MMsPred: a bioactivity and toxicology predictive system

In the last decade, the development and use of new methods in combinatorial chemistry and high-throughput screening has dramatically increased the number of known biologically active compounds. Paradoxically, the number of drugs reaching the market has not followed the same trend, often because many of the candidate drugs present poor qualities in absorption, distribution, metabolism, excretion, and toxicological properties (ADME-Tox). The ability to recognize and discard bad candidates early in the drug discovery steps would save lost investments in time and money. Machine learning techniques could provide solutions to this problem.
The goal of my research is to develop classifiers that accurately discriminate between active and inactive molecules for a specific target. To this end, I am comparing the effectiveness of the application of different machine learning techniques to this problem.	As a source of data we have selected a set of PubChem's public BioAssays1. In addition, with the objective of realizing a real-time query service with our predictors, we aim to keep the features describing the chemical compounds relatively simple.
At the end of this process, we should better understand how to build statistical models that are able to recognize molecules active in a specific bioassay, including how to select the most appropriate classification technique, and how to describe compounds in such a way that is not excessively resource-consuming to generate, yet contains sufficient information for the classification. We see immediate applications of such technology to recognize compounds with high-risk of toxicity, and also to suggest likely metabolic pathways that would process it

the molecular motion of bovine serum albumin under physiological conditions is ion specific

Specific ion effects on the Brownian motion of BSA protein under physiological conditions give new useful insights into the electrolyte–protein interactions and the molecular mechanisms involved in the Hofmeister effect

Ion specific effects on charged interfaces

The physico-chemical phenomena occurring at charged interfaces are specifically affected by the type and the concentration of electrolytes. This has implications both in living and in inorganic systems. The discovery of the ‘ion specific effects’ dates back to Hofmeister (1888), who observed the specific effect of salts in promoting egg white proteins precipitation. Nowadays we are aware that ion specific effects are ubiquitous in all fields of science and technology where electrolytes play a role. Until few years ago the occurrence of ion specific (Hofmeister) effects, although well recognized in a huge number of cases (i.e. protein precipitation and crystallization, viscosity of aqueous solutions, colloid stability, enzyme activities, etc.), was mainly related to ion-induced change of ‘water structure’. To depict these peculiar behaviors the words ‘kosmotropic’ (order maker) and ‘chaotropic’ (disorder maker) ion were coined. Recently, Ninham and co-workers have proposed an explanation of the Hofmeister phenomena based on the consideration that non- electrostatic ion-specific dispersion forces have to be evaluated at the same level of electrostatics in the Poisson-Boltzmann description of ion-ion and ion-surface interactions. The investigation of the effects that the type of salt and its concentration have on the properties (surface charge and potential, electrochemical behavior) of some proteins (BSA, cytochrome c, lysozyme) and of silica-based ordered mesoporours material (OMM) chosen as model systems, was the main purpose of this thesis. In particular, the present work is devoted to reach the following aims: I) To investigate the ion specific effects due to added electrolytes in different systems where soft or hard matter charged interfaces occur; II) To ascertain the interpretation of different experimental results through Ninham’s theory modeling; III) To show how the comprehension of Hofmeister effects may be used for technological purposes, for instance in the development of ‘controlled release systems’. This thesis can be outlined in two parts. The first part is dedicated to a description of the intermolecular forces in terms of the classical and new theories, which permits to understand ion specific effects at charged interfaces, and to the presentation of the experimental techniques that were used to investigate the various systems. In particular, Chapter 1 gives a brief summary of the classical theories of ‘electrical double layer’ and of ‘colloid stability’ used to describe the phenomena occurring at charged interfaces. Chapter 2 gives an overview of the most important ion-specific phenomena since the famous Hofmeister’s experiment, and of the most recent theoretical approaches currently used to explain ion specificity. Chapter 3 describes the experimental methods and the techniques that were used for the investigation of ion specific effects along the PhD work. In the second part of the thesis the papers where the properties of the charged interfaces were studied as a function of the ionic strength and the type of electrolyte are reported. Papers I and II deal with the model protein Bovine Serum Albumin (BSA) in aqueous solution where a liquid-liquid charged interface is formed. In paper I the surface charge (Zp) and the Zeta potential (ζ) of BSA were determined by means of potentiometric titrations (PT) and electrophoretic light scattering (ELS), respectively. The measurements were carried on as a function of the pH and the ionic strength of the background electrolyte (NaCl) used in the measurements. The isoionic point (IIP) and the isoelectric point (IEP) of the protein were determined as the intercept of the surface charge and zeta potential curves with pH axis, respectively. The shift in the values of IIP (to higher pH) and of IEP (to lower pH), that occurs with increasing ionic strength, depends on the specific interaction of the ions of the background electrolyte with the surface of BSA. The experimental values of IIP and IEP were compared with the respective theoretical values calculated by means of the charge regulation model. In this model the H+ concentration at the protein surface (surface pH), is calculated introducing a term that takes into account the additional potential due to the dispersion forces proposed by Ninham. The same experimental techniques were used in paper II for the determination of the surface charge (Zp) and the electrophoretic mobility (μe) of BSA in the presence of different sodium salts at fixed ionic strength. In this case the values of electrophoretic mobility were used to calculate the effective charge (Zeff) of the protein by means of Henry’s equation. Zp is the net (proton) charge of the protein in the absence of other bound ions. Zeff, instead, is the charge of the protein including the ions (cations and anions) adsorbed on its surface. The difference between these two values (Zp-Zeff) calculated at a given pH, gives an estimation of ion-binding, that is the number of ions (cations and anions) bound to the protein surface. Paper III focuses on a silica-based Ordered Mesoporous Material (OMM), namely SBA-15, dispersed in an aqueous solution and thus forming a solid-liquid charged interface. Potentiometric titrations (PT) were used to estimate the surface charge density (σ) of silica surface of SBA-15 particles in water at different pH values. The surface charge density/pH curve was studied in the presence of salts with different cations but same anion. The experimental results were compared with the theoretical surface charge density (σ) vs pH curves calculated through Ninham’s theory. The theoretical curves for SBA-15 surface charge density were obtained using Ninham’s charge regulation model mentioned above for Paper I. Paper IV highlights the electrochemical behavior of cytochrome c (cyt c) as a function of salt type and concentration. The electrochemical properties of cytochrome c, a redox protein, were investigated by means of differential pulse voltammetry (DPV) as a function of the ionic strength and the type of the supporting electrolyte used to guarantee the electrical conductivity of the solution. This work was carried out during my stay at the laboratory of Prof. Edmond Magner at the University of Limerick (Ireland). The redox potential (E°’) and the intensity of the current measured in the electrochemical experiments were firstly investigated as a function of the ionic strength using NaCl as the supporting electrolyte. The values of the redox potential were fitted using a model derived from the Debye-Hückel extended law. Then, the redox potential and the intensity of current were investigated in the presence of different electrolytes (cations and anions of the Hofmeister series) at a fixed ionic strength. The values of redox potential measured at different temperatures were used to obtain thermodynamic information (H°’ and S°’) about the redox process. Paper V reports a possible application of the electrolyte effects on charged interfaces for the development of a “controlled drug release system”. The adsorption and the release of Lysozyme (Lyz), a protein with antimicrobial activity, from two OMMs (SBA-15 and MSE) were investigated. The work focused on the effect of two weak electrolytes (buffers) used to fix the pH of the adsorbing solution. SBA-15 and MSE have both a hexagonal mesoporous structure, but different chemical composition and surface properties. In particular MSE is characterized by a higher “hydrophobic” character due to the presence of bridged ethylene groups linked to the silicon skeleton. The adsorption of the lysozyme on the two OMMs was carried out at two different pHs (pH 7.0 and 9.6) using two suitable buffers. Lysozyme release in ‘in-vitro’ physiological conditions was investigated. It was found that the Lysozyme loading changes very much, depending on the surface charge and on the type of surface-protein interactions. Non-electrostatic interactions, mainly involved in the adsorption/release process at the Lyz/MSE interface, seems to produce a stronger protein binding while electrostatic forces dominate at the Lyz/SBA-15 interface. Another very significant parameter that affects both adsorption and release is the pH of the adsorbing solution. The changing in the charge of the surfaces allows for a potential modulation of the global performance, both in terms of protein’s loaded amount, and in terms of release’s rate. The main conclusions of this work can be sketched by the following important remarks: I) All kinds of soft or hard matter charged interfaces (liquid-liquid and solid-liquid) are strongly affected by ion specific effects, in striking agreement with Hofmeister series (almost always). II) Theoretical modeling based on the modified Poisson-Boltzmann equation that includes ion dispersion potentials calculated introducing ab-initio ion polarizabilities of differently hydrated ions allowed to reproduce experimental electrochemical properties at a semi-quantitative level, thus validating further Ninham’s theoretical approach for intermolecular forces. III) In the case of OMMs used for immobilizing proteins, both adsorption and release can be modulated by the choice of different buffers (that modifies the pH). Ultimately, it can be asserted that the choice of background salt used in the adsorbing solutions may address different biotechnological purposes for instance a drug delivery system or a biocatalyst

Ion specific effects on charged interfaces

The physico-chemical phenomena occurring at charged interfaces are specifically affected by the type and the concentration of electrolytes. This has implications both in living and in inorganic systems. The discovery of the ‘ion specific effects’ dates back to Hofmeister (1888), who observed the specific effect of salts in promoting egg white proteins precipitation. Nowadays we are aware that ion specific effects are ubiquitous in all fields of science and technology where electrolytes play a role. Until few years ago the occurrence of ion specific (Hofmeister) effects, although well recognized in a huge number of cases (i.e. protein precipitation and crystallization, viscosity of aqueous solutions, colloid stability, enzyme activities, etc.), was mainly related to ion-induced change of ‘water structure’. To depict these peculiar behaviors the words ‘kosmotropic’ (order maker) and ‘chaotropic’ (disorder maker) ion were coined. Recently, Ninham and co-workers have proposed an explanation of the Hofmeister phenomena based on the consideration that non- electrostatic ion-specific dispersion forces have to be evaluated at the same level of electrostatics in the Poisson-Boltzmann description of ion-ion and ion-surface interactions. The investigation of the effects that the type of salt and its concentration have on the properties (surface charge and potential, electrochemical behavior) of some proteins (BSA, cytochrome c, lysozyme) and of silica-based ordered mesoporours material (OMM) chosen as model systems, was the main purpose of this thesis. In particular, the present work is devoted to reach the following aims: I) To investigate the ion specific effects due to added electrolytes in different systems where soft or hard matter charged interfaces occur; II) To ascertain the interpretation of different experimental results through Ninham’s theory modeling; III) To show how the comprehension of Hofmeister effects may be used for technological purposes, for instance in the development of ‘controlled release systems’. This thesis can be outlined in two parts. The first part is dedicated to a description of the intermolecular forces in terms of the classical and new theories, which permits to understand ion specific effects at charged interfaces, and to the presentation of the experimental techniques that were used to investigate the various systems. In particular, Chapter 1 gives a brief summary of the classical theories of ‘electrical double layer’ and of ‘colloid stability’ used to describe the phenomena occurring at charged interfaces. Chapter 2 gives an overview of the most important ion-specific phenomena since the famous Hofmeister’s experiment, and of the most recent theoretical approaches currently used to explain ion specificity. Chapter 3 describes the experimental methods and the techniques that were used for the investigation of ion specific effects along the PhD work. In the second part of the thesis the papers where the properties of the charged interfaces were studied as a function of the ionic strength and the type of electrolyte are reported. Papers I and II deal with the model protein Bovine Serum Albumin (BSA) in aqueous solution where a liquid-liquid charged interface is formed. In paper I the surface charge (Zp) and the Zeta potential (ζ) of BSA were determined by means of potentiometric titrations (PT) and electrophoretic light scattering (ELS), respectively. The measurements were carried on as a function of the pH and the ionic strength of the background electrolyte (NaCl) used in the measurements. The isoionic point (IIP) and the isoelectric point (IEP) of the protein were determined as the intercept of the surface charge and zeta potential curves with pH axis, respectively. The shift in the values of IIP (to higher pH) and of IEP (to lower pH), that occurs with increasing ionic strength, depends on the specific interaction of the ions of the background electrolyte with the surface of BSA. The experimental values of IIP and IEP were compared with the respective theoretical values calculated by means of the charge regulation model. In this model the H+ concentration at the protein surface (surface pH), is calculated introducing a term that takes into account the additional potential due to the dispersion forces proposed by Ninham. The same experimental techniques were used in paper II for the determination of the surface charge (Zp) and the electrophoretic mobility (μe) of BSA in the presence of different sodium salts at fixed ionic strength. In this case the values of electrophoretic mobility were used to calculate the effective charge (Zeff) of the protein by means of Henry’s equation. Zp is the net (proton) charge of the protein in the absence of other bound ions. Zeff, instead, is the charge of the protein including the ions (cations and anions) adsorbed on its surface. The difference between these two values (Zp-Zeff) calculated at a given pH, gives an estimation of ion-binding, that is the number of ions (cations and anions) bound to the protein surface. Paper III focuses on a silica-based Ordered Mesoporous Material (OMM), namely SBA-15, dispersed in an aqueous solution and thus forming a solid-liquid charged interface. Potentiometric titrations (PT) were used to estimate the surface charge density (σ) of silica surface of SBA-15 particles in water at different pH values. The surface charge density/pH curve was studied in the presence of salts with different cations but same anion. The experimental results were compared with the theoretical surface charge density (σ) vs pH curves calculated through Ninham’s theory. The theoretical curves for SBA-15 surface charge density were obtained using Ninham’s charge regulation model mentioned above for Paper I. Paper IV highlights the electrochemical behavior of cytochrome c (cyt c) as a function of salt type and concentration. The electrochemical properties of cytochrome c, a redox protein, were investigated by means of differential pulse voltammetry (DPV) as a function of the ionic strength and the type of the supporting electrolyte used to guarantee the electrical conductivity of the solution. This work was carried out during my stay at the laboratory of Prof. Edmond Magner at the University of Limerick (Ireland). The redox potential (E°’) and the intensity of the current measured in the electrochemical experiments were firstly investigated as a function of the ionic strength using NaCl as the supporting electrolyte. The values of the redox potential were fitted using a model derived from the Debye-Hückel extended law. Then, the redox potential and the intensity of current were investigated in the presence of different electrolytes (cations and anions of the Hofmeister series) at a fixed ionic strength. The values of redox potential measured at different temperatures were used to obtain thermodynamic information (H°’ and S°’) about the redox process. Paper V reports a possible application of the electrolyte effects on charged interfaces for the development of a “controlled drug release system”. The adsorption and the release of Lysozyme (Lyz), a protein with antimicrobial activity, from two OMMs (SBA-15 and MSE) were investigated. The work focused on the effect of two weak electrolytes (buffers) used to fix the pH of the adsorbing solution. SBA-15 and MSE have both a hexagonal mesoporous structure, but different chemical composition and surface properties. In particular MSE is characterized by a higher “hydrophobic” character due to the presence of bridged ethylene groups linked to the silicon skeleton. The adsorption of the lysozyme on the two OMMs was carried out at two different pHs (pH 7.0 and 9.6) using two suitable buffers. Lysozyme release in ‘in-vitro’ physiological conditions was investigated. It was found that the Lysozyme loading changes very much, depending on the surface charge and on the type of surface-protein interactions. Non-electrostatic interactions, mainly involved in the adsorption/release process at the Lyz/MSE interface, seems to produce a stronger protein binding while electrostatic forces dominate at the Lyz/SBA-15 interface. Another very significant parameter that affects both adsorption and release is the pH of the adsorbing solution. The changing in the charge of the surfaces allows for a potential modulation of the global performance, both in terms of protein’s loaded amount, and in terms of release’s rate. The main conclusions of this work can be sketched by the following important remarks: I) All kinds of soft or hard matter charged interfaces (liquid-liquid and solid-liquid) are strongly affected by ion specific effects, in striking agreement with Hofmeister series (almost always). II) Theoretical modeling based on the modified Poisson-Boltzmann equation that includes ion dispersion potentials calculated introducing ab-initio ion polarizabilities of differently hydrated ions allowed to reproduce experimental electrochemical properties at a semi-quantitative level, thus validating further Ninham’s theoretical approach for intermolecular forces. III) In the case of OMMs used for immobilizing proteins, both adsorption and release can be modulated by the choice of different buffers (that modifies the pH). Ultimately, it can be asserted that the choice of background salt used in the adsorbing solutions may address different biotechnological purposes for instance a drug delivery system or a biocatalyst

Adsorption and release of ampicillin antibiotic from ordered mesoporous silica

In this work the adsorption and the release of ampicillin - a β-lactam penicillin-like antibiotic - from MCM-41, SBA-15, and (amino functionalized) SBA-15-NH2 ordered mesoporous silica (OMS) materials were investigated. The silica matrices differ for their pore size (SBA-15 vs. MCM-41) mainly, and also for surface charge (SBA-15 and MCM-41, vs. SBA-15-NH2). OMS samples were characterized through small-angle X-rays scattering (SAXS), transmission electron microscopy (TEM), N2 adsorption–desorption isotherms, Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and potentiometric titrations. The quantification of immobilized and released ampicillin was monitored by mean of UV–Vis spectroscopy. Experimental adsorption isotherms evidenced that ampicillin's loading is not related to the pore size (dBJH) of the adsorbent. Indeed the maximal loadings were 237 mg/g for SBA-15 (dBJH = 6.5 nm), 278 mg/g for MCM-41 (dBJH = 2.2 nm), and 333 mg/g for SBA-15-NH2 (dBJH = 5.6 nm). Loading seems, instead, to be related to the surface charge density (σ) of the sorbent surface. Indeed, at pH 7.4 ampicillin drug is negatively charged and likely prefers to interact with SBA-15-NH2 (σSBA-15-NH2 = +0.223 C m−2) rather than the slightly negatively charged silicas (σSBA-15 = −0.044 C m−2 and σMCM-41 = −0.033 C m−2). Similarly, ampicillin release is affected by interfacial interactions. Indeed, we found a burst release from pure silica samples (SBA-15 and MCM-41), whereas a sustained one from SBA-15-NH2 sample. We explain this behavior as a result of an attractive interaction between the protonated amino group of SBA-15-NH2 and the negatively charged carboxylate group of ampicillin. In summary, in order to obtain a sustained drug release, the chemical nature of the matrix's surface plays a role which is more important than its textural features. SBA-15-NH2 matrix is hence a suitable candidate for local sustained release of antibiotic drugs

Adsorption of malachite green and alizarin red S dyes using Fe-BTC metal organic framework as adsorbent

peer-reviewedSynthetic organic dyes are widely used in various industrial sectors but are also among the most harmful water pollutants. In the last decade, significant efforts have been made to develop improved materials for the removal of dyes from water, in particular, on nanostructured adsorbent materials. Metal organic frameworks (MOFs) are an attractive class of hybrid nanostructured materials with an extremely wide range of applications including adsorption. In the present work, an iron-based Fe-BTC MOF, prepared according to a rapid, aqueous-based procedure, was used as an adsorbent for the removal of alizarin red S (ARS) and malachite green (MG) dyes from water. The synthesized material was characterized in detail, while the adsorption of the dyes was monitored by UV-Vis spectroscopy. An optimal adsorption pH of 4, likely due to the establishment of favorable interactions between dyes and Fe-BTC, was found. At this pH and at a temperature of 298 K, adsorption equilibrium was reached in less than 30 min following a pseudo-second order kinetics, with k” of 4.29 × 10−3 and 3.98 × 10−2 g·mg−1 min−1 for ARS and MG, respectively. The adsorption isotherm followed the Langmuir model with maximal adsorption capacities of 80 mg·g−1(ARS) and 177 mg·g −1 (MG), and KL of 9.30·103 L·mg−1 (ARS) and 51.56·103 L·mg−1 (MG)

Heat-Driven Iontronic Nanotransistors

Thermoelectric polyelectrolytes are emerging as ideal material platform for self-powered bio-compatible electronic devices and sensors. However, despite the nanoscale nature of the ionic thermodiffusion processes underlying thermoelectric efficiency boost in polyelectrolytes, to date no evidence for direct probing of ionic diffusion on its relevant length and time scale has been reported. This gap is bridged by developing heat-driven hybrid nanotransistors based on InAs nanowires embedded in thermally biased Na+-functionalized (poly)ethyleneoxide, where the semiconducting nanostructure acts as a nanoscale probe sensitive to the local arrangement of the ionic species. The impact of ionic thermoelectric gating on the nanodevice electrical response is addressed, investigating the effect of device architecture, bias configuration and frequency of the heat stimulus, and inferring optimal conditions for the heat-driven nanotransistor operation. Microscopic quantities of the polyelectrolyte such as the ionic diffusion coefficient are extracted from the analysis of hysteretic behaviors rising in the nanodevices. The reported experimental platform enables simultaneously the ionic thermodiffusion and nanoscale resolution, providing a framework for direct estimation of polyelectrolytes microscopic parameters. This may open new routes for heat-driven nanoelectronic applications and boost the rational design of next-generation polymer-based thermoelectric materials

Investigating the Role of the Human Element in Maritime Accidents using Semi-Supervised Hierarchical Methods

Navigation safety is a priority both at European and global level. Despite the important progress made over the years, sea accidents remain a major concern and much work is still needed to enhance maritime safety. Knowing the causes and precursors of past accidents is essential to identify the elements on which to intervene to improve safety and reduce the possibility of an accident to occur again. In this study, 1.079 sea accidents from the International Maritime Organization (IMO) database are analyzed using Semi-supervised Recursively Partitioned Mixture Models in an attempt to identify and categorize causal themes from accident data. Special attention is devoted to the human element, which is widely recognized as a primary or precursory cause in most accidents

Inflammation, underweight, malignancy and a marked catabolic state as predictors for worse outcomes in COVID-19 patients with moderate-to-severe disease admitted to Internal Medicine Unit

Introduction: During COVID-19 pandemic, Internal Medicine Units (IMUs) accounted for about 70% of patients hospitalized. Although a large body of data has been published regarding the so-called first wave of the pandemic, little is known about the characteristics and predictors of worse outcomes of patients managed in IMUs during the second wave. Methods: We prospectively assessed demographics, comorbidities, treatment and outcomes, including ventilation support (VS) and death, in patients admitted to our IMU for SARS-CoV-2 between October 13th, 2020 and January 21st, 2021. Clinical evolution and biochemical testing 1, 7 and 14 days after COVID-19 diagnosis were recorded. Results: We studied 120 patients (M/F 56/64, age 71±14.5 years) admitted to our IMU. Most of them had at least one comorbidity (80%). Patients who died were older, more frequently underweight, affected by malignant neoplasms and on statin therapy compared to patients eventually discharged. Both worse outcome groups (VS and death) presented higher neutrophils, ferritin, IL-6 and lower total proteins levels than controls. Age was significantly associated with mortality but not with VS need. The multivariate analysis showed age and gender independent association of mortality with underweight, malignancy and antibiotics use at the admission. With regard to biochemical parameters, both unfavourable outcomes were positively associated with high WBC count, neutrophils, blood urea nitrogen and low serum total proteins. Conclusions: Our study identified inflammation, underweight, malignancy and a marked catabolic state as the main predictors for worse outcomes in COVID-19 patients admitted to IMU during the so-called second wave of the pandemic

The Italian National Register of infants with congenital hypothyroidism: twenty years of surveillance and study of congenital hypothyroidism

All the Italian Centres in charge of screening, diagnosis, and follow-up of infants with congenital hypothyroidism participate in the Italian National Registry of affected infants, which performs the nationwide surveillance of the disease. It was established in 1987 as a program of the Health Ministry and is coordinated by the Istituto Superiore di Sanità. The early diagnosis performed by the nationwide newborn screening programme, the prompt treatment and the appropriate clinical management of the patients carried out by the Follow-up Centres, and the surveillance of the disease performed by the National Register of infants with congenital hypothyroidism are the components of an integrated approach to the disease which has been successfully established in our country