Unraveling the molecular dynamics of sugammadex-rocuronium complexation: A blueprint for cyclodextrin drug design

A comprehensive nomenclature system for cyclodextrins

Modified cyclodextrins (CDs) are cyclic oligosaccharides with many applications in drug delivery, catalysis, and as active pharmaceutical ingredients. In general, they exist as distributions of structurally diverse molecules rather than single-isomer compounds. Their performance depends on the number of glucopyranose units (GPUs), and the type, number, and position of chemical substitutions in their hydroxyl groups. Effectively targeting individual species within these distributions is essential for optimizing CDs for specific applications. Computational techniques can generate large datasets to AI-driven structural optimization, but the absence of a standardized nomenclature system for modified CDs presents a major barrier to progress in this direction. This lack of consensus limits effective communication, data sharing, automation, and collaboration. To address this, a clear and extensible nomenclature for modified CDs is proposed. In this framework, GPUs are treated like amino-acid residues, with unsubstituted GPUs as reference building-blocks and substituted ones considered as mutations. This approach precisely defines substitution types and patterns, resolves cyclic permutation ambiguities, and offers versatility for both simple and complex modifications, including chiral center alterations and covalently linked CD oligomers. By introducing this standardized nomenclature, we aim to enhance molecular design, improve reproducibility, and streamline both experimental and computational research in the CD field.

Unveiling cyclodextrin conjugation as multidentate excipients: An exploratory journey across industries

The discovery of branched molecules like dextrin by Schardinger in 1903 marked the inception of cyclodextrin (CD) utilization, catalyzing its journey from laboratory experimentation to widespread commercialization within the pharmaceutical industry. CD, a cyclic oligosaccharide containing glucopyranose units, acts as a versatile guest molecule, forming inclusion complexes (ICs) with various host molecules. Computational studies have become instrumental in elucidating the intricate interactions between β-CD and guest molecules, enabling the prediction of binding energy, forces, affinity, and complex stability. The computational approach has established robust correlations with experimental outcomes, enhancing our understanding of CD-mediated complexation phenomena. This comprehensive review delves into the CD based Inclusion complex (CDIC) formation and a myriad of components, including drug molecules, amino acids, vitamins, and volatile oils. These complexes find applications across diverse industries, ranging from pharmaceuticals to nutraceuticals, food, fragrance, and beyond. In the pharmaceutical realm, β- CDICs offer innovative solutions for enhancing drug solubility, stability, and bioavailability, thus overcoming formulation challenges associated with poorly water-soluble drugs. Furthermore, the versatility of CDs extends beyond pharmaceuticals, with applications in the encapsulation of phytoactive compounds in nutraceuticals and the enhancing flavor, aroma in food and fragrance industries. This review underscores the pivotal role of CDs conjugation in modern drug delivery systems, emphasizing the importance of interdisciplinary approaches that integrate computational modeling with experimental validation. As the pharmaceutical landscape continues to evolve, CDs-based formulations stand poised to drive innovation and address the ever-growing demand for efficacious and patient-friendly drug delivery solutions.

Formation and stabilization mechanism of Ginsenoside Rg3 inclusion complexes based on molecular simulation

The formation of inclusion complexes between Ginsenoside Rg3 and cyclodextrins represents a promising strategy to enhance the solubility of G-Rg3. Nevertheless, the molecular mechanisms underlying the interaction between G-Rg3 and cyclodextrins have yet to be fully elucidated. In this study, we employed a combination of molecular simulation and experimental methodologies to identify the most effective solubilizing carriers among G-Rg3, β-cyclodextrin (β-CD), 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), and 2,6-dimethyl-β-cyclodextrin (DM-β-CD). The inclusion complexes formed with HP-β-CD demonstrates superior stability and water solubility compared to those formed with β-CD and DM-β-CD. The preparation process for the inclusion complexes of G-Rg3 and HP-β-CD was optimized through an orthogonal testing approach. The optimal conditions were determined to be a mass ratio of G-Rg3 to HP-β-CD of 1:125, an inclusion time of 2 h, and an inclusion temperature of 30 °C. The formation of the inclusion complexes was confirmed using DSC, Fourier Transform Infrared FTIR, and XRD techniques. In vitro solubility tests indicated that the solubility of the G-Rg3 inclusion complexes was 2.9 times greater than that of G-Rg3. Molecular dynamics (MD) simulations provided insights into the mechanisms that stabilize the inclusion complexes and enhance their water solubility. The primary interaction force between G-Rg3 and HP-β-CD was identified as the van der Waals force.

Cyclodextrins: Establishing building blocks for AI-driven drug design by determining affinity constants in silico

Cyclodextrins (CDs) are cyclic carbohydrate polymers that hold significant promise for drug delivery and industrial applications. Their effectiveness depends on their ability to encapsulate target molecules with strong affinity and specificity, but quantifying affinities in these systems accurately is challenging for a variety of reasons. Computational methods represent an exceptional complement to in vitro assays because they can be employed for existing and hypothetical molecules, providing high resolution structures in addition to a mechanistic, dynamic, kinetic, and thermodynamic characterization. Here, we employ potential of mean force (PMF) calculations obtained from guided metadynamics simulations to characterize the 1:1 inclusion complexes between four different modified βCDs, with different type, number, and location of substitutions, and two sterol molecules (cholesterol and 7-ketocholesterol). Our methods, validated for reproducibility through four independent repeated simulations per system and different post processing techniques, offer new insights into the formation and stability of CD-sterol inclusion complexes. A systematic distinct orientation preference where the sterol tail projects from the CD's larger face and significant impacts of CD substitutions on binding are observed. Notably, sampling only the CD cavity's wide face during simulations yielded comparable binding energies to full-cavity sampling, but in less time and with reduced statistical uncertainty, suggesting a more efficient approach. Bridging computational methods with complex molecular interactions, our research enables predictive CD designs for diverse applications. Moreover, the high reproducibility, sensitivity, and cost-effectiveness of the studied methods pave the way for extensive studies of massive CD-ligand combinations, enabling AI algorithm training and automated molecular design.