Molecular Insights into the Inhibitory Effect of GV971 Components Derived from Marine Acidic Oligosaccharides against the Conformational Transition of Aβ42 Monomers

Diversity, mechanism and structure-activity relationships of marine anticoagulant-active polysaccharides: A review

Thrombosis is a major complication of cardiovascular disease that can lead to fatal myocardial infarction, acute ischemic stroke and venous thromboembolism, posing a significant threat to human health and even life. Recent research showed that polysaccharides from marine organisms, including marine plants and marine animals, exhibit excellent anticoagulant activity. However, different marine anticoagulant-active polysaccharides (MAPs) exhibit significant differences in both the structure and anticoagulant activity. This review systematically summarizes the diversity and structure of MAPs from the last 30 years. We compared the anticoagulant activity and drug development potential of MAPs from different organisms including red algae, green algae, brown algae, marine fish, sea urchins and sea cucumbers, etc., and analyzed the structure-activity relationships of some MAPs with specific structures. In addition, we also discuss the current challenges and future perspectives of MAPs for the development of novel anticoagulant drugs. This review not only offers a comprehensive understanding of the diversity of marine anticoagulant polysaccharides but also provides valuable reference and guidance for the development of novel anticoagulant drugs in the future.

From pixels to druggable leads: A CADD strategy for the design and synthesis of potent DDR1 inhibitors

BACKGROUND AND OBJECTIVE

While numerous in silico tools exist for target-based drug discovery, the inconsistent integration of in vitro data with predictive models hinders research and development productivity. This is particularly apparent during the Hit-to-Lead stage, where unreliable in-silico tools often lead to suboptimal lead selection. Herein, we address this challenge by presenting a CADD-guided pipeline that successfully integrates rational drug design with in-silico hits to identify a promising DDR1 lead.

METHODS

2 × 1000 ns MD simulations along with their respective FEL and MMPBSA analyses were employed to guide the rational design and synthesis of 12 novel compounds which were evaluated for their DDR inhibition.

RESULTS

The molecular dynamics investigation of the initial hit led to the identification of key structural features within the DDR1 binding pocket. The identified key features were used to guide the rational design and synthesis of twelve novel derivatives. SAR analysis, biological evaluation, molecular dynamics, and free energy calculations were carried out for the synthesized derivatives to understand their mechanism of action. Compound 4c exhibited the strongest inhibition and selectivity for DDR1, with an IC50 of 0.11 µM.

CONCLUSIONS

The MD simulations led to the identification of a key hydrophobic groove in the DDR1 binding pocket. The integrated approach of SAR analysis with molecular dynamics led to the identification of compound 4c as a promising lead for further development of potent and selective DDR1 inhibitors. Moreover, this work establishes a protocol for translating in silico hits to real world bioactive druggable leads.

GV-971 attenuates α-Synuclein aggregation and related pathology

RATIONALE

Synucleinopathies, including Parkinson's disease (PD), multiple system atrophy (MSA), and dementia with Lewy bodies (DLB), share a distinct pathological feature, that is, a widespread accumulation of α-synuclein (α-syn) in the brain. There is a significant clinical unmet need for disease-modifying treatments for synucleinopathies. Recently, a seaweed-derived mixture of oligosaccharides sodium oligomannate, GV-971, was approved for Phase 2 clinical trials for PD. This study aimed to further evaluate the therapeutic effects of GV-971 on synucleinopathies using cellular and animal models and explore its associated molecular mechanisms.

METHODS

α-Syn aggregation was assessed, in vitro and ex vivo, by ThT assay. A dopaminergic neuron cell line, Prnp-SNCAA53T mice, and brain slices from PD and DLB patients were used to determine the efficacy of GV-971 in ameliorating α-syn pathology. Measurements of motor functions, including pole, cylinder, and rotarod tests, were conducted on Prnp-SNCAA53T mice 4 weeks after intragastric administration of GV-971 (200 mg day-1  kg-1 ).

RESULTS

GV-971 effectively prevented α-syn aggregation and even disassembled pre-aggregated α-syn fibrils, in vitro and ex vivo. In addition, GV-971 was able to rescue α-syn-induced neuronal damage and reduced release of extracellular vesicles (EVs), likely via modulating Alix expression. In the Prnp-SNCAA53T mouse model, when treated at the age of 5 months, GV-971 significantly decreased α-syn deposition in the cortex, midbrain, and cerebellum regions, along with ameliorating the motor dysfunctions.

CONCLUSIONS

Our results indicate that GV-971, when administered at a relatively early stage of the disease process, significantly reduced α-syn accumulation and aggregation in Prnp-SNCAA53T mice. Furthermore, GV-971 corrected α-syn-induced inhibition of EVs release in neurons, contributing to neuronal protection. Future studies are needed to further assess GV-971 as a promising disease-modifying therapy for PD and other synucleinopathies.

Synthesis of mannan oligosaccharide-sialic acid conjugates and its inhibition on Aβ42 aggregation

In this work, a mannan-oligosaccharide conjugate with sialic acid capable of perturbing Aβ42 aggregation was designed and synthesized. Mannan oligosaccharides with degree polymerization of 3-13 were obtained by stepwise hydrolysis of locust bean gum using β-mannanase and α-galactosidase, named as LBOS. The activated LBOS was further chemically conjugated with sialic acid (Sia, N-acetylneuraminic acid) by fluoro-mercapto chemical coupling to synthesize a conjugate LBOS-Sia, and then phosphorylated to obtain pLBOS-Sia. The successful synthesis of pLBOS-Sia was confirmed by infrared1 chromatography, mass spectrometry, and ¹H NMR. The soluble protein analysis, microscopic observation, thioflavin T-labeling, and circular dichroism spectroscopy revealed that both LBOS-Sia and pLBOS-Sia can inhibit Aβ42 aggregation. MTT assay showed that LBOS-Sia and pLBOS-Sia had no cytotoxicity to BV-2 cells, and could substantially reduce the release of pro-inflammatory factor TNF-α induced by Aβ42 in BV-2 cells, and inhibit the occurrence of neuroinflammation. In future, this novel structure of mannan oligosaccharide-sialic acid conjugate can be potentially used to for the development of glycoconjugates against AD targeting Aβ.

Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations

The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.

A Lead-Based Fragment Library Screening of the Glycosyltransferase WaaG from Escherichia coli

Glucosyl transferase I (WaaG) in E. coli catalyzes the transfer of an α-d-glucosyl group to the inner core of the lipopolysaccharide (LPS) and plays an important role in the biogenesis of the outer membrane. If its activity could be inhibited, the integrity of the outer membrane would be compromised and the bacterium would be susceptible to antibiotics that are normally prevented from entering the cell. Herein, three libraries of molecules (A, B and C) were docked in the binding pocket of WaaG, utilizing the docking binding affinity as a filter to select fragment-based compounds for further investigations. From the results of the docking procedure, a selection of compounds was investigated by molecular dynamics (MD) simulations to obtain binding free energy (BFE) and K_D values for ligands as an evaluation for the binding to WaaG. Derivatives of 1,3-thiazoles (A7 and A4) from library A and 1,3,4-thiadiazole (B33) from library B displayed a promising profile of BFE, with K_D < mM, viz., 0.11, 0.62 and 0.04 mM, respectively. Further root-mean-square-deviation (RMSD), electrostatic/van der Waals contribution to the binding and H-bond interactions displayed a favorable profile for ligands A4 and B33. Mannose and/or heptose-containing disaccharides C1–C4, representing sub-structures of the inner core of the LPS, were also investigated by MD simulations, and compound C4²⁻ showed a calculated K_D = 0.4 µM. In the presence of UDP-Glc²⁻, the best-docked pose of disaccharide C4²⁻ is proximate to the glucose-binding site of WaaG. A study of the variation in angle and distance was performed on the different portions of WaaG (N-, the C- domains and the hinge region). The Spearman correlation coefficient between the two variables was close to unity, where both variables increase in the same way, suggesting a conformational rearrangement of the protein during the MD simulation, revealing molecular motions of the enzyme that may be part of the catalytic cycle. Selected compounds were also analyzed by Saturation Transfer Difference (STD) NMR experiments. STD effects were notable for the 1,3-thiazole derivatives A4, A8 and A15 with the apo form of the protein as well as in the presence of UDP for A4.