A prospective overview of the essential requirements in molecular modeling for nanomedicine design

Research in the Field of Drug Design and Development

The processes used by academic and industrial scientists to discover new drugs have recently experienced a true renaissance, with many new and exciting techniques being developed over the past 5-10 years alone. Drug design and discovery, and the search for new safe and well-tolerated compounds, as well as the ineffectiveness of existing therapies, and society's insufficient knowledge concerning the prophylactics and pharmacotherapy of the most common diseases today, comprise a serious challenge. This can influence not only the quality of human life, but also the health of whole societies, which became evident during the COVID-19 pandemic. In general, the process of drug development consists of three main stages: drug discovery, preclinical development using cell-based and animal models/tests, clinical trials on humans and, finally, forward moving toward the step of obtaining regulatory approval, in order to market the potential drug. In this review, we will attempt to outline the first three most important consecutive phases in drug design and development, based on the experience of three cooperating and complementary academic centers of the Visegrád group; i.e., Medical University of Lublin, Poland, Masaryk University of Brno, Czech Republic, and Comenius University Bratislava, Slovak Republic.

Nanotechnology and artificial intelligence to enable sustainable and precision agriculture

Climate change, increasing populations, competing demands on land for production of biofuels and declining soil quality are challenging global food security. Finding sustainable solutions requires bold new approaches and integration of knowledge from diverse fields, such as materials science and informatics. The convergence of precision agriculture, in which farmers respond in real time to changes in crop growth with nanotechnology and artificial intelligence, offers exciting opportunities for sustainable food production. Coupling existing models for nutrient cycling and crop productivity with nanoinformatics approaches to optimize targeting, uptake, delivery, nutrient capture and long-term impacts on soil microbial communities will enable design of nanoscale agrochemicals that combine optimal safety and functionality profiles.

The Current Landscape of Novel Formulations and the Role of Mathematical Modeling in Their Development

Drug delivery is an integral part of the drug development process, influencing safety and efficacy of active pharmaceutical ingredients. The application of nanotechnology has enabled the discovery of novel formulations for numerous therapeutic purposes across multiple disease areas. However, evaluation of novel formulations in clinical scenarios is slow and hampered due to various ethical and logistical barriers. Computational models have the ability to integrate existing domain knowledge and mathematical correlations, to rationalize the feasibility of using novel formulations for safely enhancing drug delivery, identifying suitable candidates, and reducing the burden on preclinical and clinical studies. In this review, types of novel formulations and their application through several routes of administration and the use of modeling approaches that can find application in different stages of the novel formulation development process are discussed.

In silico analytico-mathematical interpretation of biopolymeric assemblies: Quantification of energy surfaces and molecular attributes via atomistic simulations

Static-lattice atomistic simulations, in vacuum and solvent phase, have been recently employed to quantify the "in vitro-in vivo-in silico" performance-correlation profile of various drug delivery systems and biomaterial scaffolds. The reactional profile of biopolymers was elucidated by exploring the spatial disposition of the molecular components with respect to the formulation conditions and the final release medium. This manuscript provides a brief overview of recently completed and published studies related to molecular tectonics of: (a) the nanoformation and solvation properties of the surfactant-emulsified polymeric systems; (b) the formation and chemistry of polyelectrolyte complexes; (c) the effect of a plasticizer and/or drug on the physicomechanical properties of biomedical archetypes; (d) the molecular modeling templates to predict stimuli- and environmentally esponsive systems; and (e) the polymer-mucopeptide complexes and intermacromolecular networks. Furthermore, this report provides a detailed account of the role of molecular mechanics energy relationships toward the interpretation and understanding of the mechanisms that control the formation, fabrication, selection, design, performance, complexation, interaction, stereospecificity, and preference of various biopolymeric systems for biomedical applications.

Antibiotics: where to throw the spanner in the ribosomal machinery?

The sheer molecular scale of the ribosome is intimidating to the traditional drug designer. By analyzing the ribosome as a series of 12 key target sites, this review seeks to make the ribosome ligand design process more manageable. Analysis of recently evaluated ribosomal structures, particularly those with bound antibiotics, indicates where the ligand target sites are located. This review employs current research data to map antibiotic binding across the ribosome. A number of neighboring ligand-binding sites are often contiguous and can be combined. Ligands that bind in close proximity can be combined into hybrid structures. The different ways antibiotics disrupt ribosomal function are also discussed. Antibiotics tend to inhibit conformational changes that are essential to the ribosomal mechanism.

Immobilization of iron oxide nanoparticles within alginate nanogels for enhanced MR imaging applications

We report the design of iron oxide (Fe3O4) nanoparticle (NP)-immobilized alginate (AG) nanogels (NGs) as a novel contrast agent for enhanced magnetic resonance (MR) imaging applications. In this study, an aqueous solution of AG activated by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride was double emulsified to form NGs, followed by in situ cross-linking with polyethyleneimine (PEI)-coated Fe3O4 NPs (PEI-Fe3O4 NPs). The resultant Fe3O4 NP-immobilized AG NGs (AG/PEI-Fe3O4 NGs) were characterized via different techniques. Our results reveal that the hybrid NGs with a size of 186.1 ± 33.1 nm are water dispersible, colloidally stable, and cytocompatible in the given concentration range. Importantly, these NGs have a high r2 relaxivity (170.87 mM(-1) s(-1)) due to the high loading of Fe3O4 NPs within the NGs, and can be more significantly uptaken by cancer cells when compared with carboxylated Fe3O4 NPs. The formed AG/PEI-Fe3O4 NGs are able to be used as an effective contrast agent for the MR imaging of cancer cells in vitro and the xenografted tumor model in vivo after intravenous injection. The developed AG/PEI-Fe3O4 NGs may hold great promise for use as a novel contrast agent for the enhanced MR imaging of different biological systems.