Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation

Molecular mechanism of ZER1-mediated recognition of N-terminal glycine in protein degradation

The N-terminal glycine (Gly/N-degron) serves as a degradation signal recognized by specific E3 ligases, playing a crucial role in protein quality control and maintaining intracellular protein homeostasis. Zinc finger E3 ubiquitin protein ligase 1 (ZER1), a substrate receptor of the Cullin 2-RING E3 ubiquitin ligase, recognizes N-terminal glycine and other small N-terminal residues (such as serine, alanine, and cysteine), mediating protein degradation through the Gly/N-degron pathway. In this study, we employed all-atom molecular dynamics (MD) simulations and binding free energy calculations to study the binding mode of ZER1 with N-terminal glycine and the effects of key residue mutations on this recognition process. The results show that the binding of glycine-containing peptides and key residue mutations have minimal impact on ZER1 structural stability. During ZER1-peptide binding, van der Waals and electrostatic interactions are the primary driving forces. Residues W552, N553, D556, N597, I678, N579, R681, and K716 play significant roles in the recognition process, with mutations in these residues affecting the electrostatic distribution and hydrophobic properties of the ZER1 binding site, thereby influencing peptide binding. Additionally, ZER1 forms a complex hydrogen-bond network with the peptide, which stabilizes the peptide like an anchor. D556A and N597A disrupt the hydrogen bond between the N-terminal residue (G1) and ZER1. These findings provide a molecular-level understanding of the N-terminal degron pathway and lay a foundation for future related research.

A Study on the Binding Mechanism and the Impact of Key Residue Mutations between SND1 and MTDH Peptide through Molecular Dynamics Simulations

Metastasis of breast cancer is the main cause of death for patients with breast cancer. The interaction between metadherin (MTDH) and staphylococcal nuclease domain 1 (SND1) plays a pivotal role in promoting breast cancer development. However, the binding details between MTDH and SND1 remain unclear. In this study, we employed all-atom molecular dynamics simulations (MDs) and conducted binding energy calculations to investigate the binding details and the impact of key residue mutations on binding. The mutations in key residues have not significantly affected the overall stability of the structure and the fluctuation of residues near the binding site; they have exerted a substantial impact on the binding of SND1 and MTDH peptide. The electrostatic interactions and van der Waals interactions play an important role in the binding of SND1 and the MTDH peptide. The mutations in the key residues have a significant impact on electrostatic and van der Waals interactions, resulting in weakened binding. The energy contributions of key residues mainly come from the electrostatic energy and van der Waals interactions of the side chain. In addition, the key residues form an intricate and stable network of hydrogen bonds and salt-bridge interactions with the MTDH peptide. The mutations in key residues have directly disrupt the interactions formed between SND1 and MTDH peptide, consequently leading to changes in the binding mode of the MTDH peptide. These analyses unveil the detailed atomic-level interaction mechanism between SND1 and the MTDH peptide, providing a molecular foundation for the development of antibreast cancer drugs.

Exploring binding modes of the selected inhibitors to SND1 by all-atom molecular dynamics simulations

Breast cancer is the leading cause of cancer-related deaths in women. Previous studies have indicated that disrupting the interaction between Metadherin (MTDH) and Staphylococcal nuclease domain containing 1 (SND1) can inhibit breast cancer development. Understanding the binding mode of small molecule inhibitors with SND1 is of great significance for designing drugs targeting the MTDH-SND1 complex. In this study, we conducted all-atom molecular dynamics (MD) simulations in solution and performed binding energy calculations to gain insights into the binding mechanism of small molecules to SND1. The binding site of SND1 for small molecules is relatively rigid, and the binding of the small molecule and the mutation of key residues have little effect on the conformation of the binding site. SND1 binds more tightly to C26-A6 than to C26-A2, as C26-A2 undergoes a 180° directional change during the simulation process. The key residue mutations have a direct effect on the position and orientation of small molecule in the binding site. The key residues make primary contributions to the binding energy through van der Waals interaction and nonpolar solvation energy, although the contribution from nonpolar solvation is relatively minor. The key residue mutations also affect the formation of hydrogen bonds and ultimately the stability of the small molecule-SND1 complex.Communicated by Ramaswamy H. Sarma.

Revealing the binding mechanism of BACE1 inhibitors through molecular dynamics simulations

Alzheimer's disease is a debilitating neurodegenerative disorder, and the Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) is a key therapeutic target in its treatment. This study employs molecular dynamics simulations and binding energy analysis to investigate the binding interactions between BACE1 and four selected small molecules: CNP520, D9W, NB641, and NB360. The binding model analysis indicates that the binding of BACE1 with four molecules are stable, except the loop regions show significant fluctuation. The binding free energy analyses reveal that NB360 exhibits the highest binding affinity with BACE1, surpassing other molecules (CNP520, D9W, and NB641). Detailed energy component assessments highlight the critical roles of electrostatic interactions and van der Waals forces in the binding process. Furthermore, residue contribution analysis identifies key amino acids influencing the binding process across all systems. Hydrogen bond analysis reveals a limited number of bonds between BACE1 and each small molecule, highlighting the importance of structural modifications to enable more stable hydrogen bonds. This research provides valuable insights into the molecular mechanisms of potential Alzheimer's disease therapeutics, guiding the way for improved drug design and the development of effective treatments targeting BACE1.

Recent advances in computational methods for biosensor design

Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.

Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics

Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.

Effectively remediating spiramycin from production wastewater through hydrolyzing its functional groups using solid superacid TiO2/SO4

Breaking down the structural bonds and eliminating the functional groups are more efficient than destroying the whole molecule in antibiotic production wastewater (APW) pretreatment before further biotreatment. Two sulfated titania (TiO₂/SO₄) solid superacids, SSA1 and SSA2 were synthesized, characterized and used for hydrolytic pretreatment of spiramycin in APW. Spiramycin removal followed an order of SSA2>SSA1>TiO₂≈pH = 3>control. The hydrolytic efficiencies increased at elevated temperature from 25 °C to 65 °C. The hydrolytic kinetics followed a first-order model and SSA2 performed the fastest. The performances were positively correlated with both the total acidity determined by n-butylamine titration and the strength of acid sites measured by NH₃-temperature-programmed desorption (TPD). The residual solution for SSA2 presented the least antibacterial potency and anaerobic inhibition among all treatments. The hydrolyzed product was identified as the m/z 699.4321 fragment using UPLC-Q/TOF-MS, which was formed after losing a functional mycarose moiety from the parent molecular. The solid superacids were effective in selectively eliminating 433 mg/L of spiramycin and the antibacterial potencies of the spiramycin production wastewater, which contained very high concentrations of COD (33,000 mg/L). This hydrolytic method avoids using and handling hazardous and corrosive mineral acids on site. It is attractive as a selective catalytic pretreatment method to cleave antibiotics' functional groups and to reduce its inhibitory effects before sequential biotreatments.