The Role of in silico Research in Developing Nanoparticle-Based Therapeutics

Utilizing machine learning and molecular dynamics for enhanced drug delivery in nanoparticle systems

Materials data science and machine learning (ML) are pivotal in advancing cancer treatment strategies beyond traditional methods like chemotherapy. Nanotherapeutics, which merge nanotechnology with targeted drug delivery, exemplify this advancement by offering improved precision and reduced side effects in cancer therapy. The development of these nanotherapeutic agents depends critically on understanding nanoparticle (NP) properties and their biological interactions, often analyzed through molecular dynamics (MD) simulations. This study enhances these analyses by integrating ML with MD simulations, significantly improving both prediction accuracy and computational efficiency. We introduce a comprehensive three-stage methodology for predicting the solvent-accessible surface area (SASA) of NPs, which is crucial for their therapeutic efficacy. The process involves training an ML model to forecast the many-body tensor representation (MBTR) for future time steps, applying data augmentation to increase dataset realism, and refining the SASA predictor with both augmented and original data. Results demonstrate that our methodology can predict SASA values 299 time steps ahead with a 40-fold speed improvement and a 25% accuracy increase over existing methods. Importantly, it provides a 300-fold increase in computational speed compared to traditional simulation techniques, offering substantial cost and time savings for nanotherapeutic research and development.

Recent Progress in Terrestrial Biota Derived Antibacterial Agents for Medical Applications

Conventional antibiotic and multidrug treatments are becoming less and less effective and the discovery of new effective and safe antibacterial agents is becoming a global priority. Returning to a natural antibacterial product is a relatively new current trend. Terrestrial biota is a rich source of biologically active substances whose antibacterial potential has not been fully utilized. The aim of this review is to present the current state-of-the-art terrestrial biota-derived antibacterial agents inspired by natural treatments. It summarizes the most important sources and newly identified or modified antibacterial agents and treatments from the last five years. It focuses on the significance of plant- animal- and bacteria-derived biologically active agents as powerful alternatives to antibiotics, as well as the advantages of utilizing natural antibacterial molecules alone or in combination with antibiotics. The main conclusion is that terrestrial biota-derived antibacterial products and substances open a variety of new ways for modern improved therapeutic strategies. New terrestrial sources of known antibacterial agents and new antibacterial agents from terrestrial biota were discovered during the last 5 years, which are under investigation together with some long-ago known but now experiencing their renaissance for the development of new medical treatments. The use of natural antibacterial peptides as well as combinational therapy by commercial antibiotics and natural products is outlined as the most promising method for treating bacterial infections. In vivo testing and clinical trials are necessary to reach clinical application.

Exploring nanoparticular platform in delivery of repurposed drug for Alzheimer's disease: current approaches and future perspectives

INTRODUCTION

Alzheimer's disease (AD) stands as significant challenge in realm of neurodegenerative disorder. It is characterized by gradual decline in cognitive function and memory loss. It has already expanded its prevalence to 55 million people worldwide and is expected to rise significantly. Unfortunately, there exists a limited therapeutic option that would mitigate its progression. Repurposing existing drugs and employing nanoparticle as delivery agent presents a potential solution to address the intricate pathology of AD.

AREAS COVERED

In this review, we delve into utilization of nanoparticular platforms to enhance the delivery of repurposed drugs for treatment of AD. Firstly, the review begins with the elucidation of intricate pathology underpinning AD, subsequently followed by rationale behind drug repurposing in AD. Covered are explorations of nanoparticle-based repurposing of drugs in AD, highlighting their clinical implication. Further, the associated challenges and probable future perspective are delineated.

EXPERT OPINION

The article has highlighted that extensive research has been carried out on the delivery of repurposed nanomedicines against AD. However, there is a need for advanced and long-term research including clinical trials required to shed light upon their safety and toxicity profile. Furthermore, their scalability in pharmaceutical set-up should also be validated.

Potential of Exosomes as Multifunctional Nanocarriers for Targeted Drug Delivery

Exosomes are small vesicles that form when multivesicular bodies fuse with the plasma membrane and are released into body fluids. They play a vital role in facilitating communication between cells by transferring different biomolecules, including DNA, RNA, proteins, and lipids, over both short and long distances. They also function as vital mediators in both states of health and disease, exerting an impact on several physiological processes. Exosomes have been modified to overcome the limitations of natural exosomes to enhance their potential as carriers for drug delivery systems, and these modifications aim to improve the drug delivery efficiency, enhance tissue and organ targeting, and prolong the circulating half-life of exosomes. This review discussed recent advancements in exosome nanotechnology, as well as the progression and use of exosomes for drug delivery. The potential commercialisation and challenges associated with the use of exosome-based drug delivery systems were also discussed, aiming to motivate the development of exosome-based theranostic nanoplatforms and nanotechnology for improved healthcare treatments.

Nanoparticle-Based Drug Delivery Systems in Inhaled Therapy: Improving Respiratory Medicine

Inhaled nanoparticle (NP) therapy poses intricate challenges in clinical and pharmacodynamic realms. Recent strides have revolutionized NP technology by enabling the incorporation of diverse molecules, thus circumventing systemic clearance mechanisms and enhancing drug effectiveness while mitigating systemic side effects. Despite the established success of systemic NP delivery in oncology and other disciplines, the exploration of inhaled NP therapies remains relatively nascent. NPs loaded with bronchodilators or anti-inflammatory agents exhibit promising potential for precise distribution throughout the bronchial tree, offering targeted treatment for respiratory diseases. This article conducts a comprehensive review of NP applications in respiratory medicine, highlighting their merits, ranging from heightened stability to exacting lung-specific delivery. It also explores cutting-edge technologies optimizing NP-loaded aerosol systems, complemented by insights gleaned from clinical trials. Furthermore, the review examines the current challenges and future prospects in NP-based therapies. By synthesizing current data and perspectives, the article underscores the transformative promise of NP-mediated drug delivery in addressing chronic conditions such as chronic obstructive pulmonary disease, a pressing global health concern ranked third in mortality rates. This overview illuminates the evolving landscape of NP inhalation therapies, presenting optimistic avenues for advancing respiratory medicine and improving patient outcomes.

Development of an ultrasound-mediated nano-sized drug-delivery system for cancer treatment: from theory to experiment

Aim: To establish a methodology for understanding how ultrasound (US) induces drug release from nano-sized drug-delivery systems (NSDDSs) and enhances drug penetration and uptake in tumors. This aims to advance cancer treatment strategies.Materials & methods: We developed a multi-physics mathematical model to elucidate and understand the intricate mechanisms governing drug release, transport and delivery. Unique in vitro models (monolayer, multilayer, spheroid) and a tailored US exposure setup were introduced to evaluate drug penetration and uptake.Results: The results highlight the potential advantages of US-mediated NSDDSs over conventional NSDDSs and chemotherapy, notably in enhancing drug release and inducing cell death.Conclusion: Our sophisticated numerical and experimental methods aid in determining and quantifying drug penetration and uptake into solid tumors.

Para- and Transcellular Transport Kinetics of Nanoparticles across Lymphatic Endothelial Cells

Lymphatic vessels have received significant attention as drug delivery targets, as they shuttle materials from peripheral tissues to the lymph nodes, where adaptive immunity is formed. Delivery of immune modulatory materials to the lymph nodes via lymphatic vessels has been shown to enhance their efficacy and also improve the bioavailability of drugs when delivered to intestinal lymphatic vessels. In this study, we generated a three-compartment model of a lymphatic vessel with a set of kinematic differential equations to describe the transport of nanoparticles from the surrounding tissues into lymphatic vessels. We used previously published data and collected additional experimental parameters, including the transport efficiency of nanoparticles over time, and also examined how nanoparticle formulation affected the cellular transport mechanisms using small molecule inhibitors. These experimental data were incorporated into a system of kinematic differential equations, and nonlinear, least-squares curve fitting algorithms were employed to extrapolate transport coefficients within our model. The subsequent computational framework produced some of the first parameters to describe transport kinetics across lymphatic endothelial cells and allowed for the quantitative analysis of the driving mechanisms of transport into lymphatic vessels. Our model indicates that transcellular mechanisms, such as micro- and macropinocytosis, drive transport into lymphatics. This information is crucial to further design strategies that will modulate lymphatic transport for drug delivery, particularly in diseases like lymphedema, where normal lymphatic functions are impaired.

Exploring and Analyzing the Systemic Delivery Barriers for Nanoparticles

Most nanomedicines require efficient in vivo delivery to elicit diagnostic and therapeutic effects. However, en route to their intended tissues, systemically administered nanoparticles often encounter delivery barriers. To describe these barriers, we propose the term "nanoparticle blood removal pathways" (NBRP), which summarizes the interactions between nanoparticles and the body's various cell-dependent and cell-independent blood clearance mechanisms. We reviewed nanoparticle design and biological modulation strategies to mitigate nanoparticle-NBRP interactions. As these interactions affect nanoparticle delivery, we studied the preclinical literature from 2011-2021 and analyzed nanoparticle blood circulation and organ biodistribution data. Our findings revealed that nanoparticle surface chemistry affected the in vivo behavior more than other nanoparticle design parameters. Combinatory biological-PEG surface modification improved the blood area under the curve by ~418%, with a decrease in liver accumulation of up to 47%. A greater understanding of nanoparticle-NBRP interactions and associated delivery trends will provide new nanoparticle design and biological modulation strategies for safer, more effective, and more efficient nanomedicines.

Improving ADMET Prediction Accuracy for Candidate Drugs: Factors to Consider in QSPR Modeling Approaches

Quantitative Structure-Property Relationship (QSPR) employs mathematical and statistical methods to reveal quantitative correlations between the pharmacokinetics of compounds and their molecular structures, as well as their physical and chemical properties. QSPR models have been widely applied in the prediction of drug absorption, distribution, metabolism, excretion, and toxicity (ADMET). However, the accuracy of QSPR models for predicting drug ADMET properties still needs improvement. Therefore, this paper comprehensively reviews the tools employed in various stages of QSPR predictions for drug ADMET. It summarizes commonly used approaches to building QSPR models, systematically analyzing the advantages and limitations of each modeling method to ensure their judicious application. We provide an overview of recent advancements in the application of QSPR models for predicting drug ADMET properties. Furthermore, this review explores the inherent challenges in QSPR modeling while also proposing a range of considerations aimed at enhancing model prediction accuracy. The objective is to enhance the predictive capabilities of QSPR models in the field of drug development and provide valuable reference and guidance for researchers in this domain.

Ultrasound-mediated nano-sized drug delivery systems for cancer treatment: Multi-scale and multi-physics computational modeling

Computational modeling enables researchers to study and understand various complex biological phenomena in anticancer drug delivery systems (DDSs), especially nano-sized DDSs (NSDDSs). The combination of NSDDSs and therapeutic ultrasound (TUS), that is, focused ultrasound and low-intensity pulsed ultrasound, has made significant progress in recent years, opening many opportunities for cancer treatment. Multiple parameters require tuning and optimization to develop effective DDSs, such as NSDDSs, in which mathematical modeling can prove advantageous. In silico computational modeling of ultrasound-responsive DDS typically involves a complex framework of acoustic interactions, heat transfer, drug release from nanoparticles, fluid flow, mass transport, and pharmacodynamic governing equations. Owing to the rapid development of computational tools, modeling the different phenomena in multi-scale complex problems involved in drug delivery to tumors has become possible. In the present study, we present an in-depth review of recent advances in the mathematical modeling of TUS-mediated DDSs for cancer treatment. A detailed discussion is also provided on applying these computational models to improve the clinical translation for applications in cancer treatment. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.

The Long Journey of Extracellular Vesicles towards Global Scientific Acclamation

Extracellular vesicles (EVs) are a heterogeneous class of cell-derived vesicles that are responsible for eliciting a wide array of biological processes. After decades of intense investigation, the therapeutic potential of EVs will be finally explored in a series of upcoming clinical trials. EVs are rapidly changing the understanding of human physiology and will undoubtedly transform the field of medicine. The applicability of EVs as diagnostic biomarkers and treatment vectors has captured the attention of the scientific community and investors, facilitating the rapid progression of numerous EVs-based platforms. This mini-review provides an outline of the pioneering discoveries, and their respective significances, on progressing EVs toward clinical use. We focus the attention of the readers on several promising classes of EVs that hold major opportunities to translate in clinical practice. Market analysis and future challenges facing EVs-based therapies are also discussed.

Perspectives on Usage of Functional Nanomaterials in Antimicrobial Therapy for Antibiotic-Resistant Bacterial Infections

The clinical applications of nanotechnology are emerging as widely popular, particularly as a potential treatment approach for infectious diseases. Diseases associated with multiple drug-resistant organisms (MDROs) are a global concern of morbidity and mortality. The prevalence of infections caused by antibiotic-resistant bacterial strains has increased the urgency associated with researching and developing novel bactericidal medicines or unorthodox methods capable of combating antimicrobial resistance. Nanomaterial-based treatments are promising for treating severe bacterial infections because they bypass antibiotic resistance mechanisms. Nanomaterial-based approaches, especially those that do not rely on small-molecule antimicrobials, display potential since they can bypass drug-resistant bacteria systems. Nanoparticles (NPs) are small enough to pass through the cell membranes of pathogenic bacteria and interfere with essential molecular pathways. They can also target biofilms and eliminate infections that have proven difficult to treat. In this review, we described the antibacterial mechanisms of NPs against bacteria and the parameters involved in targeting established antibiotic resistance and biofilms. Finally, yet importantly, we talked about NPs and the various ways they can be utilized, including as delivery methods, intrinsic antimicrobials, or a mixture.

Integration of In Vitro and In Vivo Models to Predict Cellular and Tissue Dosimetry of Nanomaterials Using Physiologically Based Pharmacokinetic Modeling

Nanomaterials (NMs) have been increasingly used in a number of areas, including consumer products and nanomedicine. Target tissue dosimetry is important in the evaluation of safety, efficacy, and potential toxicity of NMs. Current evaluation of NM efficacy and safety involves the time-consuming collection of pharmacokinetic and toxicity data in animals and is usually completed one material at a time. This traditional approach no longer meets the demand of the explosive growth of NM-based products. There is an emerging need to develop methods that can help design safe and effective NMs in an efficient manner. In this review article, we critically evaluate existing studies on in vivo pharmacokinetic properties, in vitro cellular uptake and release and kinetic modeling, and whole-body physiologically based pharmacokinetic (PBPK) modeling studies of different NMs. Methods on how to simulate in vitro cellular uptake and release kinetics and how to extrapolate cellular and tissue dosimetry of NMs from in vitro to in vivo via PBPK modeling are discussed. We also share our perspectives on the current challenges and future directions of in vivo pharmacokinetic studies, in vitro cellular uptake and kinetic modeling, and whole-body PBPK modeling studies for NMs. Finally, we propose a nanomaterial in vitro to in vivo extrapolation via physiologically based pharmacokinetic modeling (Nano-IVIVE-PBPK) framework for high-throughput screening of target cellular and tissue dosimetry as well as potential toxicity of different NMs in order to meet the demand of efficient evaluation of the safety, efficacy, and potential toxicity of a rapidly increasing number of NM-based products.