Elucidating Daptomycin's Antibacterial Efficacy: Insights into the Tripartite Complex with Lipid II and Phospholipids in Bacterial Septum Membrane.

This study elucidated the mechanism of formation of a tripartite complex containing daptomycin (Dap), lipid II, and phospholipid phosphatidylglycerol in the bacterial septum membrane, which was previously reported as the cause of the antibacterial action of Dap against gram-positive bacteria via molecular dynamics and enhanced sampling methods. Others have suggested that this transient complex ushers in the inhibition of cell wall synthesis by obstructing the downstream polymerization and cross-linking processes involving lipid II, which is absent in the presence of cardiolipin lipid in the membrane. In this work, we observed that the complex was stabilized by Ca2+-mediated electrostatic interactions between Dap and lipid head groups, hydrophobic interaction, hydrogen bonds, and salt bridges between the lipopeptide and lipids and was associated with Dap concentration-dependent membrane depolarization, thinning of the bilayer, and increased lipid tail disorder. Residues Orn6 and Kyn13, along with the DXDG motif, made simultaneous contact with constituent lipids, hence playing a crucial role in the formation of the complex. Incorporating cardiolipin into the membrane model led to its competitively displacing lipid II away from the Dap, reducing the lifetime of the complex and the nonexistence of lipid tail disorder and membrane depolarization. No evidence of water permeation inside the membrane hydrophobic interior was noted in all of the systems studied. Additionally, it was shown that using hydrophobic contacts between Dap and lipids as collective variables for enhanced sampling gave rise to a free energy barrier for the translocation of the lipopeptide. A better understanding of Dap's antibacterial mechanism, as studied through this work, will help develop lipopeptide-based antibiotics for rising Dap-resistant bacteria.

Mononuclear organogermanium(IV) catalysts for a [3 + 2] cycloaddition reaction.

Three mononuclear Ge(IV) compounds, [(C6H5)2Ge(C13H8N2O4)] (1), [(C6H5)2Ge(C14H10N2O5)] (2), and [(C6H5)2Ge(C14H11NO3)] (3), have been synthesized by the reaction of pro-ligands H2L1 (C13H10N2O4), H2L2 (C14H12N2O5), and H2L3 (C14H13NO3) with (C6H5)2GeCl2 in the presence of triethylamine. All compounds were characterized by FT-IR spectroscopy and NMR spectroscopy. Single crystal X-ray diffraction analysis shows that the germanium(IV) atom exhibits a five-coordinated geometry in compounds 1 and 2. All compounds were screened as Lewis acid catalysts in the [3 + 2] cycloaddition reaction between sodium azide and various nitriles. The reactions resulted in the formation of 5-substituted 1H-tetrazoles with yields of up to 96%. Based on the experimental findings and DFT calculations, a plausible mechanism is proposed for the [3 + 2] cycloaddition reaction.

Design of saccharide based organic binder for low-grade iron ore pelletization using atomistic simulations and machine learning methods.

Inorganic binders like bentonite, used for pelletization of low-grade iron ore, generate iron ore slimes with comparatively high silica and alumina content necessitating extra steps for their removal during iron making process. This demands the usage of organic binders as full or partial replacement of bentonite for iron ore pelletization. In this work, adsorption of organic binders with saccharides skeleton and -H, -OH, -CH2OH and -CH2CH2OH as polar substituents, on goethite surface was studied using density functional theory, molecular dynamics and machine learning. It was observed that adsorption energy of binders on goethite surface had weak dependence on number of hydrogen bonds between them. With this favorable interaction in mind, a library containing 64 organic binders was constructed and adsorption energy of 30 of these binders was computed using molecular dynamics, followed by training of a linear regression model, which was then used to predict the adsorption energy of rest of the binders in the library. It was found that the introduction of -CH2CH2OH at R2 position resulted in statistically significant higher adsorption energy. Binder34 and Binder44 were identified as viable candidates for both goethite and hematite ore pelletization and adsorption of their n-mers on goethite and hematite surfaces was also quantified.

Formate dehydrogenase activity by a Cu(II)-based molecular catalyst and deciphering the mechanism using DFT studies.

Due to the requirement to establish renewable energy sources, formic acid (FA), one of the most probable liquid organic hydrogen carriers (LOHCs), has received great attention. Catalytic formic acid dehydrogenation in an effective and environmentally friendly manner is still a challenge. The N3Q3 ligand (N3Q3 = N,N-bis(quinolin-8-ylmethyl)quinolin-8-amine) and the square pyramidal [Cu(N3Q3)Cl]Cl complex have been synthesised in this work and characterised using several techniques, such as NMR spectroscopy, mass spectrometry, EPR spectroscopy, cyclic voltammetry, X-ray diffraction and DFT calculations. This work investigates the dehydrogenation of formic acid using a molecular and homogeneous catalyst [Cu(N3Q3)Cl]Cl in the presence of HCOONa. The mononuclear copper complex exhibits catalytic activity towards the dehydrogenation of formic acid in H2O with the evolution of a 1 : 1 CO2 and H2 mixture. The activation energy of formic acid dehydrogenation was calculated to be Ea = 86 kJ mol-1, based on experiments carried out at various temperatures. The Gibbs free energy was found to be 82 kJ at 298 K for the decomposition of HCOOH. The DFT studies reveal that [Cu(N3Q3)(HCOO-)]+ undergoes an uphill process of rearrangement followed by decarboxylation to generate [Cu(N3Q3)(H-)]+. The initial uphill step for forming a transition state is the rate-determining step. The [Cu(N3Q3)(H-)]+ follows an activated state in the presence of HCOOH to liberate H2 and generate the [Cu(N3Q3)(OH2)]2+.

Enhanced Uptake of Anticancer C6-Pep Dimer in a Model Membrane Caused by Differential pKa in Acidic Microenvironment.

Acidic tumor microenvironment (TME) presents a challenge for the action of antitumor drugs by acting as an additional barrier for the passive crossing of the cell membrane by chemotherapic agents playing a critical role in the proliferation of tumor cells. Anticancer lipopeptide C6-Pep dimer containing the leucine zipper motif shows an increased uptake into the model tumor membrane in TME, and application of external heat might lead to the uncoiling of the zipper, which could result in cell lysis. This work investigated the cause of this increased uptake of C6-Pep dimer into the bilayer model in TME. Accurate protonation states of all the titratable residues of the C6-Pep dimer in TME were determined using constant pH molecular dynamics. In TME, except for two terminal Glu5 residues, all other Glu residues in the C6-Pep dimer were permanently protonated. The remaining Glu5 residues had differential pKa values, leading to the construction of four possible dimers with different fixed protonation states, and molecular dynamics was used to study their interaction with the anionic bilayer. Except for the dimer at a physiological pH, the other dimers were positively charged and could readily adsorb on the membrane surface. The free energy of insertion of these dimers in the bilayer was lower for single and double protonated Glu5-containing dimers than for the others. After the insertion of the lipopeptides into the membrane, thinning of the bilayer in the vicinity of dimers and an increase in area per lipid of the bilayer were observed for all systems, indicating destabilization of the bilayer due to this intercalation. This study shows that the anticancer lipopeptide C6-Pep utilizes the TME around a tumor cell for insertion into the membrane.

Telescoping-Solvation-Box Protocol-Based Umbrella Sampling Method for Potential Mean Force Estimation.

Previously, it was shown that the telescoping box scheme, in combination with adaptive steered molecule dynamics (ASMD), can be used to estimate the potential of mean force (PMF) with a decrease in computational cost associated with large solvation boxes. Since ASMD reduces to umbrella sampling (US) in the limit of infinitely slow pulling velocity, a hypothesis was made that the telescoping box scheme can be extended to include the US method. The hypothesis was tested using the unfolding pathway of a polyalanine peptide in a water box and translocation of α-tocopherol through the human membrane. Two different approaches were tried: telescoping US (TELUS), in which the number of solvent molecules was linearly coupled to the reaction coordinate, and Block-TELUS, which was a compromise between the fixed solvation box of the US and the window-wise variable solvation box of TELUS. In the case of polyalanine peptide in a water box, both approaches gave overlapping potential of mean force (PMF) concerning the benchmark US-PMF. Window-wise comparison of properties like root-mean-square inner product, Ramachandran plot, α-helix content, and hydrogen bond formation was used to verify that both approaches captured the same dynamics as the US method. Applying the Block-TELUS protocol in the system with diffusing α-tocopherol through the bilayer resulted in overlapping PMF to its US benchmark. A comparison between the window-wise orientation of the chromanol headgroup also produced almost identical results. This study concluded that with the careful application of telescoping solvation boxes, a less computationally expensive US could be performed for systems where the effect of distant solvent molecules on the configurational space sampled in the window depends on the value of the reaction coordinate.

Self-Uptake Mechanism of Polymyxin-Based Lipopeptide against Gram-Negative Bacterial Membrane: Role of the First Adsorbed Lipopeptide.

Research in the continuously increasing threat of polymyxin-resistant multidrug-resistant Pseudomonas aeruginosa, which causes severe infection in immunocompromised patients, has resulted in the development of several polymyxin-derived cyclic lipopeptides containing l-α-γ- diamino butyric acid-like FADDI-019 (F19). In this work, F19's insertion into a minimal model of the asymmetric outer membrane of the bacterium, which contained only penta-acylated lipid A (LipA) and lacked keto-d-octulosonic acid and O-antigens, in the top leaflet and phospholipids in the bottom leaflet, was studied. F19 exhibited all of the hallmarks of the self-uptake mechanism into the asymmetric bilayer. While a single monomer of the lipopeptide did not get partitioned into the inside of the bilayer, it competitively displaced Ca2+ from the membrane surface, observed as a decrease in Ca2+ coordination number with phosphate groups (1.89 vs 1.718), resulting in membrane destabilization. This resulted in an increment of the average defect size and the probability of interplay between lipid tails and hydrophobic residues of another F19. When more than one monomer was present in the system, the first monomer remained docked on the surface, while other monomers intercalated into the bilayer interior with their hydrophobic moieties "sleeved" by lipid acyl chains. The free energy barrier for partial insertion of the lipopeptide into a bilayer in the presence of surface-docked second F19 was recorded at ∼1.3 kcal/mol using two-dimensional (2D) well-tempered metadynamics, making it a low barrier process at 300 K. This study is an attempt to demonstrate the self-uptake mechanism of F19 during intercalation process into the bilayer interior, which may help in the design of better alternates for polymyxins to work against polymyxin resistance.

Photoresponsive transformation from spherical to nanotubular assemblies: anticancer drug delivery using macrocyclic cationic gemini amphiphiles.

We developed NIR-light-responsive macrocyclic cationic gemini amphiphiles, one of which displayed various favorable properties of lipids. The NIR-light-mediated cleavage of the strained dioxacycloundecine ring led to the conversion of the spherical to a nanotubular self-assembly in the aqueous medium. This photo-mediated transformation from the spherical to nanotubular self-assembly resulted in the release of encapsulated hydrophobic anticancer drug molecule doxorubicin (Dox) in a controlled manner. The potent cationic gemini amphiphile also displayed lower cytotoxicity and efficient NIR-light-mediated Dox release efficacy to cancerous cells.