In silico investigation of the structural stability as the origin of the pathogenicity of α-synuclein protofibrils.

α-Synuclein is a presynaptic neuronal protein. The fibril form of α-synuclein is a major constituent of the intraneuronal inclusion called Lewy body, a characteristic hallmark of Parkinson's disease. Recent ssNMR and cryo-EM experiments of wild-type α-synuclein fibrils have shown polymorphism and observed two major polymorphs, rod and twister. To associate the cytotoxicity of α-synuclein fibrils with their structural features, it is essential to understand the origins of their structural stability. In this study, we performed molecular dynamics simulations of the two major polymorphs of wild-type α-synuclein fibrils. The predominance of specific fibril polymorphs was rationalized in terms of relative structural stability in aqueous environments, which was attributed to the cooperative contributions of various stabilizing features. The results of the simulations indicated that highly stable structures in aqueous environments could be maintained by the cooperation of compact sidechain packing in the hydrophobic core, backbone geometry of the maximal ß-sheet content wrapping the hydrophobic core, and solvent-exposed sidechains with large fluctuations maximizing the solvation entropy. The paired structure of the two protofilaments provides additional stability, especially at the interface region, by forming steric zipper interactions and hiding the hydrophobic residues from exposure to water. The sidechain interaction analyses and pulling simulations showed that the rod polymorph has stronger sidechain interactions and exhibits higher dissociation energy than the twister polymorph. It is expected that our study will provide a basis for understanding the pathogenic behaviors of diverse amyloid strains in terms of their structural properties.Communicated by Ramaswamy H. Sarma.

Target-Specific Drug Discovery of Natural Products against SARS-CoV-2 Life Cycle and Cytokine Storm in COVID-19.

Coronavirus disease 2019 (COVID-19) is currently a worldwide pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, there are no drugs that can specifically combat SARS-CoV-2. Besides, multiple SARS-CoV-2 variants are circulating globally. These variants may lead to immune escape or drug resistance. Natural products may be appropriate for this need due to their cost efficiency, fewer side effects, and antiviral activities. Considering these circumstances, there is a need to develop or discover more compounds that have potential to target SARS-CoV-2. Therefore, we searched for articles on natural products describing anti-SARS-CoV-2 activities by targeting the SARS-CoV-2 life cycle and the cytokine storm in COVID-19 from academic databases. We reviewed anti-SARS-CoV-2 activities of natural products, especially those that target the SARS-CoV-2 life cycle (angiotensin-converting enzyme 2, transmembrane serine protease 2, cathepsin L, 3CL protease, PL protease, RNA-dependent RNA polymerase, and helicase) and cytokine storm in COVID-19. This review may provide a repurposed approach for the discovery of specific medications using natural products to treat COVID-19 through targeting the SARS-CoV-2 life cycle and the cytokine storm in COVID-19.

Cost-utility analysis of emicizumab prophylaxis in haemophilia A patients with factor VIII inhibitors in Korea.

AIMS: Haemophilia A patients with factor VIII inhibitors (HAPI) experience frequent spontaneous bleeding, approximately once a week, and require expensive bypassing agent (BPA) treatments to control bleeding over their lifetime. According to the HAVEN 1 trial, weekly emicizumab (Hemlibra®) prophylaxis injection reduces annualized bleeding rates (ABR) by 87% compared with BPA on-demand treatment (BPA-OD) administered at the time of bleeding. Our study aimed to assess the cost-effectiveness of emicizumab prophylaxis in HAPI in Korea. METHODS: Using a lifetime Markov model with health states of 'alive with bleeds' and 'dead', we simulated the experience of HAPI receiving emicizumab prophylaxis (treatment arm) or BPA-OD (control arm) and estimated expected clinical and economic outcomes under each treatment arm. Model parameters included comparative effectiveness, clinical and epidemiologic characteristics of Korean HAPI, costs of drug treatment and medical events and utility for 'alive with bleeds' state under each treatment. We utilized local data, including National Health Insurance claims data, national statistics, literature and expert surveys with haematologists. RESULTS: Base-case analysis results showed that compared with BPA-OD, lifetime emicizumab prophylaxis prevented 807 bleedings, extended 3.04 quality-adjusted life-years and reduced costs by 2.6 million US dollars. Thus, emicizumab prophylaxis is a dominant treatment option with better effectiveness and lower costs than BPA-OD. A series of one-way sensitivity analyses consistently showed dominant results, confirming that lifetime emicizumab prophylaxis is a cost-saving intervention for HAPI. CONCLUSION: Emicizumab prophylaxis is an excellent treatment choice reducing ABR, improving quality of life and reducing costs.

Computational Study on Structure and Aggregation Pathway of Aß42 Amyloid Protofibril.

Amyloid deposits of Aß protein in neuronal cells are known to be a major symptom of Alzheimer's disease. In particular, Aß42 shows relatively high toxicity among the different Aß isoforms, and its toxicity is thought to be because of its structural features. Recent ssNMR and cryo-EM experiments identified that Aß42 shows an S-shaped triple-ß structure, in contrast to the previously suggested U-shaped ß-arch structure. In order to associate the high toxicity of Aß42 with its structural features, it is essential to explain the conformational stability and aggregation mechanisms of this triple-ß motif. We utilized several different simulation methods, including extensive straight molecular dynamics simulation, steered molecular dynamics simulation, and replica-exchange molecular dynamics simulation. The S-shaped triple-ß motif showed remarkable structural stability because of its complex residual interactions that form stable hydrophobic cores. The triple-ß structure of Aß42 is primarily made up of three ß-sheet regions and two hydrophobic cores formed between ß-sheet regions. Our analysis of ß-sheet rupture patterns between adjacent chains showed that its two hydrophobic cores have different degrees of stability, indicating a lock phase mechanism. Our analysis of the docking pathway of monomeric Aß42 to the fibril motif using REMD simulations showed that each of the three ß-sheet sequences plays a distinct role in the docking process by changing their conformational features. Our results provide an understanding for the stability and consequent high toxicity of the triple-ß structure Aß42.

Cost-effectiveness analysis of the implementation of a National Immunization Program for rotavirus vaccination in a country with a low rotavirus gastroenteritis-related mortality: A South Korean study.

Rotavirus is a leading cause of severe gastroenteritis among children younger than 5 years in South Korea. Two rotavirus vaccines (RVs), pentavalent human-bovine reassortant vaccine (Rotateq®; RV5) and attenuated human strain originated monovalent vaccine (Rotarix®; RV1), have been available for voluntary vaccination using out-of-pocket payment since 2007 and 2008, respectively. Yet, RVs are not included in the National Immunization Program (NIP), partly because of the low associated mortality rate. We assessed the cost-effectiveness of RVs to assist the evidence-based decision-making process for NIP implementation in South Korea. Using a transparent age-structured static cohort model, we simulated the experience of ten annual birth cohorts of South Korean children from 2018 to 2027. Model inputs included rotavirus gastroenteritis (RVGE) incidence and mortality rates, RVGE treatment costs, vaccine coverage and timeliness, and vaccine effectiveness and price. The incremental costs of including RVs in the NIP compared to no vaccination were 59,662,738 USD and 152,444,379 USD for RV1 and RV5, respectively. The introduction of RV1 and RV5 can prevent 4799 disability-adjusted life years (DALYs) and 5068 DALYs. From the societal perspective, the incremental cost-effectiveness ratios (ICERs) for adopting RV into the NIP versus no vaccination were 12,432 USD per DALY averted for RV1 and 30,081 USD per DALY averted for RV 5. The weighted average for the ICERs of the two vaccines computed using the market share of each vaccine in the current voluntary use as a weight, was 21,698 USD per DALY averted. The estimated ICER was below 1 × gross domestic product per capita (30,000 USD), which has been a commonly used willingness-to-pay threshold for health care technology assessment in South Korea, suggesting that introducing RVs into the NIP would be cost-effective.

Evaluation of bleeding-related adverse events following acupuncture treatment in patients on anticoagulant or antiplatelet drugs: A prospective observational study.

OBJECTIVE: To evaluate the risk of bleeding-related adverse events after acupuncture treatment in patients receiving anticoagulant or antiplatelet drugs. DESIGN AND SETTING: A total of 428 inpatients who received acupuncture treatment underwent two assessments for bleeding-related adverse events, such as micro-bleeding, hematoma, and ecchymosis: 1) immediately after acupuncture treatment on the first day and 2) before acupuncture treatment on the following day. Additional analyses were performed using the number of acupuncture needles as independent variables. Multivariable analysis using factors likely related to bleeding and subgroup analysis according to regions of needle insertion were also performed. RESULTS: A total of 169 patients receiving anticoagulant or antiplatelet drugs (exposure group) and 259 patients not receiving either drug (non-exposure group) were studied. Sixty-five (38.5%) patients in the exposure group and 115 (44.4%) patients in the non-exposure group had bleeding-related mild adverse events. There was no difference in the risk of bleeding-related adverse events between the two groups per sessions (relative risk (RR) 0.87, 95% confidence interval (CI), 0.69-1.10) and per needles (RR 0.89, 95% CI 0.70-1.13). In multivariable analysis, thickness of needle only increased risk of bleeding. Subgroup analysis showed that taking these drugs did not increase the risk of bleeding in any of the regions. CONCLUSION: Our findings suggest that anticoagulant and antiplatelet drugs do not increase the incidence of bleeding-related adverse events after acupuncture treatment.

Graphene quantum dots prevent α-synucleinopathy in Parkinson's disease.

Though emerging evidence indicates that the pathogenesis of Parkinson's disease is strongly correlated to the accumulation1,2 and transmission3,4 of α-synuclein (α-syn) aggregates in the midbrain, no anti-aggregation agents have been successful at treating the disease in the clinic. Here, we show that graphene quantum dots (GQDs) inhibit fibrillization of α-syn and interact directly with mature fibrils, triggering their disaggregation. Moreover, GQDs can rescue neuronal death and synaptic loss, reduce Lewy body and Lewy neurite formation, ameliorate mitochondrial dysfunctions, and prevent neuron-to-neuron transmission of α-syn pathology provoked by α-syn preformed fibrils5,6. We observe, in vivo, that GQDs penetrate the blood-brain barrier and protect against dopamine neuron loss induced by α-syn preformed fibrils, Lewy body/Lewy neurite pathology and behavioural deficits.

Note: Development of a wideband amplifier for cryogenic scanning tunneling microscopy.

A wideband cryogenic amplifier has been developed for low temperature scanning tunneling microscopy. The amplifier consisting of a wideband complementary metal oxide semiconductor field effect transistors operational amplifier together with a feedback resistor of 100 kΩ and a capacitor is mounted within a 4 K Dewar. This amplifier has a wide bandwidth and is successfully applied to scanning tunneling microscopy applications at low temperatures down to ∼7 K. The quality of the designed amplifier is validated by high resolution imaging. More importantly, the amplifier has also proved to be capable of performing scanning tunneling spectroscopy measurements, showing the detection of the Shockley surface state of the Au(111) surface and the superconducting gap of Nb(110).

Conformational sampling of metastable states: Tq-REM as a novel replica exchange method.

Although the replica exchange methods (REMs) were developed as efficient conformational sampling methods for bio-molecular simulations, their application to very large bio-systems is somewhat limited. We propose a new replica exchange scheme (Tq-REM) created by combining the conventional temperature-REM (T-REM) and one of the Hamiltonian-REMs, q-REM, using the effective potential with reduced barriers. In the proposed Tq-REM scheme, high temperature replicas in T-REM are substituted with q-replicas. This combined scheme is expected to exploit advantages of the T-REM and q-REM resulting in improved sampling efficiency while minimizing the drawbacks of both approaches. We investigated the performance of Tq-REM compared with T-REM by performing all-atom MD simulations on Met-enkephalin, (AAQAA)3, and Trpzip2. It was found that convergence of the free energy surfaces was improved by Tq-REM over the conventional T-REM. In particular, the trajectories of Tq-REM were able to sample the relevant conformations for all of the metastable folding intermediates, while some of the local minimum structures are poorly represented by T-REM. The results of the present study suggest that Tq-REM can provide useful tools to investigate systems where metastable states play important roles.

Energy Bandgap and Edge States in an Epitaxially Grown Graphene/h-BN Heterostructure.

Securing a semiconducting bandgap is essential for applying graphene layers in switching devices. Theoretical studies have suggested a created bulk bandgap in a graphene layer by introducing an asymmetry between the A and B sub-lattice sites. A recent transport measurement demonstrated the presence of a bandgap in a graphene layer where the asymmetry was introduced by placing a graphene layer on a hexagonal boron nitride (h-BN) substrate. Similar bandgap has been observed in graphene layers on metal substrates by local probe measurements; however, this phenomenon has not been observed in graphene layers on a near-insulating substrate. Here, we present bulk bandgap-like features in a graphene layer epitaxially grown on an h-BN substrate using scanning tunneling spectroscopy. We observed edge states at zigzag edges, edge resonances at armchair edges, and bandgap-like features in the bulk.

Fast on-site diagnosis of influenza A virus by Palm PCR and portable capillary electrophoresis.

A method combining Palm polymerase chain reaction (PCR) and portable capillary electrophoresis (CE) was developed for rapid on-site analysis of influenza A (H1N1) virus. The portable CE system was suitable for rapid diagnosis which was able to detect a sample in ∼4 min after sample loading, while the 'Palm PCR' system allowed for high-speed nucleic acid amplification in ∼16 min. The analysis time from DNA sample to analysis of amplified target DNA molecule was only ∼20 min, which was significantly less than slab gel electrophoresis with other commercially available PCR machine. When the 100-bp DNA ladder was separated, the relative standard deviation values (n=5) for the migration times and peak areas of the 100 and 200-bp DNA molecules were 0.26 and 8.9%. The detection limits were 6.3 and 7.2 pg/µL, respectively. The combined method was also able to identify two influenza A-associated genes (the HA and NP genes of the novel H1N1 influenza). CE separation was achieved with a sieving matrix of 1% poly(vinylpyrrolidone) (Mr=1,300,000) in 1× TBE buffer (pH 8.45). The combined Palm PCR-portable CE system should provide an improved, fast on-site molecular genetic diagnostic method.

DA-125, a new antitumor agent, inhibits topoisomerase II as topoisomerase poison and DNA intercalator simultaneously.

DA-125, a novel derivative of adriamycin, is known for its anti-cancer activity. In this study, the inhibitory mechanism of DA-125 on topoisomerase was investigated in the simian virus 40 (SV40) replicating CV-1 cell by studying the SV40 DNA replication intermediates and DNA-topoisomerase complexes. DNA-protein complexes that were formed in the drug-treated cells were quantitated by using a glass filter assay. SV40 DNA replication intermediates that were accumulated in the drug-treated CV-1 cell were analyzed in a high resolution gel. DA-125 did not accumulate B-dimers of SV40 DNA replication intermediates which were found in the adriamycin-treated CV-1 cells. DA-125 induced a dose-dependent formation of the DNA-protein complexes, while adriamycin did not. When adriamycin and etoposide (VP16) were added to the SV40-infected cells at the same time, adriamycin blocked the formation of the DNA-protein complexes induced by VP16 in a dose-dependent manner. However, DA-125 blocked the formation of the DNA-protein complexes induced by VP16 up to the maximum level of the DNA-protein complexes that were induced by DA-125 alone. Adriamycin and DA-125 did not inhibit the formation of the DNA-protein complexes that were caused by camptothecin, a known topoisomerase I poison. DA-125 is bifunctional in inhibiting topoisomerase II because it simultaneously has the properties of the topoisomerase II poison and the DNA intercalator. As a topoisomerase II poison, DA-125 alone induced dose-dependent formation of the DNA-protein complexes. However, as a DNA intercalator, it quantitatively inhibited the formation of the DNA-protein complexes induced by a strong topoisomerase II poison VP16. Furthermore considering that the levels of the DNA-protein complex induced by VP16 were decreased by DA-125 in terms of the topoisomerase II poison, we suggest that DA-125 has a higher affinity to the drug-binding sites of DNA than VP16 has.