Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors

A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a −1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.

The Role of Homoaromaticity in the Tropylium-Catalyzed Carboxylic Acid O-H Insertion with Diazoesters

The tropylium catalyzed carboxylic acid O-H insertion with diazoesters providing α-hydroxy esters was reported recently through an activated carbene as the key intermediate. We report a revised mechanism involving a unique homoaromatic intermediate with the tropylium ion and the diazoester based on the DFT calculations. Our computational model provides a clear insight into the binding of the tropylium ion with the diazoester providing the homoaromatic intermediate. The reaction profiles of four different pathways were compared. The energies of the intermediates and the transition states are reported at B97-D3(SMD)/def2TZVP//B97-D3/def2TZVP (in dichloromethane). The energy profiles were compared across a few computational methods to study the sensitivity of our model across methods.

Catalytic atroposelective synthesis of axially chiral benzonitriles via chirality control during bond dissociation and CN group formation

The applications of axially chiral benzonitriles and their derivatives remain mostly unexplored due to their synthetic difficulties. Here we disclose an unusual strategy for atroposelective access to benzonitriles via formation of the nitrile unit on biaryl scaffolds pre-installed with stereogenic axes in racemic forms. Our method starts with racemic 2-arylbenzaldehydes and sulfonamides as the substrates and N-heterocyclic carbenes as the organocatalysts to afford axially chiral benzonitriles in good to excellent yields and enantioselectivities. DFT calculations suggest that the loss of p-toluenesulfinate group is both the rate-determining and stereo-determining step. The axial chirality is controlled during the bond dissociation and CN group formation. The reaction features a dynamic kinetic resolution process modulated by both covalent and non-covalent catalytic interactions. The axially chiral benzonitriles from our method can be easily converted to a large set of functional molecules that show promising catalytic activities for chemical syntheses and anti-bacterial activities for plant protections.

Nanoscale Chemical Imaging of Coadsorbed Thiolate Self-assembled Monolayers on Au(111) by Tip-Enhanced Raman Spectroscopy

Self-assembled monolayers (SAMs) of thiolates on metal surfaces are of key importance for engineering surfaces with tunable properties. However, it remains challenging to understand binary thiolate SAMs on metals at the nanoscale under ambient conditions. Here we employ tip-enhanced Raman spectroscopy (TERS) and density functional theory (DFT) calculations to investigate local information of binary SAMs on Au(111) coadsorbed from an equimolar mixture of p-cyanobenzenethiol (pCTP) and p-aminothiophenol (pATP), including chemical composition, coadsorption behavior, phase segregation, plasmon-induced photocatalysis, and solvation effects. We found that upon competitive adsorption of pCTP and pATP on Au(111) from a methanolic solution, the coadsorption initially occurs randomly and homogeneously; eventually, pATP is replaced by pCTP through gradual growth of pCTP nanodomains. TERS imaging also allows for visualization of the plasmon-induced coupling of pATP to p,p’-dimercaptoazobenzene (DMAB) and the solvation-induced phase segregation of the binary SAMs into nanodomains, with a spatial resolution of ~9 nm under ambient conditions. According to DFT calculations, these aromatic thiolates differing only in their functional groups, -CN versus –NH2, show different adsorption energy on Au(111) in vacuum and methanol, and thus the solvation effect on adsorption energy of these thiolates in methanol can determine the dispersion state and replacement order of the binary thiolates on Au(111).

Exploring novel fluorine rich fuberidazole derivatives as hypoxic cancer inhibitors: design, synthesis, pharmacokinetics, molecular docking and DFT evaluations

Sixteen fuberidazole derivatives as potential new anticancer bioreductive prodrugs are prepared and characterized. The in vitro anticancer potential is examined to explore their cytotoxic properties employing apoptosis, DNA damage, and proliferation tests on chosen hypoxic cancer cells. Overall, eight substances (Compound 5a, 5c, 5d, 5e, 5g, 5h, 5i, and 5m) showed good cytotoxic properties. The potential of compounds is also examined through in silico studies (against human serum albumin), including chem-informatics to understand the structure-activity relationship (SAR), pharmacochemical strength, and the mode of interactions responsible for their action. The DFT calculations revealed that only 5b compound showed the lowest ΔET (2.29 eV) while 5i showed relatively highest βtot (69.89 x 10-31 esu), highest αave (3.18 x 10-23 esu), and dipole moment (6.49 Debye). This study presents a novel class of fuberidazole derivatives with selectivity toward hypoxic cancer cells.