Low Conformational Changes Research Articles

Forging of nicotine for the effective management of diabetic wounds: A hybrid of scaffold hopping and molecular dynamics simulation approaches

Diabetic wound (DW) is a huge threat to the health care community and is always challenging to treat. The main biochemical culprits in DW recalcitrance are elevated inflammatory mediators, proteases, cell proliferation and migration suppressors, anti-angiogenic factors, and bacterial infections. In this scenario, using a scaffold to target important factors at each stage of pathogenesis can accelerate the healing process. Many shreds of evidence disclosed the role of nicotine scaffold in handling inflammation, infection, proliferation, migration, and angiogenesis. All these factors made us forge nicotine by employing a scaffold hopping approach. The hops were then subjected to molecular docking and binding free energy calculations against Matrix metallopeptidase 9, Glycogen synthase kinase 3 beta, Tumor necrosis factor alpha, MurC and ParE enzymes. Gratifyingly, molecule H1 was found to possess significant inhibitory activity against the selected receptors as evidenced by their high negative glide score and binding energy. Furthermore, 100 ns of molecular dynamics simulation studies (MD) was performed for the five H1/4XCT, H1/5F95, H1/2AZ5, H1/4C13 and H1/4MOT complexes to get insight into the binding modes and stability. The MD results showed significant stability as evidenced by the low conformational changes of the H1 with the chosen receptors. Hence, H1 might be a druggable candidate in the therapeutic management of DW. However, further research is strongly recommended to advance the drug into the therapeutic pipeline.

Curious Binding Energy Increase between the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein and Angiotensin-Converting Enzyme 2 Adsorbed on a Silane Monolayer from Molecular Dynamics Simulations.

In the context of the COVID-19 outbreak since December 2019, antigenic tests are widely used, for diagnosis purposes, to detect the SARS-CoV-2 spike protein in nasopharyngeal fluid through its interactions with specific antibodies. However, the SARS-CoV-2 spike protein is subject to rapid mutations yielding more and more variants that might lose their affinity toward the currently used antibodies. The virus entry into the host cell involves interactions between the angiotensin-converting enzyme 2 (ACE2) and the SARS-CoV-2 spike protein receptor-binding domain. Consequently, ACE2 could be a target with limited mutation escaping possibilities. However, as the enzyme has not evolved to recognize the virus, its affinity with the spike protein receptor-binding domain is lower than that with specific antibodies. The present molecular dynamics simulations study suggests that the adsorption of the ACE2 on specific silane monolayers could increase its affinity toward the spike protein receptor-binding domain. Indeed, silane monolayers, combining silane molecules with short alkyl chains and positively charged head groups and silane molecules without charged head groups, could adsorb the ACE2 while maintaining its bioactivity (orientation compatible with the spike protein trapping, low conformational changes) and increasing its interactions with the spike protein receptor-binding domain (number of hydrogen bonds and electrostatic interactions) to lead to an increase by 20% both in the binding free energy and in the enzyme /receptor-binding domain rupture force. This work could help develop biosensing tools efficient toward any variants of the SARS-CoV-2 spike protein.

Discovery of methoxy-naphthyl linked N-(1-benzylpiperidine) benzamide as a blood-brain permeable dual inhibitor of acetylcholinesterase and butyrylcholinesterase.

The cholinesterase enzymes play a vital role in maintaining balanced levels of the neurotransmitter acetylcholine in the central nervous system. However, the overexpression of these enzymes results in hampered neurotransmission. Both the major forms of cholinesterase enzymes viz. acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) play a crucial role in blocking neurotransmission; therefore, in recent years, a strategy of dual cholinesterase inhibition is being explored. Herein, we developed an energy-optimized e-pharmacophore hypothesis AHHPRR from AChE-donepezil complex and screened a set of 15 scaffolds that were designed imaginarily. The ligand with N-(1-benzylpyridinium) benzamide framework has shown the highest fitness and volume score, which was chosen for synthesis and validation. A series of pyridinium benzamides were synthesized and screened for cholinesterase inhibition that led to the identification of 7b, a naphthalene containing N-(1-benzylpiperidine) benzamide as a potent dual AChE and BChE inhibitor with IC50 values of 0.176, and 0.47μM, respectively. The kinetic study indicated that 7b inhibits AChE in a non-competitive manner with Ki value of 0.21μM, and BChE in a mixed-fashion with Ki of 0.15μM. The observed mode of inhibition was corroborated with molecular docking studies. The MD simulation studies pointed out that both AChE and BChE undergo low conformational changes in complex with 7b. The benzamide 7b displayed high BBB permeability in PAMPA assay, which indicates its potential for further exploration in preclinical studies for Alzheimer's disease.