A dual diffusion model enables 3D molecule generation and lead optimization based on target pockets.

Structure-based generative chemistry is essential in computer-aided drug discovery by exploring a vast chemical space to design ligands with high binding affinity for targets. However, traditional in silico methods are limited by computational inefficiency, while machine learning approaches face bottlenecks due to auto-regressive sampling. To address these concerns, we have developed a conditional deep generative model, PMDM, for 3D molecule generation fitting specified targets. PMDM consists of a conditional equivariant diffusion model with both local and global molecular dynamics, enabling PMDM to consider the conditioned protein information to generate molecules efficiently. The comprehensive experiments indicate that PMDM outperforms baseline models across multiple evaluation metrics. To evaluate the applications of PMDM under real drug design scenarios, we conduct lead compound optimization for SARS-CoV-2 main protease (Mpro) and Cyclin-dependent Kinase 2 (CDK2), respectively. The selected lead optimization molecules are synthesized and evaluated for their in-vitro activities against CDK2, displaying improved CDK2 activity.

Liquid-liquid phase separation (LLPS) in DNA and chromatin systems from the perspective of colloid physical chemistry.

DNA is a highly charged polyelectrolyte and is prone to associative phase separation driven by the presence of multivalent cations, charged surfactants, proteins, polymers and colloids. The process of DNA phase separation induced by positively charged species is often called DNA condensation. Generally, it refers to either intramolecular DNA compaction (coil-globule transition) or intermolecular DNA aggregation with macroscopic phase separation, but the formation of a DNA liquid crystalline system is also displayed. This has traditionally been described by polyelectrolyte theory and qualitative (Flory-Huggins-based) polymer theory approaches. DNA in the cell nucleus is packed into chromatin wound around the histone octamer (a protein complex comprising two copies each of the four histone proteins H2A, H2B, H3 and H4) to form nucleosomes separated by linker DNA. During the last decade, the phenomenon of the formation of biomolecular condensates (dynamic droplets) by liquid-liquid phase separation (LLPS) has emerged as a generally important mechanism for the formation of membraneless organelles from proteins, nucleic acids and their complexes. DNA and chromatin droplet formation through LLPS has recently received much attention by in vitro as well as in vivo studies that established the importance of this for compartmentalisation in the cell nucleus. Here, we review DNA and chromatin LLPS from a general colloid physical chemistry perspective. We start with a general discussion of colloidal phase separation in aqueous solutions and review the original (pre-LLPS era) work on DNA (macroscopic) phase separation for simpler systems with DNA in the presence of multivalent cations and well-defined surfactants and colloids. Following that, we discuss and illustrate the similarities of such macroscopic phase separation with the general behaviour of LLPS droplet formation by associative phase separation for DNA-protein systems, including chromatin; we also note cases of segregative association. The review ends with a discussion of chromatin LLPS in vivo and its physiological significance.

Estabilidad fisicoquímica y microbiológica de un colirio de insulina 10 UI/mL / Physicochemical and microbiological stability of a 10 IU/mL insulin eye drop

Objetivo: Los pacientes con defectos epiteliales corneales persistentes son, a menudo, refractarios a los tratamientos convencionales. La insulina tópica surge como una posible alternativa, habiendo demostrado su efectividad y seguridad. Sin embargo, en la bibliografía actual disponible, hay una falta de estudios de estabilidad. El objetivo del presente trabajo fue evaluar la estabilidad fisicoquímica y microbiológica de un colirio de insulina 10 UI/ml durante 28 días. Método: Estudio de estabilidad fisicoquímica y microbiológica. Se elaboraron 2 lotes (A y B) de colirios de insulina 10 UI/ml, manteniendo el lote B cerrado hasta el día 15. Las variables fisicoquímicas analizadas fueron la concentración de insulina mediante inmunoanálisis quimioluminiscente, pH y osmolaridad. El estudio microbiológico se realizó mediante pruebas de esterilidad mientras que el estudio descriptivo se analizó mediante visualización directa. Resultados: No se observaron cambios significativos de concentración (±10%) en los colirios a excepción de 2 valores en una de las muestras del lote B. El pH y la osmolaridad se mantuvieron dentro de los rangos fisiológicos del ojo. No se observó crecimiento microbiano ni cambios en las características organolépticas. Conclusiones: Se puede considerar al colirio de insulina 10 UI/ml estable durante 28 días en refrigeración manteniendo el frasco abierto desde el día de su elaboración.(AU)

Objective: Patients with persistent corneal epithelial defects are often refractory to conventional treatments. Topical insulin emerges as a possible alternative of proven effectiveness and safety. However, in the current available literature, there is a lack of stability studies. The main objective of this study was to evaluate the physicochemical and microbiological stability of a 10 IU/ml insulin eye drop for 28 days. Methods: Physicochemical and microbiological stability study. Two batches (A and B) of 10 IU/ml insulin eye drops were prepared, keeping batch B closed until day 15. The physicochemical variables analysed were insulin concentration by chemiluminescent immunoassay, pH and osmolarity. The microbiological study was performed by sterility tests while the descriptive study was assessed by direct visualization. Results: No significant concentration changes (±10%) were observed in the eye drops except for 2 values in one of the samples from batch B. The pH and osmolarity remained within the physiological ranges of the eye. No microbiological growth or changes in organoleptic characteristics were observed. Conclusions: Insulin 10 UI/ml eye drops can be considered stable for 28 days under refrigeration if the bottle is kept open from the day of its preparation.(AU)

Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail.

We provide a molecular-level description of the thermodynamics and mechanistic aspects of drug permeation through the cell membrane. As a case study, we considered the antimalaria FDA approved drug chloroquine. Molecular dynamics simulations of the molecule (in its neutral and protonated form) were performed in the presence of different lipid bilayers, with the aim of uncovering key aspects of the permeation process, a fundamental step for the drug's action. Free energy values obtained by well-tempered metadynamics simulations suggest that the neutral form is the only permeating protomer, consistent with experimental data. H-bond interactions of the drug with water molecules and membrane headgroups play a crucial role for permeation. The presence of the transmembrane potential, investigated here for the first time in a drug permeation study, does not qualitatively affect these conclusions.

C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids.

Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.

Organically Templated Uranyl Sulfates and Selenates: Structural Complexity and Crystal Chemical Restrictions for Isotypic Compounds Formation.

This paper reviews the state of the art in the structural chemistry of organically templated uranyl sulfates and selenates, which are considered as the most representative groups of U-bearing synthetic compounds. In total, there are 194 compounds known for both groups, the crystal structures of which include 84 various organic molecules. Structural studies and topological analysis clearly indicate complex crystal chemical limitations in terms of the isomorphic substitution implementation, since the existence of isotypic phases has to date been confirmed only for 24 compounds out of 194, which is slightly above 12%. The structural architecture of the entire compound depends on the combination of the organic and oxyanion parts, changes in which are sometimes realized even while maintaining the topology of the U-bearing complex. An increase in the size of the hydrocarbon part and number of charge functional groups of the organic cation leads to the formation of rare and more complex topologies. In addition, the crystal structures of two novel uranyl sulfates and one uranyl selenate, templated by isopropylammonium cations, are reported.

Recent Progress in Crystalline Borates with Edge-Sharing BO4 Tetrahedra.

Crystalline borates have received great attention due to their various structures and wide applications. For a long time, the corner-sharing B-O unit is considered a basic rule in borate structural chemistry. The Dy4B6O15 synthesized under high-pressure is the first oxoborate with edge-sharing [BO4] tetrahedra, while the KZnB3O6 is the first ambient pressure borate with the edge-sharing [BO4] tetrahedra. The edge-sharing connection modes greatly enrich the structural chemistry of borates and are expected to expand new applications in the future. In this review, we summarize the recent progress in crystalline borates with edge-sharing [BO4] tetrahedra. We discuss the synthesis, fundamental building blocks, structural features, and possible applications of these edge-sharing borates. Finally, we also discuss the future perspectives in this field.

Teaching and assessing undergraduate collaboration skills scaffolded through the biochemistry curriculum using collaboration rubrics and student learning contracts.

The Department of Chemistry and Biochemistry at St. Mary's College of Maryland has scaffolded collaboration skills throughout the Biochemistry curriculum and developed several assessment tools to evaluate these skills. Biochemistry I and II have used team contracts at the beginning of extensive team projects where students identify their strengths, review expectations, and plan for group communication. At the conclusion of each project, each student assesses their own contributions and team members for various parts of the project. A common collaboration rubric was also applied in Biochemistry I and II as well as in two other courses, General Chemistry II Lab and Physical Chemistry I Lab, for students to evaluate themself and team members using the following subcategories: quality of work, commitment, leadership, communication, and analysis. In Biochemistry I and II, we used this rubric for multiple assignments that are part of the projects in the lecture courses. In the General Chemistry II Lab, we provided elements of this rubric within an evaluation form that reflects these collaboration attributes after each lab experience, so students can assess and report privately on their experiences as part of their collaboration grade for the course. A similar collaboration rubric is completed by students for each team-based laboratory within Physical Chemistry I. We also demonstrate different ways that instructors can use the data from these assessment tools. In our department, we are using these tools to frame the importance of collaboration skills and collecting data to inform our teaching of these skills. Preliminary data suggest that our curriculum is successfully teaching students how to be good collaborators.

Molecular Fingerprint Detection Using Raman and Infrared Spectroscopy Technologies for Cancer Detection: A Progress Review.

Molecular vibrations play a crucial role in physical chemistry and biochemistry, and Raman and infrared spectroscopy are the two most used techniques for vibrational spectroscopy. These techniques provide unique fingerprints of the molecules in a sample, which can be used to identify the chemical bonds, functional groups, and structures of the molecules. In this review article, recent research and development activities for molecular fingerprint detection using Raman and infrared spectroscopy are discussed, with a focus on identifying specific biomolecules and studying the chemical composition of biological samples for cancer diagnosis applications. The working principle and instrumentation of each technique are also discussed for a better understanding of the analytical versatility of vibrational spectroscopy. Raman spectroscopy is an invaluable tool for studying molecules and their interactions, and its use is likely to continue to grow in the future. Research has demonstrated that Raman spectroscopy is capable of accurately diagnosing various types of cancer, making it a valuable alternative to traditional diagnostic methods such as endoscopy. Infrared spectroscopy can provide complementary information to Raman spectroscopy and detect a wide range of biomolecules at low concentrations, even in complex biological samples. The article concludes with a comparison of the techniques and insights into future directions.