot to the formation of ordered extended β-sheet states. However, network pathway analysis from the most populated disordered state indicates that the formation of extended β-sheet states is quite slow (at the millisecond level), as large structural rearrangement is needed from disordered states. We speculate that the formation process of the extended β-sheet folded states may represent an important event during the early formation of prion oligomers and the results of our study provide insights into the molecular details of the early stage of prion aggregation.

The aggregation of human islet amyloid polypeptide (hIAPP) is closely related with the occurrence of type 2 diabetes (T2D). Natural flavonoid morin was confirmed to not only inhibit the amyloid formation of hIAPP, but disaggregate its preformed amyloid fibrils. In this study, with the goal of elucidating the molecular mechanism of inhibition and destabilization of morin on the full-length hIAPP1–37 oligomer, molecular dynamics simulations were performed for hIAPP1–37 pentamer in the presence and absence of morin. The obtained results show that during the protein–inhibitor interaction, morin can notably alter the structural properties of hIAPP1–37 pentamer, such as morphology, solvent accessible surface area and secondary structure. Moreover, we identified three possible binding sites of morin on hIAPP, all of which located near the amyloidogenic region of this protein. From the binding free energy calculations, we found that Site II was the most possible one. Further conformational analysis together with energy decomposition showed that the residues His18, Phe23 and Ile26 play a key role in the binding with morin by hydrogen bond, π–π and hydrophobic interactions. The proposal of the theoretical mechanism of morin against hIAPP aggregation will provide valuable information for the development of new drugs to inhibit hIAPP aggregation.