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1. Aquaglyceroporin AQP7's affinity for its substrate glycerol. Have we reached convergence in the computed values of glycerol-aquaglyceroporin affinity?

   https://doi.org/10.1039/D1RA07367B  

   Falato, Michael; Chan, Ruth; Chen, Liao Y. (January 2022, RSC Advances)

   AQP7 is one of the four human aquaglyceroporins that facilitate glycerol transport across the cell membrane, a biophysical process that is essential in human physiology. Therefore, it is interesting to compute AQP7's affinity for its substrate (glycerol) with reasonable certainty to compare with the experimental data suggesting high affinity in contrast with most computational studies predicting low affinity. In this study aimed at computing the AQP7-glycerol affinity with high confidence, we implemented a direct computation of the affinity from unbiased equilibrium molecular dynamics (MD) simulations of three all-atom systems constituted with 0.16 M, 4.32 M, and 10.23 M atoms, respectively. These three sets of simulations manifested a fundamental physics law that the intrinsic fluctuations of pressure in a system are inversely proportional to the system size (the number of atoms in it). These simulations showed that the computed values of glycerol-AQP7 affinity are dependent upon the system size (the inverse affinity estimations were, respectively, 47.3 mM, 1.6 mM, and 0.92 mM for the three model systems). In this, we obtained a lower bound for the AQP7-glycerol affinity (an upper bound for the dissociation constant). Namely, the AQP7-glycerol affinity is stronger than 1087/M (the dissociation constant is less than 0.92 mM). Additionally, we conducted hyper steered MD (hSMD) simulations to map out the Gibbs free-energy profile. From the free-energy profile, we produced an independent computation of the AQP7-glycerol dissociation constant being approximately 0.18 mM. 

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2. Kinetics and free energy of ligand dissociation using weighted ensemble milestoning.

   https://doi.org/10.1063/5.0021953  

   Ray, D; Gokey, T; Mobley, DL; Andricioaei, I. (October 2020, Chemical physics)

   null (Ed.)

   We consider the recently developed weighted ensemble milestoning (WEM) scheme [D. Ray and I. Andricioaei, J. Chem. Phys. 152, 234114 (2020)] and test its capability of simulating ligand-receptor dissociation dynamics. We performed WEM simulations on the following host-guest systems: Na+/Cl- ion pair and 4-hydroxy-2-butanone ligand with FK506 binding protein. As a proof of principle, we show that the WEM formalism reproduces the Na+/Cl- ion pair dissociation timescale and the free energy profile obtained from long conventional MD simulation. To increase the accuracy of WEM calculations applied to kinetics and thermodynamics in protein-ligand binding, we introduced a modified WEM scheme called weighted ensemble milestoning with restraint release (WEM-RR), which can increase the number of starting points per milestone without adding additional computational cost. WEM-RR calculations obtained a ligand residence time and binding free energy in agreement with experimental and previous computational results. Moreover, using the milestoning framework, the binding time and rate constants, dissociation constants, and committor probabilities could also be calculated at a low computational cost. We also present an analytical approach for estimating the association rate constant (kon) when binding is primarily diffusion driven. We show that the WEM method can efficiently calculate multiple experimental observables describing ligand-receptor binding/unbinding and is a promising candidate for computer-aided inhibitor design. 

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3. Analysis of Drug Interactions with Serum Proteins and Related Binding Agents by Affinity Capillary Electrophoresis: A Review

   https://doi.org/10.1002/elps.202200191  

   Sharmeen, Sadia; Kyei, Isaac; Hatch, Arden; Hage David S. (December 2022, Electrophoresis)

   Biomolecules such as serum proteins can interact with drugs in the body and influence their pharmaceutical effects. Specific and precise methods that analyze these interactions are critical for drug development or monitoring and for diagnostic purposes. Affinity capillary electrophoresis (ACE) is one technique that can be used to examine the binding between drugs and serum proteins, or other agents found in serum or blood. This article will review the basic principles of ACE, along with related affinity-based CE methods, and examine recent developments that have occurred in this field as related to the characterization of drug-protein interactions. An overview will be given of the various formats that can be used in ACE and CE for such work, including the relative advantages or weaknesses of each approach. Various applications of ACE and affinity-based CE methods for the analysis of drug interactions with serum proteins and other binding agents will also be presented. Applications of ACE and related techniques that will be discussed include drug interaction studies with serum agents, chiral drug separations employing serum proteins, and the use of CE in hybrid methods to characterize drug binding with serum proteins. 

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4. An octahedral coordination cage with six Fe( iii ) centers as a T ₁ MRI probe

   https://doi.org/10.1039/d4cc03681f  

   Dissanayake, Aruni; Spernyak, Joseph A; Morrow, Janet R (October 2024, Chemical Communications)

   A coordination cage containing six high-spin Fe(iii) centers is an effectiveT₁relaxation agent through second-sphere water interactions. The cage is robust towards dissociation and binds avidly to serum albumin through electrostatic interactions. 

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5. Chromatographic‐Based Binding and Thermodynamic Studies of Antibiotic Micropollutants with Humic Acid Using Affinity Microcolumns

   https://doi.org/10.1002/jssc.70345  

   Sharmeen, Sadia; Kyei, Isaac; Poddar, Saumen; Iftekhar, Sazia; Sajeeb, BK; Graham, Lillian M; Snow, Daniel D; Hage, David S (January 2026, Journal of Separation Science)

   High‐performance affinity microcolumns with entrapped humic acid were utilized to investigate interactions between this natural carrier agent and several classes of antibiotics that are common emerging environmental contaminants, or micropollutants. Aldrich humic acid was used as a general model for this type of binding agent. Chromatographic studies under various temperature and mobile phase conditions were used to characterize interactions of the humic acid with the antibiotics sulfadiazine and sulfamethoxazole (sulfonamides), clarithromycin (a macrolide), and lincomycin (a lincosamide). It was determined by this approach that sulfadiazine and sulfamethoxazole had moderate affinities for the humic acid at pH 7.0 and 25°C, with distribution equilibrium constants (KD) of ∼2–3 × 10^1 L/kg and global affinities (nK’a) of ∼0.8–1.0 × 10^3 M^−1. Lincomycin and clarithromycin had stronger binding, with KD and nK’a values of 3.8–7.5 × 10^2 L/kg and 1.3–2.6 × 10^4 M^−1. All the antibiotics had a negative for this binding, representing spontaneous reactions, and a negative change in enthalpy; however, the change in free energy due to entropy was positive in some cases but negative in others. The binding strength decreased in each case as the ionic strength increased. A change in pH also affected binding, as was consistent with the presence of significant electrostatic interactions from some of the antibiotics. These experiments demonstrated how affinity microcolumns could be employed to study such interactions quickly and with only small amounts of binding agent. The fundamental information obtained through this analytical technique should be valuable in characterizing the transport and activity of these antibiotics in the environment and in adapting this approach to the study of other binding agents and micropollutants that may be found in water. 

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