Tuning the lanthanide binding tags for preferential actinide chelation: an all atom molecular dynamics study.

The present study focuses on designing mutant peptides derived from the lanthanide binding tag (LBT) to enhance selectivity for trivalent actinide (An) ions over lanthanide (Ln) metal ions (M). The LBT is a short peptide consisting of only 17 amino acids, and is known for its high affinity towards Ln. LBT was modified by substituting hard-donor ligands like asparagine (ASN or N) and aspartic acid (ASP or D) with softer ligand cysteine (CYS or C) to create four mutant peptides: M-LBT (wild-type), M-N103C, M-D105C, and M-N103C-D105C.

Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study.

Uranium is routinely handled in various stages of nuclear fuel cycle and its association with human serum albumin (HSA) has been reported in literature, however, their binding characteristics still remains obscure. The present study aims to understand interaction of uranium with HSA by employing all atom molecular dynamics simulation of the HSA-metal ion complex. His67, His247 and Asp249 residues constitute the major binding site of HSA, which capture the uranyl ion (UO).

Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein.

The first direful biomolecular event leading to COVID-19 disease is the SARS-CoV-2 virus surface spike (S) protein-mediated interaction with the human transmembrane protein, angiotensin-converting enzyme 2 (hACE2). Prevention of this interaction presents an attractive alternative to thwart SARS-CoV-2 replications. The development of monoclonal antibodies (mAbs) in the convalescent plasma treatment, nanobody, and designer peptides, which recognizes epitopes that overlap with hACE2 binding sites in the receptor-binding domain (RBD) of S protein (S/RBD) and thereby blocking the infection has been the center stage of therapeutic research.

Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation.

The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which , is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies.

MD simulation reveals differential binding of Cm(III) and Th(IV) with serum transferrin at acidic pH.

The iron carrier human serum transferrin (sTf) is known to transport other metals, including some actinides (An). Radiotoxic An are routinely involved in the nuclear fuel cycle and the possibility of their accidental exposure cannot be ruled out. Understanding An interaction with sTf assumes a greater significance for the development of safe and efficacious chelators for their removal from the blood stream.

Molecular dynamics simulations of plutonium binding and its decorporation from the binding-cleft of human serum transferrin.

The possibility of plutonium (Pu) intake by radiation workers can not be ruled out. Transportation of Pu(IV) to various organs/cells is mainly carried through iron-carrying protein, serum transferrin (sTf), by receptor-mediated endocytosis. Understanding the Pu-sTf interaction is a primary step toward future design of its decorporating agents.

Quantum chemical and well-tempered metadynamics study to design adenine analogs for orthogonal Preq riboswitch.

Communicated by Ramaswamy H. Sarma.

Binding of Cm(III) and Th(IV) with Human Transferrin at Serum pH: Combined QM and MD Investigations.

Human serum transferrin (sTf) can also function as a noniron metal transporter since only 30% of it is typically saturated with a ferric ion. While this function of sTf can be fruitfully utilized for targeted delivery of certain metal therapeutics, it also runs the risk of trafficking the lethal radionuclides into cells. A large number of actinide (An) ions are known to bind to the iron sites of sTf although molecular-level understanding of their binding is unclear.

Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water.

Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters.

Stereoselective Metabolism of Omeprazole by Cytochrome P450 2C19 and 3A4: Mechanistic Insights from DFT Study.

The efficacy of S-omeprazole as a proton pump inhibitor compared with that of its enantiomer R-omeprazole is studied using density functional theoretical calculations. The pharmacokinetic studies suggest that the efficacy of S-omeprazole presumably depends on metabolic pathway and excretion from the human body. The density functional theory calculations at SMD-B3LYP-D3/6-311+G(d,p)/LANL2DZ//B3LYP/6-31G(d)/LANL2DZ with triradicaloid model active species, [PorFe(SH)O], of CYP2C19 enzyme with high-spin quartet and low-spin doublet states demonstrate C-H bond activation mechanism through a two-state rebound process for the hydroxylation of R-omeprazole and S-omeprazole.

Dynamic Mechanism of a Fluorinated Oxime Reactivator Unbinding from AChE Gorge in Polarizable Water.

A well-tempered metadynamics simulation is performed to study the unbinding process of a fluorinated oxime (FHI-6) drug from the active-site gorge of acetylcholinesterase enzyme in a polarizable water medium. Cation-π interactions and water bridge and hydrogen bridge formations between the protein and the drug molecule are found to strongly influence the unbinding process, forming basins and barriers along the gorge pathway. Distinct unbinding pathways are found when FHI-6 was compared with its recently reported nonfluorinated analogue, HI-6.

Designed inhibitors with hetero linkers for gastric proton pump H,K-ATPase: Steered molecular dynamics and metadynamics studies.

Acid suppressant SCH28080 and its derivatives reversibly reduce acid secretion activity of the H,K-ATPase in a K competitive manner. The results on homologation of the SCH28080 by varying the linker chain length suggested the improvement in efficacy. However, the pharmacokinetic studies reveal that the hydrophobic nature of the CH linker units may not help it to function as a better acid suppressant.

Divalent ions are potential permeating blockers of the non-selective NaK ion channel: combined QM and MD based investigations.

The bacterial NaK ion channel is distinctly different from other known ion channels due to its inherent non-selective feature. One of the unexplored and rather interesting features is its ability to permeate divalent metal ions (such as Ca and Ba) and not monovalent alkali metal ions. Several intriguing questions about the energetics and structural aspects still remain unanswered.

Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study.

Oral polio vaccine is considered to be the most thermolabile of all the common childhood vaccines. Despite heavy water (DO) having been known for a long time to stabilise attenuated viral RNA against thermodegradation, the molecular underpinnings of its mechanism of action are still lacking. Whereas, understanding the basis of DO action is an important step that might reform the way other thermolabile drugs are stored and could possibly minimize the cold chain problem.

Unbinding of fluorinated oxime drug from the AChE gorge in polarizable water: a well-tempered metadynamics study.

Despite the fact that fluorination makes a drug more lipophilic, the molecular level understanding of protein-fluorinated drug interactions is very poor. Due to their enhanced ability to penetrate the blood brain barrier, they are suitable for reactivation of organophosphorus inactivated acetylcholinesterase (AChE) in the central nervous system. We systematically studied the unbinding of fluorinated obidoxime (FOBI) and non-fluorinated obidoxime (OBI) from the active site gorge of the serine hydrolase AChE in mean field polarizable water by employing all atom molecular dynamics simulations.

Revealing the Mechanistic Pathway of Acid Activation of Proton Pump Inhibitors To Inhibit the Gastric Proton Pump: A DFT Study.

Acid-related gastric diseases are associated with disorder of digestive tract acidification due to the acid secretion by gastric proton pump, H,K-ATPase. Omeprazole is one of the persuasive irreversible inhibitor of the proton pump H,K-ATPase. However, the reports on the mechanistic pathway of irreversible proton pump inhibitors (PPIs) on the acid activation and formation of disulfide complex are scarce in the literature.

Efficient Separation of Europium Over Americium Using Cucurbit-[5]-uril Supramolecule: A Relativistic DFT Based Investigation.

Achieving an efficient separation of chemically similar Am(3+)/Eu(3+) pair in high level liquid waste treatment is crucial for managing the long-term nuclear waste disposal issues. The use of sophisticated supramolecules in a rigid framework could be the next step toward solving the long-standing problem. Here, we have investigated the possibility of separating Am(3+)/Eu(3+) pair with cucurbit-[5]-uril (CB[5]), a macrocycle from the cucurbit-[n]-uril family, using relativistic density functional theory (DFT) based calculations.

Protein-Drug Interactions with Effective Polarization in Polarizable Water: Oxime Unbinding from AChE Gorge.

Despite the fact that polarizability of water is different in the bulk and in protein, simulations of protein-ligand complexes are mostly carried out in nonpolarizable water media. We present oxime (HI-6) unbinding from the active site gorge of AChE, known to be strongly influenced by intermolecular cation-π, hydrogen bridge (HB) and water bridge (WB) interactions and by molecular simulations with effective polarization in polarizable mean-field model of TIP3P water. Enabled by the recent availability of a method of obtaining microkinetics of rare events, we set out to investigate the rate constants of unbinding transitions from one basin to the other through a combination of metadynamics and hyperdynamics simulations.

Selectivity of a Singly Permeating Ion in Nonselective NaK Channel: Combined QM and MD Based Investigations.

Ion channels, such as potassium channels are known to discriminate ions to achieve remarkable selective transportation of K(+) over Na(+) through the membrane. The recently reported NaK ion channel, on the contrary, seems to be an exception, as it is observed to permeate most of the group IA alkali metal cations and hence is suggested to be nonselective in nature. However, does that correspond to a complete annihilation of selectivity inside the selectivity filter (SF) of the channel? What is the origin of such nonselectivity/selectivity, if any? The present computational study is an extensive multiscale modeling approach to find the probable answers to these intriguing questions.

Ortho-7 bound to the active-site gorge of free and OP-conjugated acetylcholinesterase: cation-π interactions.

Despite the immense importance of cation-π interactions prevailing in bispyridinium drug acetylcholinesterase (AChE) complexes, a precise description of cation-π interactions at molecular level has remained elusive. Here, we consider a bispyridinium drug, namely, ortho-7 in three different structures of AChE, with and without complexation with organophosphorus (OP) compounds for detailed investigation using all atom molecular dynamics simulation. By quantum mechanical calculations, Y72, W86, Y124, W286, Y337, and Y341 aromatic residues of the enzyme are investigated for possible cation-π interactions with ortho-7.

Water-Mediated Differential Binding of Strontium and Cesium Cations in Fulvic Acid.

The migration of potentially harmful radionuclides, such as cesium ((137)Cs) and strontium ((90)Sr), in soil is governed by the chemical and biological reactivity of soil components. Soil organic matter (SOM) that can be modeled through fulvic acid (FA) is known to alter the mobility of radionuclide cations, Cs(+) and Sr(2+). Shedding light on the possible interaction mechanisms at the atomic level of these two ions with FA is thus vital to explain their transport behavior and for the design of new ligands for the efficient extraction of radionuclides.

An ultrafast molecular rotor based ternary complex in a nanocavity: a potential "turn on" fluorescence sensor for the hydrocarbon chain.

Formation of a ternary complex by an ultrafast molecular rotor (UMR) with a macrocyclic cavitand has been investigated for the sensitive detection of the alkyl chain of a surfactant. A benzothiazole based UMR, Thioflavin-T (ThT), has been used as a fluorescent probe. It is shown that ThT forms a very weak inclusion complex with γ-cyclodextrin (γ-CD) with an association constant of 8.

Deciphering the binding modes of hematoporphyrin to bovine serum albumin.

Interaction of proteins with small molecules is important in understanding delivery and transport of different therapeutic agents, including drugs. In the present study, we investigated the interaction between hematoporphyrin (HP), the principal component of photosensitizing drug with bovine serum albumin (BSA) in aqueous buffer solution using UV-Vis absorption spectroscopy and fluorescence measurements. The results were further substantiated by molecular docking and molecular dynamics (MD) simulation.

Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation.

Because of the pivotal role that the nerve enzyme, acetylcholinesterase plays in terminating nerve impulses at cholinergic synapses. Its active site, located deep inside a 20 Å gorge, is a vulnerable target of the lethal organophosphorus compounds. Potent reactivators of the intoxicated enzyme are nucleophiles, such as bispyridinium oxime that binds to the peripheral anionic site and the active site of the enzyme through suitable cation-π interactions.