Two Novel Metformin Carboxylate Salts and the Accidental Discovery of Two 1,3,5-Triazine Antihyperglycemic Agent

Metformin (MET), commonly marketed as a hydrochloride salt (MET-HCl) for better pharmacokinetic profile over the free base, would release a high concentration of chloride ions and cause adverse gastrointestinal effects. The preparation of chloride-free MET salts could potentially circumvent this issue. In this study, seven carboxylic acids (formic acid, acetic acid, malonic acid, succinic acid, fumaric acid, cinnamic acid, and acetylsalicylic acid) were used for preparing MET carboxylate salts. When compared with MET-HCl, all MET salts/salt hydrates show lower dissolution rates in pH 6.8 phosphate buffer. However, the cinnamic acid and acetylsalicylic acid show significantly higher dissolution rates in the forms of MET salt/salt hydrate. In the permeability test, the permeability of the MET in all of the salts was not improved. However, the permeability of cinnamic acid in the MET cinnamate is reduced, and the permeability of acetylsalicylic acid in the MET acetylsalicylate is increased. Meanwhile, at a higher crystallization temperature, the acetone solvent and a hydrolyzed product of acetylsalicylic acid react with MET respectively, leading to two unexpected 1,3,5-triazine derivatives. The results of in vitro bioactivity assays indicate that one of the triazine molecules promote glucose consumption more effectively than MET-HCl, and had relatively weak lactate production ability at low concentration. This glucose metabolism regulating compound may serve as a novel lead antihyperglycemic agent for further optimization.

Modeling of Olfactory Receptors

Olfactory receptors (ORs) form the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date. Homology modeling has become a popular strategy to propose plausible OR models, in order to study the structure-function relationships of the receptors and to aid the discovery and development of ligands capable of modulating receptor activity. In this chapter, we provide a general guideline for OR structure construction, including the collection of candidate templates, structure-based sequence alignment, 3D structure construction, ligand docking, and molecular dynamic simulation.

Translocation Mechanism of Allosteric Sodium Ions in β2-Adrenoceptor

The allosteric modulation of G-protein-coupled receptors (GPCRs) by sodium ions has received significant attention as the crystal structures of several receptors show the binding of sodium ions (Na⁺) at the conserved D^2.50. Theoretical studies have shown that extracellular Na⁺ would enter the allosteric D^2.50 via the orthosteric site. However, it remains unclear how the bound allosteric Na⁺ would leave the GPCRs. In this study, we performed molecular dynamics (MD) simulations to illustrate the energy barriers of Na⁺ transfer through the transmembrane helix bundle of β₂AR. In contrast to the postulations from other GPCRs, the translocation of this allosteric Na⁺ into the intracellular side is found to be significantly difficult. Hence, the translocation direction could be receptor-specific.

MolADI: A Web Server for Automatic Analysis of Protein-Small Molecule Dynamic Interactions

Protein-ligand interaction analysis is important for drug discovery and rational protein design. The existing online tools adopt only a single conformation of the complex structure for calculating and displaying the interactions, whereas both protein residues and ligand molecules are flexible to some extent. The interactions evolved with time in the trajectories are of greater interest. MolADI is a user-friendly online tool which analyzes the protein-ligand interactions in detail for either a single structure or a trajectory. Interactions can be viewed easily with both 2D graphs and 3D representations. MolADI is available as a web application.

Phase solubility diagrams and energy surface calculations support the solubility enhancement with low hygroscopicity of Bergenin: 4-Aminobenzamide (1: 1) cocrystal

Herein, we reported a new bergenin: 4-aminobenzamide (BGN-4AM) cocrystal with significantly enhanced solubility and low hygroscopicity probed from two aspects such as phase solubility diagrams and theoretical calculations. Compared with anhydrous BGN, BGN-4AM solubilities in water and different buffer solutions (pH = 1.2, 4.5, 6.8) increase significantly. It is noted that BGN-4AM solubility in pH = 6.8 buffer solution presents 32.7 times higher than anhydrous BGN. Interestingly, BGN-4AM (0.31 ± 0.07%) showcases lower hygroscopicity than anhydrous BGN (9.31 ± 0.16%). The predicted and experimental solubilities agree with each other when considering solubility product (K_sp) and solution binding constant (K₁₁) in phase solubility diagrams, indicating the solution complexes formation occurs. Further crystal surface-water interactions and Bravais, Friedel, Donnay-Harker (BFDH) analyses based on Density Functional Theory with dispersion correction (DFT-d) methods support the enhanced solubility. The water probe demonstrates an average interaction energy of -6.48 kcal/mol on the 002 plane of BGN-4AM, and only -5.47 kcal/mol on the 011 plane of BGN monohydrate. The lower lattice energy of BGN-4AM guarantees its lower hygroscopicity than BGN monohydrate. BGN-4AM with enhanced solubility and low hygroscopicity can be a potential candidate for further formulation development.

Clinical HDAC Inhibitors Are Effective Drugs to Prevent the Entry of SARS-CoV2

The outbreak of COVID-19 by the end of 2019 has posed serious health threats to humanity and jeopardized the global economy. However, no effective drugs are available to treat COVID-19 currently and there is a great demand to fight against it. Here, we combined computational screening and an efficient cellular pseudotyped virus system, confirming that clinical HDAC inhibitors can efficiently prevent SARS-CoV-2 and potentially be used to fight against COVID-19.

Exploring a new ligand binding site of G protein-coupled receptors

Identifying a target ligand binding site is an important step for structure-based rational drug design as shown here for G protein-coupled receptors (GPCRs), which are among the most popular drug targets. We applied long-time scale molecular dynamics simulations, coupled with mutagenesis studies, to two prototypical GPCRs, the M3 and M4 muscarinic acetylcholine receptors. Our results indicate that unlike synthetic antagonists, which bind to the classic orthosteric site, the endogenous agonist acetylcholine is able to diffuse into a much deeper binding pocket. We also discovered that the most recently resolved crystal structure of the LTB4 receptor comprised a bound inverse agonist, which extended its benzamidine moiety to the same binding pocket discovered in this work. Analysis on all resolved GPCR crystal structures indicated that this new pocket could exist in most receptors. Our findings provide new opportunities for GPCR drug discovery.

GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection

GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.

Designing Safer Analgesics via μ-Opioid Receptor Pathways

Pain is both a major clinical and economic problem, affecting more people than diabetes, heart disease, and cancer combined. While a variety of prescribed or over-the-counter (OTC) medications are available for pain management, opioid medications, especially those acting on the μ-opioid receptor (μOR) and related pathways, have proven to be the most effective, despite some serious side effects including respiration depression, pruritus, dependence, and constipation. It is therefore imperative that both academia and industry develop novel μOR analgesics which retain their opioid analgesic properties but with fewer or no adverse effects. In this review we outline recent progress towards the discovery of safer opioid analgesics.

The Principles of Ligand Specificity on beta-2-adrenergic receptor

G protein-coupled receptors are recognized as one of the largest families of membrane proteins. Despite sharing a characteristic seven-transmembrane topology, G protein-coupled receptors regulate a wide range of cellular signaling pathways in response to various physical and chemical stimuli, and prevail as an important target for drug discovery. Notably, the recent progress in crystallographic methods led to a breakthrough in elucidating the structures of membrane proteins. The structures of β₂-adrenergic receptor bound with a variety of ligands provide atomic details of the binding modes of agonists, antagonists and inverse agonists. In this study, we selected four representative molecules from each functional class of ligands and investigated their impacts on β₂-adrenergic receptor through a total of 12 × 100 ns molecular dynamics simulations. From the obtained trajectories, we generated molecular fingerprints exemplifying propensities of protein-ligand interactions. For each functional class of compounds, we characterized and compared the fluctuation of the protein backbone, the volumes in the intracellular pockets, the water densities in the receptors, the domain interaction networks as well as the movements of transmembrane helices. We discovered that each class of ligands exhibits a distinct mode of interactions with mainly TM5 and TM6, altering the shape and eventually the state of the receptor. Our findings provide insightful prospective into GPCR targeted structure-based drug discoveries.

The Molecular Mechanism of P2Y1 Receptor Activation

Human purinergic G protein-coupled receptor P2Y1 (P2Y1 R) is activated by adenosine 5'-diphosphate (ADP) to induce platelet activation and thereby serves as an important antithrombotic drug target. Crystal structures of P2Y1 R revealed that one ligand (MRS2500) binds to the extracellular vestibule of this GPCR, whereas another (BPTU) occupies the surface between transmembrane (TM) helices TM2 and TM3. We introduced a total of 20 μs all-atom long-timescale molecular dynamic (MD) simulations to inquire why two molecules in completely different locations both serve as antagonists while ADP activates the receptor. Our results indicate that BPTU acts as an antagonist by stabilizing extracellular helix bundles leading to an increase of the lipid order, whereas MRS2500 blocks signaling by occupying the ligand binding site. Both antagonists stabilize an ionic lock within the receptor. However, binding of ADP breaks this ionic lock, forming a continuous water channel that leads to P2Y1 R activation.

Can picolinamide be a promising cocrystal former?

Picolinamide was shown to demonstrate the potential to be a promising cocrystal former. 8 novel cocrystals were found.