Molecular basis for the inhibitory effects of 5-hydroxycyclopenicillone on the conformational transition of Aβ40 monomer

Bionics design of affinity peptide inhibitors for SARS-CoV-2 RBD to block SARS-CoV-2 RBD-ACE2 interactions

Coronavirus Disease 2019 (COVID-19), has already posed serious threats and impacts on the health of the population and the country's economy. Therefore, it is of great theoretical significance and practical application value to better understand the process of COVID-19 infection and develop effective therapeutic drugs. It is known that the receptor-binding structural domain (SARS-CoV-2 RBD) on the spike protein of the novel coronavirus directly mediates its interaction with the host receptor angiotensin-converting enzyme 2 (ACE2), and thus blocking SARS-CoV-2 RBD-ACE2 interaction is capable of inhibiting SARS-CoV-2 infection. Firstly, the interaction mechanism between SARS-CoV-2RBD-ACE2 was explored using molecular dynamics simulation (MD) coupled with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation method. The results of energy analysis showed that the key residues R403, R408, K417, and Y505 of SARS-CoV-2 RBD and the key residues D30, E37, D38, and Y41 of ACE2 were identified. Therefore, according to the hotspot residues of ACE2 and their distribution, a short peptide library of high-affinity SARS-CoV-2 RBD was constructed. And by using molecular docking virtual screening, six short peptides including DDFEDY, DEFEDY, DEYEDY, DFVEDY, DFHEDY, and DSFEDY with high affinity for SARS-CoV-2 RBD were identified. The results of MD simulation further confirmed that DDFEDY, DEYEDY, and DFVEDY are expected to be effective inhibitors. Finally, the allergenicity, toxicity and solubility properties of the three peptide inhibitors were validated.

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

GV971 derived from marine acidic oligosaccharides has been used to cure Alzheimer's disease (AD). However, the molecular mechanism of its inhibition of the conformational transition of amyloid β-proteins (Aβ) is still unclear. Herein, molecular dynamics simulations were used to explore the molecular mechanism of the main GV971 components including DiM, TetraM, HexaM, and OctaM to inhibit the conformational conversion of the Aβ42 monomer. It is found that the GV971 components inhibit the conformational transition from α-helix to β-sheet and the hydrophobic collapse of the Aβ42 monomer. In addition, the binding energy analysis implies that both electrostatic and van der Waals interactions are beneficial to the binding of GV971 components to the Aβ42 monomer. Among them, electrostatic interactions occupy the dominant position. Moreover, the GV971 components mainly interact directly with the charged residues D1, R5, K16, and K28 by forming salt bridges and hydrogen bonds, which specifically bind to the N-terminal region of Aβ42.