Application of Genetic Programming (GP) Formalism for Building Disease Predictive Models from Protein-Protein Interactions (PPI) Data

Novel Properties of Old Propranolol-Assessment of Antiglycation Activity through In Vitro and In Silico Approaches

Hypertension has earned the "silent killer" nickname since it may lead to a number of comorbidities, including diabetes and cardiovascular diseases. Oxidative stress and protein glycation play vital roles in the pathogenesis of hypertension. Several studies have shown that they profoundly account for vascular dysfunction, endothelial damage, and disruption of blood pressure regulatory mechanisms. Of particular note are advanced glycation end products (AGEs). AGEs alter vascular tissues' functional and mechanical properties by binding to receptors for advanced glycation end products (RAGE), stimulating inflammation and free radical-mediated pathways. Propranolol, a nonselective beta-adrenergic receptor antagonist, is one of the most commonly used drugs to treat hypertension and cardiovascular diseases. Our study is the first to analyze propranolol's effects on protein glycoxidation through in vitro and in silico approaches. Bovine serum albumin (BSA) was utilized to evaluate glycoxidation inhibition by propranolol. Propranolol (1 mM) and BSA (0.09 mM) were incubated with different glycating (0.5 M glucose, fructose, and galactose for 6 days and 2.5 mM glyoxal and methylglyoxal for 12 h) or oxidizing agents (chloramine T for 1 h). Biomarkers of protein glycation (Amadori products (APs), β-amyloid (βA), and advanced glycation end products (AGEs)), protein glycoxidation (dityrosine (DT), kynurenine (KYN), and N-formylkynurenine (NFK)), protein oxidation (protein carbonyls (PCs), and advanced oxidation protein products (AOPPs)) were measured by means of colorimetric and fluorimetric methods. The scavenging of reactive oxygen species (hydrogen peroxide, hydroxyl radical, and nitric oxide) and the antioxidant capacity (2,2-diphenyl-1-picrylhydrazyl radical and ferrous ion chelating (FIC) assays)) of propranolol were also evaluated. Additionally, in silico docking was performed to showcase propranolol's interaction with BSA, glycosides, and AGE/RAGE pathway proteins. The products of protein glycation (↓APs, ↓βA, ↓AGEs), glycoxidation (↓DT, ↓KYN, ↓NFK), and oxidation (↓PCs, ↓AOPPs) prominently decreased in the BSA samples with both glycating/oxidizing factors and propranolol. The antiglycoxidant properties of propranolol were similar to those of aminoguanidine, a known protein oxidation inhibitor, and captopril, which is an established antioxidant. Propranolol showed a potent antioxidant activity in the FIC and H2O2 scavenging assays, comparable to aminoguanidine and captopril. In silico analysis indicated propranolol's antiglycative properties during its interaction with BSA, glycosidases, and AGE/RAGE pathway proteins. Our results confirm that propranolol may decrease protein oxidation and glycoxidation in vitro. Additional studies on human and animal models are vital for in vivo verification of propranolol's antiglycation activity, as this discovery might hold the key to the prevention of diabetic complications among cardiology-burdened patients.

A Genetic Programming Approach to Engineering MRI Reporter Genes

Here we develop a mechanism of protein optimization using a computational approach known as "genetic programming". We developed an algorithm called Protein Optimization Engineering Tool (POET). Starting from a small library of literature values, the use of this tool allowed us to develop proteins that produce four times more MRI contrast than what was previously state-of-the-art. Interestingly, many of the peptides produced using POET were dramatically different with respect to their sequence and chemical environment than existing CEST producing peptides, and challenge prior understandings of how those peptides function. While existing algorithms for protein engineering rely on divergent evolution, POET relies on convergent evolution and consequently allows discovery of peptides with completely different sequences that perform the same function with as good or even better efficiency. Thus, this novel approach can be expanded beyond developing imaging agents and can be used widely in protein engineering.

Antiglycoxidative properties of amantadine – a systematic review and comprehensive in vitro study

An important drug used in the treatment of Parkinson’s disease is amantadine. We are the first to perform a comprehensive study based on various glycation and oxidation factors, determining the impact of amantadine on protein glycoxidation. Sugars (glucose, fructose, galactose) and aldehydes (glyoxal, methylglyoxal) were used as glycation agents, and chloramine T was used as an oxidant. Glycoxidation biomarkers in albumin treated with amantadine were generally not different from the control group (glycation/oxidation factors), indicating that the drug did not affect oxidation and glycation processes. Molecular docking analysis did not reveal strong binding sites of amantadine on the bovine serum albumin structure. Although amantadine poorly scavenged hydroxyl radical and hydrogen peroxide, it had significantly lower antioxidant and antiglycation effect than all protein oxidation and glycation inhibitors. In some cases, amantadine even demonstrated glycoxidant, proglycation, and prooxidant properties. In summary, amantadine exhibited weak antioxidant properties and a lack of antiglycation activity.

Phloroglucinol prevents albumin glycation as well as diminishes ROS production, glycooxidative damage, nitrosative stress and inflammation in hepatocytes treated with high glucose

The treatment of diabetes mellitus aftermaths became one of medicine's most significant therapeutical and financial issues in the XXI century. Most of which are related to protein glycation and oxidative stress caused by long lasting periods of hyperglycemia. Thus, even within a venerable one, searching for new drugs, displaying anti-glycation and anti-oxidative properties seem useful as an additive therapy of diabetes. In this paper, we assessed the anti-glycating properties of phloroglucinol, a drug discovered in the XIX century and still used in many countries for its antispasmodic action. Herewith, we present its effect on protein glycation, glycoxidation, and oxidative damage in an albumin glycation/oxidation model and HepG2 cells treated with high glucose concentrations. The phloroglucinol showed the strongest and the widest protective effect within all analyzed antiglycating (aminoguanidine, pioglitazone) and anti-oxidative (vitamin C, GSH) agents. To the very best of our knowledge, this is the first study showing the properties of phloroglucinol in vitro what once is proven in other models might deepen its clinical applications.

Exploring Energy Profiles of Protein-Protein Interactions (PPIs) Using DFT Method

Background:

Large-scale energy landscape characterization of protein-protein interactions (PPIs) is important to understand the interaction mechanism and protein-protein docking methods. The experimental methods for detecting energy landscapes are tedious and the existing computational methods require longer simulation time.

Objective:

The objective of the present work is to ascertain the energy profiles at the interface regions in a rapid manner to analyze the energy landscape of protein-protein interactions.

Methods:

The atomic coordinates obtained from the X-ray and NMR spectroscopy data are considered as inputs to compute cumulative energy profiles for experimentally validated protein-protein complexes. The energies computed by the program were comparable to the standard molecular dynamics simulations.

Results:

The PPI Profiler not only enables rapid generation of energy profiles but also facilitates the detection of hot spot residue atoms involved therein.

Conclusion:

The hotspot residues and their computed energies matched with the experimentally determined hot spot residues and their energies which correlated well by employing the MM/GBSA method. The proposed method can be employed to scan entire proteomes across species at an atomic level to study the key PPI interactions.