The pH (low) insertion peptide (pHLIP) is a family of peptides that are able to insert into a lipid bilayer at acidic pH. The molecular mechanism of pHLIPs insertion, folding and stability in the membrane at low pH is based on multiple protonation events, which are challenging to study at molecular level. More specifically, the relation between the experimental pK of insertion (pKexp) of pHLIPs and the pKa of the key residues is yet to be clarified. We carried out a computational study, complemented with new experimental data, and established the influence of (de)protonation of key titrable residues on the stability of the peptide membrane-inserted state. Constant-pH molecular dynamics simulations were employed to calculate the pKa values of these residues along the membrane normal. In the wt-pHLIP, we identified Asp14 as the key residue for the stability of the membrane-inserted state, and its pKa value is strongly correlated with the experimental pKexp measured in thermodynamics studies. Also, in order to narrow down the pH range at which pHLIP is stable in the membrane, we designed a new pHLIP variant, L16H, where Leu in the 16th position was replaced by a titrable His residue. Our results showed that the L16H variant undergoes two transitions. The calculated pK and experimentally observed pKexp values are in good agreement. Two distinct pKexp values delimit a pH range where the L16H peptide is stably inserted in the membrane while, outside this range, the membrane-inserted state is destabilized and the peptide exits from the bilayer. pHLIP peptides have been successfully used to target cancer cells for the delivery of diagnostics and therapeutic agents to acidic tumors. The fine tuning of the stability of pHLIP inserted state and its restriction to a narrow well-defined pH range might allow the design of new pHLIPs, able to discriminate between tissues with different extracellular pH values.

Peptides and proteins protonation equilibrium is strongly influenced by its surrounding media. Remarkably, until now, there have been no quantitative and systematic studies reporting the pK(a) shifts in the common titrable amino acids upon lipid membrane insertion. Here, we applied our recently developed CpHMD-L method to calculate the pK(a) values of titrable amino acid residues incorporated in Ala-based pentapeptides at the water/membrane interface. We observed that membrane insertion leads to desolvation and a clear stabilization of the neutral forms, and we quantified the increases/decreases of the pK(a) values in the anionic/cationic residues along the membrane normal. This work highlights the importance of properly modeling the protonation equilibrium in peptides and proteins interacting with membranes using molecular dynamics simulations.

Biological membranes are complex systems that have recently attracted a significant scientific interest. Due to the presence of many different anionic lipids, these membranes are usually negatively charged and sensitive to pH. The protonation states of lipids and the ion distribution close to the bilayer are two of the main challenges in biomolecular simulations of these systems. These two problems have been circumvented by using ionized (deprotonated) anionic lipids and enough counterions to preserve the electroneutrality. In this work, we propose a method based on the Poisson-Boltzmann equation to estimate the counterion and co-ion concentration close to a lipid bilayer that avoids the need for neutrality at this microscopic level. The estimated number of ions was tested in molecular dynamics simulations of a 25% DMPA/DMPC lipid bilayer at different ionization levels. Our results show that the system neutralization represents an overestimation of the number of counterions. Consequently, the resulting lipid bilayer becomes too ordered and practically insensitive to ionization. On the other hand, our proposed approach is able to correctly model the ionization dependent isothermal phase transition of the bilayer observed experimentally. Furthermore, our approach is not too computationally expensive and can easily be used to model diverse charged biomolecular systems in molecular dynamics simulations.

We describe the synthesis of the new Zn–N‐heterocyclic carbene (NHC) alkoxide complexes [(S,CNHC)ZnCl(OBn)]2 (5) and [(O,CNHC)ZnCl(OBn)]2 (6) for use as ring‐opening polymerization (ROP) initiators for lactide polymerization. Complexes 5 and 6 are readily available through an alcoholysis reaction between BnOH and the corresponding Zn–NHC ethyl species [(S,CNHC)ZnCl(Et)] (3) and [(O,CNHC)ZnCl(Et)] (4), and species 3 and 4 were obtained from the reaction of ZnEt2 with the N‐methyl‐N'‐ethylphenylsulfide (1⋅HCl) and N‐methyl‐N'‐ethylmethylether (2⋅HCl) imidazolium salts, respectively. Both solution and solid‐state structural data for Zn benzyloxide species 5 and 6 agree with dimeric structures under the studied conditions (reaction conditions: CH2Cl2 or THF, room temperature). A computational analysis of species 3 and 4 supports a dimeric structure in solution. The ZnII alkoxide species 5 and 6 were found to mediate either the ROP of lactide (in an effective and controlled manner) to produce chain length‐controlled polylactide (PLA) or, in the presence of an alcohol source such as MeOH, the controlled degradation of PLA through extensive transesterification reactions to afford methyl lactate as the major product. A thorough DFT computational analysis of the ROP of lactide initiated by complex 5 was performed, which revealed that the operating coordination–insertion mechanism was assisted by the second Zn center, leading to a lower‐energy ROP process; this result may be of interest for the future design of well‐defined and high‐performance metal‐based catalysts.

pH is a very important property, influencing all important biomolecules such as proteins, nucleic acids, and lipids. The effect of pH on proteins has been the subject of many computational works in recent years. However, the same has not been done for lipids, especially in their most biologically relevant environment: the bilayer. A reason for this is the inherent technical difficulty in dealing with this type of periodic systems. Here, we tackle this problem by developing a Poisson-Boltzmann-based method that takes in consideration the periodic boundary conditions of lipid bilayer patches. We used this approach with a linear response approximation to calculate the pKa value of a DMPC molecule when diluted in zwitterionic lipids. Our results show that DMPC protonation only becomes relevant at quite low pH values (2-3). However, when it happens, it has a strong impact on lipid conformations, leading to significant heterogeneity in the membrane.

Inhibiting glucose reabsorption by sodium glucose co-transporter proteins (SGLTs) in the kidneys is a relatively new strategy for treating type 2 diabetes. Selective inhibition of SGLT2 over SGLT1 is critical for minimizing adverse side effects associated with SGLT1 inhibition. A library of C-glucosyl dihydrochalcones and their dihydrochalcone and chalcone precursors was synthesized and tested as SGLT1/SGLT2 inhibitors using a cell-based fluorescence assay of glucose uptake. The most potent inhibitors of SGLT2 (IC = 9-23 nM) were considerably weaker inhibitors of SGLT1 (IC = 10-19 μM). They showed no effect on the sodium independent GLUT family of glucose transporters, and the most potent ones were not acutely toxic to cultured cells. The interaction of a C-glucosyl dihydrochalcone with a POPC membrane was modeled computationally, providing evidence that it is not a pan-assay interference compound. These results point toward the discovery of structures that are potent and highly selective inhibitors of SGLT2.

The protonation of titratable residues has a significant impact on the structure and function of biomolecules, influencing many physicochemical and ADME properties. Thus, the importance of the estimation of protonation free energies (pK a values) is paramount in different scientific communities, including bioinformatics, structural biology, or medicinal chemistry. Here, we introduce PypKa, a flexible tool to predict Poisson–Boltzmann/Monte Carlo-based pK a values of titratable sites in proteins. This application was benchmarked using a large data set of experimental values to show that our single structure-based method is fast and has a competitive performance. This is a free and open-source tool that provides a simple, reusable, and extensible Python API and CLI for pK a calculations with a valuable trade-off between fast and accurate predictions. PypKa allows pK a calculations in existing protocols with the addition of a few extra lines of code. PypKa supports CPU parallel computing on solvated proteins obtained from the PDB repository but also from MD simulations using three common naming schemes: GROMOS, AMBER, and CHARMM. The code and documentation to this open-source project is publicly available at .

A major component of ex vivo amyloid plaques of patients with dialysis-related amyloidosis (DRA) is a cleaved variant of β2-microglobulin (ΔN6) lacking the first six N-terminal residues. Here we perform a computational study on ΔN6, which provides clues to understand the amyloidogenicity of the full-length β2-microglobulin. Contrary to the wild-type form, ΔN6 is able to efficiently nucleate fibrillogenesis in vitro at physiological pH. This behavior is enhanced by a mild acidification of the medium such as that occurring in the synovial fluid of DRA patients. Results reported in this work, based on molecular simulations, indicate that deletion of the N-terminal hexapeptide triggers the formation of an intermediate state for folding and aggregation with an unstructured strand A and a native-like core. Strand A plays a pivotal role in aggregation by acting as a sticky hook in dimer assembly. This study further predicts that the detachment of strand A from the core is maximized at pH 6.2 resulting into higher aggregation efficiency. The structural mapping of the dimerization interface suggests that Tyr10, His13, Phe30 and His84 are hot-spot residues in ΔN6 amyloidogenesis.