Peptides are fragments of proteins that carry out biological functions. They act as signaling entities via all domains of life and interfere with protein-protein interactions, which are indispensable ...in bio-processes. Short peptides include fundamental molecular information for a prelude to the symphony of life. They have aroused considerable interest due to their unique features and great promise in innovative bio-therapies. This work focusing on the current state-of-the-art short peptide-based therapeutical developments is the first global review written by researchers from all continents, as a celebration of 100 years of peptide therapeutics since the commencement of insulin therapy in the 1920s. Peptide "drugs" initially played only the role of hormone analogs to balance disorders. Nowadays, they achieve numerous biomedical tasks, can cross membranes, or reach intracellular targets. The role of peptides in bio-processes can hardly be mimicked by other chemical substances. The article is divided into independent sections, which are related to either the progress in short peptide-based theranostics or the problems posing challenge to bio-medicine. In particular, the SWOT analysis of short peptides, their relevance in therapies of diverse diseases, improvements in (bio)synthesis platforms, advanced nano-supramolecular technologies, aptamers, altered peptide ligands and in silico methodologies to overcome peptide limitations, modern smart bio-functional materials, vaccines, and drug/gene-targeted delivery systems are discussed.
This is a perspective article entitled “Frontiers in computational biophysics: understanding conformational dynamics of complex lipid mixtures relevant to biology” which is following a CECAM meeting ...with the same name.
Graphical Abstract
In order to combat bacterial and cancer resistance, we identified peptides (pugnins) with dual antibacterial l-anticancer activity from the
(
) skin transcriptome through in silico analysis. Pugnins ...A and B were selected owing to their high similarity to the DS4.3 peptide, which served as a template for their alignment to the
transcriptome, as well as their function as part of a voltage-dependent potassium channel protein. The secondary peptide structure stability in aqueous medium was evaluated as well, and after interaction with the
(
) membrane model using molecular dynamics. These pugnins were synthesized via solid-phase synthesis strategy and verified by Reverse phase high-performance liquid chromatography (RP-HPLC) and mass spectrometry. Subsequently, their alpha-helix structure was determined by circular dichroism, after which antibacterial tests were then performed to evaluate their antimicrobial activity. Cytotoxicity tests against cancer cells also showed selectivity of pugnin A toward breast cancer (MFC7) cells, and pugnin B toward prostate cancer (PC3) cells. Alternatively, flow cytometry revealed necrotic cell damage with a major cytotoxic effect on human keratinocytes (HaCaT) control cells. Therefore, the pugnins found in the transcriptome of
present dual antibacterial-anticancer activity with reduced selectivity to normal eukaryotic cells.
Following our previous work, where we described the interaction of calcium with the Cx26 hemichannel, we further explore the same system by atomistic molecular dynamics simulations considering a ...different di-cation, magnesium. Specifically, the interaction of magnesium di-cation with the previously reported calcium binding sites (ASP2, ASP117, ASP159, GLU114, GLU119, GLU120, and VAL226) was investigated to identify similarities and differences between them. In order to do so, four extensive simulations were carried out. Two of them considered a Cx26 hemichannel embedded on a POPC bilayer with one of the di-cations and a sodium-chlorine solution. For the remaining two, no di-cations were included and a sodium-chlorine or potassium-chlorine solution was considered. Potassium has a similar atomic mass to calcium, and sodium to magnesium, but they both differ in charge (1e and 2e respectively). Magnesium and calcium, even having the same charge, showed different affinity for the explored protein. From the calcium binding sites referred above, we found that the magnesium di-cations only binds strongly to the GLU114 site of one connexin. For the sodium and potassium simulations, no specific interactions with the protein were found. Altogether, these results suggest that mass and steric effects play an important role in determining cation binding to Cx26 hemichannels.
Objectives To investigate the molecular interaction between β‐cyclodextrin (βCD) or hydroxypropyl‐β‐cyclodextrin (HPβCD) and riboflavin (RF), and to test the anticancer potential of these ...formulations.
Methods The physicochemical characterization of the association between RF and CDs was performed by UV‐vis absorption, fluorescence, differential scanning calorimetry and NMR techniques. Molecular dynamics simulation was used to shed light on the mechanism of interaction of RF and CDs. Additionally, in‐vitro cell culture tests were performed to evaluate the cytotoxicity of the RF–CD complexes against prostate cancer cells.
Key findings Neither βCD nor HPβCD led to substantial changes in the physicochemical properties of RF (with the exception of solubility). Additionally, rotating frame Overhauser effect spectroscopy experiments detected no spatial correlations between hydrogens from the internal cavity of CDs and RF, while molecular dynamics simulations revealed ‘out‐of‐ring’ RF–CD interactions. Notwithstanding, both RF–βCD and RF–HPβCD complexes were cytotoxic to PC3 prostate cancer cells.
Conclusions The interaction between RF and either βCD or HPβCD, at low concentrations, seems to be made through hydrogen bonding between the flavonoid and the external rim of both CDs. Regardless of the mechanism of complexation, our findings indicate that RF–CD complexes significantly increase RF solubility and potentiate its antitumour effect.
The aim of the present work was to understand the interfacial properties of a complex mixture of wax esters (WEs) obtained from Jojoba oil (JO). Previously, on the basis of molecular area ...measurements, a hairpin structure was proposed as the hypothetical configuration of WEs, allowing their organization as compressible monolayers at the air–water interface. In the present work, we contributed with further experimental evidence by combining surface pressure (π), surface potential (ΔV), and PM-IRRAS measurements of JO monolayers and molecular dynamic simulations (MD) on a modified JO model. WEs were self-assembled in Langmuir films. Compression isotherms exhibited πlift‑off at 100 Å2/molecule mean molecular area (A lift‑off) and a collapse point at πc ≈ 2.2 mN/m and A c ≈ 77 Å2/molecule. The ΔV profile reflected two dipolar reorganizations, with one of them at A > A lift‑off due to the release of loosely bound water molecules and another one at A c < A < A lift‑off possibly due to reorientations of a more tightly bound water population. This was consistent with the maximal SP value that was calculated according to a model that considered two populations of oriented water and was very close to the experimental value. The orientation of the ester group that was assumed in that calculation was coherent with the PM-IRRAS behavior of the carbonyl group with the CO oriented toward the water and the C–O oriented parallel to the surface and was in accordance with their orientational angles (∼45 and ∼90°, respectively) determined by MD simulations. Taken together, the present results confirm a V shape rather than a hairpin configuration of WEs at the air–water interface.
We investigated the encapsulation of prilocaine (PLC), an aminoamide local anesthetic widely used in dentistry, into a small unilamellar liposome. We extended a recently developed coarse grained ...model to access the problem relevant time and length scales. Molecular dynamics (MD) simulations for different protonation states of the PLC captured important features of the PLC−vesicle interactions. We found that all neutral PLC molecules (nPLC) rapidly diffuse into the hydrophobic region of the vesicle adopting an asymmetric bimodal density distribution, with nPLC molecules jumping between the internal and external vesicle monolayers. Protonated PLC molecules (pPLC) initially placed in water were instead only found on the external monolayer, with a high rate of exchange with the water phase and no access to the inner part of the liposome. Although electrostatic interaction between pPLC tails and oppositely charged lipid head groups is shown to be structured, hydrophobicity is the driving force of PLC drug absorption within the liposome. Our simulations also show that a major percentage of pPLC remains trapped within the interior water phase of the liposome when starting from a configuration with pPLC distributed within the lipid membrane. This suggests that at low pH liposome−PLC complexes and therefore drug efficacy can strongly depend on the preparation procedure.
In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive ...molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we simulated the peptide-lipid system from three different initial configurations: (a) peptides in water in the presence of a pre-equilibrated lipid bilayer; (b) peptides inside the hydrophobic core of the membrane; and (c) random configurations that allow self-assembled molecular structures. This last approach allowed us to sample the structural space of the systems and consider cooperative effects. The peptides used in our simulations are aurein 1.2 and maculatin 1.1; two well-known antimicrobial peptides from the Australian tree frogs; and molecules that present different membrane-perturbing behaviors. Our results showed differential behaviors for each type of peptide seen in a different organization that could guide a molecular interpretation of the experimental data. While both peptides are capable of forming membrane aggregates; the aurein 1.2 ones have a pore-like structure and exhibit a higher level of organization than those conformed by maculatin 1.1. Furthermore; maculatin 1.1 has a strong tendency to form clusters and induce curvature at low peptide-lipid ratios. The exploration of the possible lipid-peptide structures; as the one carried out here; could be a good tool for recognizing specific configurations that should be further studied with more sophisticated methodologies.
In order to understand the interaction between naratriptan and a fully hydrated bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidyl-choline (POPC), we carried out molecular dynamics ...simulations. The simulations were performed considering neutral and protonated ionization states, starting from different initial conditions. At physiological pH, the protonated state of naratriptan is predominant. It is expected that neutral compounds could have larger membrane partition than charged compounds. However, for the specific case of triptans, it is difficult to study neutral species in membranes experimentally, making computer simulations an interesting tool. When the naratriptan molecules were originally placed in water, they partitioned between the bilayer/water interface and water phase, as has been described for similar compounds. From this condition, the drugs displayed low access to the hydrophobic environment, with no significant effects on bilayer organization. The molecules anchored in the interface, due mainly to the barrier function of the polar and oriented lipid heads. On the other hand, when placed inside the bilayer, both neutral and protonated naratriptan showed self-aggregation in the lipid tail environment. In particular, the protonated species exhibited a pore-like structure, dragging water through this environment.
Graphical Abstract
Different behaviour of Naratriptan and Sumatriptan, when the drugs were originally placed in the lipid core
In this work we implement a new methodology to study structural and mechanical properties of systems having spherical and planar symmetries throughout Molecular Dynamics simulations. This methodology ...is applied here to a drug delivery system based in polymersomes, as an example. The chosen model drug was the local anesthetic prilocaine due to previous parameterization within the used coarse grain scheme. In our approach, mass density profiles (MDPs) are used to obtain key structural parameters of the systems, and pressure profiles are used to estimate the curvature elastic parameters. The calculation of pressure profiles and radial MPDs required the development of specific methods, which were implemented in an in-house built version of the GROMACS 2018 code. The methodology presented in this work is applied to characterize poly(ethylene oxide)-poly(butadiene) polymersomes and bilayers loaded with the model drug prilocaine. Our results show that structural properties of the polymersome membrane could be obtained from bilayer simulations, with significantly lower computational cost compared to whole polymersome simulations, but the bilayer simulations are insufficient to get insights on their mechanical aspects, since the elastic parameters are canceled out for the complete bilayer (as consequence of the symmetry). The simulations of entire polymersomes, although more complex, offer a complementary approach to get insights on the mechanical behavior of the systems.
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