Mapping the hydropathy of amino acids based on their local solvation structure

Nanoscale Topography Dictates Residue Hydropathy in Proteins

Proteins exhibit diverse structures, including pockets, cavities, channels, and bumps, which are crucial in determining their functions. This diversity in topography also introduces significant chemical heterogeneity, with polar and charged domains often juxtaposed with nonpolar domains in proximity. Consequently, accurately assessing the hydropathy of amino acid residues within the intricate nanoscale topology of proteins is essential. This study presents quantitative hydropathy data for 277,877 amino acid residues, computed using the Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) scale. Leveraging this data set comprising 1000 structurally diverse proteins sourced from the Protein Data Bank, we examined residues situated in various nanoscale environments and analyzed hydropathy in relation to protein topography. Our findings indicate that the hydropathy of a residue is intricately linked to both its individual characteristics and the geometric features of its neighboring residues in response to water. Changes in the number and chemical identity of the neighbors, as well as the nanoscale topography surrounding a residue, are mirrored in its hydropathy profile. Our calculations reveal the intricate interplay of hydrophilic, hydroneutral, and hydrophobic residues distributed across the surface and core of proteins. Notably, we observe that protein surfaces can be ten times more hydrophilic than their cores.

An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale

The hydropathy of proteins or quantitative assessment of protein-water interactions has been a topic of interest for decades. Most hydropathy scales use a residue-based or atom-based approach to assign fixed numerical values to the 20 amino acids and categorize them as hydrophilic, hydroneutral, or hydrophobic. These scales overlook the protein's nanoscale topography, such as bumps, crevices, cavities, clefts, pockets, and channels, in calculating the hydropathy of the residues. Some recent studies have included protein topography in determining hydrophobic patches on protein surfaces, but these methods do not provide a hydropathy scale. To overcome the limitations in the existing methods, we have developed a Protocol for Assigning a Residue's Character on the Hydropathy (PARCH) scale that adopts a holistic approach to assigning the hydropathy of a residue. The parch scale evaluates the collective response of the water molecules in the protein's first hydration shell to increasing temperatures. We performed the parch analysis of a set of well-studied proteins that include the following─enzymes, immune proteins, and integral membrane proteins, as well as fungal and virus capsid proteins. Since the parch scale evaluates every residue based on its location, a residue may have very different parch values inside a crevice versus a surface bump. Thus, a residue can have a range of parch values (or hydropathies) dictated by the local geometry. The parch scale calculations are computationally inexpensive and can compare hydropathies of different proteins. The parch analysis can affordably and reliably aid in designing nanostructured surfaces, identifying hydrophilic and hydrophobic patches, and drug discovery.

Investigating the competition between ACE2 natural molecular interactors and SARS-CoV-2 candidate inhibitors

The SARS-CoV-2 pandemic still poses a threat to the global health as the virus continues spreading in most countries. Therefore, the identification of molecules capable of inhibiting the binding between the ACE2 receptor and the SARS-CoV-2 spike protein is of paramount importance. Recently, two DNA aptamers were designed with the aim to inhibit the interaction between the ACE2 receptor and the spike protein of SARS-CoV-2. Indeed, the two molecules interact with the ACE2 receptor in the region around the K353 residue, preventing its binding of the spike protein. If on the one hand this inhibition process hinders the entry of the virus into the host cell, it could lead to a series of side effects, both in physiological and pathological conditions, preventing the correct functioning of the ACE2 receptor. Here, we discuss through a computational study the possible effect of these two very promising DNA aptamers, investigating all possible interactions between ACE2 and its experimentally known molecular partners. Our in silico predictions show that some of the 10 known molecular partners of ACE2 could interact, physiologically or pathologically, in a region adjacent to the K353 residue. Thus, the curative action of the proposed DNA aptamers could recruit ACE2 from its biological functions.

Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics

We use molecular dynamics simulations to investigate the effect of polypeptoid sequence on the structure and dynamics of its hydration waters. Polypeptoids provide an excellent platform to study small-molecule hydration in disordered polymers, as they can be precisely synthesized with a variety of sidechain chemistries. We examine water behavior near a set of peptoid oligomers in which the number and placement of nonpolar versus polar sidechains are systematically varied. To do this, we leverage a new computational workflow enabling accurate sampling of polypeptoid conformations. We find that the hydration waters are less dense, are more tetrahedral, and have slower dynamics compared to bulk water. The magnitude of these shifts increases with the number of nonpolar groups. We also find that shifts in the water structure and dynamics are strongly correlated, suggesting that experimental insight into the dynamics of hydration water obtained by Overhauser dynamic nuclear polarization (ODNP) also contains information about water structural properties. We then demonstrate the ability of ODNP to probe site-specific dynamics of hydration water near these model peptoid systems.

Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

Correlation analysis based on the hydropathy properties of non-steroidal anti-inflammatory drugs in solid-phase extraction (SPE) and reversed-phase high performance liquid chromatography (HPLC) with photodiode array detection and their applications to biological samples

In the present work we analyzed the hydrophobicity and hydrophilicity properties of several non-steroidal anti-inflammatory drugs (NSAIDs) by investigating the structural changes of the dynamic hydrogen bond network in order to predict the extraction recovery of NSAIDs from biological fluids set by solid phase extraction (SPE). This work allows investigating the relationship between theoretical descriptors and experimental data using a parameter free method with a strong correlation (Pearson correlation 0.95, p-value 0.0003). The identification and quantification of analytes in human plasma were carried out by high performance liquid chromatography coupled with photodiode array detection (HPLC-PDA) using a Kinetex Evo C₁₈ (150 x 4.6 mm I.D) protected by a guard column and a mixture of acetonitrile and 10 mM phosphate buffer (pH 2.5) (50:50, v/v) as mobile phase at isocratic conditions. Accuracy (BIAS%) ranged within -2.33% and + 8.05% while precision (RSD%) was less than 5.73%.The mean extraction recovery of the carprofen (IS) was 84.1% and the recovery of NSAIDs from human plasma ranged between 81.9% to 86.6%. LODs and LOQs for all the investigated NSAIDs were 0.003 and 0.01 μg/mL, respectively. The method was validated according to the ICH guide line in the range 0.010-20.0 μg/mL.

Insights into protein sequencing with an α-Hemolysin nanopore by atomistic simulations

Single molecule protein sequencing would represent a disruptive burst in proteomic research with important biomedical impacts. Due to their success in DNA sequencing, nanopore based devices have been recently proposed as possible tools for the sequencing of peptide chains. One of the open questions in nanopore protein sequencing concerns the ability of such devices to provide different signals for all the 20 standard amino acids. Here, using equilibrium all-atom molecular dynamics simulations, we estimated the pore clogging in α-Hemolysin nanopore associated to 20 different homopeptides, one for each standard amino acid. Our results show that pore clogging is affected by amino acid volume, hydrophobicity and net charge. The equilibrium estimations are also supported by non-equilibrium runs for calculating the current blockades for selected homopeptides. Finally, we discuss the possibility to modify the α-Hemolysin nanopore, cutting a portion of the barrel region close to the trans side, to reduce spurious signals and, hence, to enhance the sensitivity of the nanopore.

Intestinal absorption and activation of decitabine amino acid ester prodrugs mediated by peptide transporter PEPT1 and enterocyte enzymes

Decitabine (DAC), a potent DNA methyltransferase (DNMT) inhibitor, has a limited oral bioavailability. Its 5'-amino acid ester prodrugs could improve its oral delivery but the specific absorption mechanism is not yet fully understood. The aim of this present study was to investigate the in vivo absorption and activation mechanism of these prodrugs using in situ intestinal perfusion and pharmacokinetics studies in rats. Although PEPT1 transporter is pH dependent, there appeared to be no proton cotransport in the perfusion experiment with a preferable transport at pH 7.4 rather than pH 6.5. This suggested that the transport was mostly dependent on the dissociated state of the prodrugs and the proton gradient might play only a limited role. In pH 7.4 HEPES buffer, an increase in P_eff was observed for L-val-DAC, D-val-DAC, L-phe-DAC and L-trp-DAC (2.89-fold, 1.2-fold, 2.73-fold, and 1.90-fold, respectively), compared with the parent drug. When co-perfusing the prodrug with Glysar, a known substrate of PEPT1, the permeabilities of the prodrugs were significantly inhibited compared with the control. To further investigate the absorption of the prodrugs, L-val-DAC was selected and found to be concentration-dependent and saturable, suggesting a carrier-mediated process (intrinsic K_m: 7.80 ± 2.61 mM) along with passive transport. Determination of drug in intestinal homogenate after perfusion further confirmed that the metabolic activation mainly involved an intestinal first-pass effect. In a pharmacokinetic evaluation, the oral bioavailability of L-val-DAC, L-phe-DAC and L-trp-DAC were nearly 1.74-fold, 1.69-fold and 1.49-fold greater than that of DAC. The differences in membrane permeability and oral bioavailability might be due to the different stability in the intestinal lumen and the distinct PEPT1 affinity which is mainly caused by the stereochemistry, hydrophobicity and steric hindrance of the side chains. In summary, the detailed investigation of the absorption mechanism by in vivo intestinal perfusion and pharmacokinetic studies showed that the prodrugs of DAC exhibited excellent permeability and oral bioavailability, which might be attributed to a hybrid (partly PEPT1-mediated and partly passive) transport mode and a rapid activation process in enterocytes.

Hydrophobicity of proteins and nanostructured solutes is governed by topographical and chemical context

Hydrophobic interactions drive many important biomolecular self-assembly phenomena. However, characterizing hydrophobicity at the nanoscale has remained a challenge due to its nontrivial dependence on the chemistry and topography of biomolecular surfaces. Here we use molecular simulations coupled with enhanced sampling methods to systematically displace water molecules from the hydration shells of nanostructured solutes and calculate the free energetics of interfacial water density fluctuations, which quantify the extent of solute-water adhesion, and therefore solute hydrophobicity. In particular, we characterize the hydrophobicity of curved graphene sheets, self-assembled monolayers (SAMs) with chemical patterns, and mutants of the protein hydrophobin-II. We find that water density fluctuations are enhanced near concave nonpolar surfaces compared with those near flat or convex ones, suggesting that concave surfaces are more hydrophobic. We also find that patterned SAMs and protein mutants, having the same number of nonpolar and polar sites but different geometrical arrangements, can display significantly different strengths of adhesion with water. Specifically, hydroxyl groups reduce the hydrophobicity of methyl-terminated SAMs most effectively not when they are clustered together but when they are separated by one methyl group. Hydrophobin-II mutants show that a charged amino acid reduces the hydrophobicity of a large nonpolar patch when placed at its center, rather than at its edge. Our results highlight the power of water density fluctuations-based measures to characterize the hydrophobicity of nanoscale surfaces and caution against the use of additive approximations, such as the commonly used surface area models or hydropathy scales for characterizing biomolecular hydrophobicity and the associated driving forces of assembly.

IKKα inibition by a glucosamine derivative enhances Maspin expression in osteosarcoma cell line

Chronic inflammation has been associated to cancer development by the alteration of several inflammatory pathways, such as Nuclear Factor-κB pathway. In particular, IκB kinase α (IKKα), one of two catalytic subunit of IKK complex, has been described to be associated to cancer progression and metastasis in a number of cancers. The molecular mechanism by which IKKα affects cancer progression is not yet completely clarified, anyway an association between IKKα and the expression of Maspin (Mammary Serine Protease Inhibitor or SerpinB5), a tumor suppressor protein, has been described. IKKα shuttles between cytoplasm and nucleus, and when is localized into the nuclei, IKKα regulates the expression of several genes, among them Maspin gene, whose expression is repressed by high amount of nuclear IKKα. Considering that high levels of Maspin have been associated with reduced metastatic progression, it could be hypothesized that the repression of IKKα nuclear translocation could be associated with the repression of metastatic phenotype. The present study is aimed to explore the ability of a glucosamine derivative, 2-(N-Carbobenzyloxy)l-phenylalanylamido-2-deoxy-β-d-glucose (NCPA), synthesized in our laboratory, to stimulate the production of Maspin in an osteosarcoma cell line, 143B. Immunofluorescence and Western blotting experiments showed that NCPA is able to inhibit IKKα nuclear translocation, and to stimulate Maspin production. Moreover, in association with stimulation of Maspin production we found the decrease of β1 Integrin expression, the down-regulation of metalloproteases MMP-9 and MMP-13 production and cell migration inhibition. Taking in account that β1 Integrin and MMP-9 and -13 have been correlated with the invasiveness of osteosarcoma, considering that NCPA affects the invasiveness of 143B cell line, we suggest that this molecule could affect the osteosarcoma metastatic ability.

Prediction of the permeability of neutral drugs inferred from their solvation properties

Motivation: Determination of drug absorption is an important component of the drug discovery and development process in that it plays a key role in the decision to promote drug candidates to clinical trials. We have developed a method that, on the basis of an analysis of the dynamic distribution of water molecules around a compound obtained by molecular dynamics simulations, can compute a parameter-free value that correlates very well with the compound permeability measured using the human colon adenocarcinoma (Caco-2) cell line assay.

Results: The method has been tested on twenty-three neutral drugs for which a consistent set of experimental data is available. We show here that our method reproduces the experimental data better than other existing tools. Furthermore it provides a detailed view of the relationship between the hydration and the permeability properties of molecules.

Contact:anna.tramontano@uniroma1.it

Supplementary information:Supplementary data are available at Bioinformatics online.