Journal articles: 'Biomolecular and medicinal chemistry'

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Prasad, Ashok K., Virinder S. Parmar, Hanumantharao G. Raj, and Daniel Jore. "Advances in biomolecular and medicinal chemistry." Biochimie 92, no. 9 (September 2010): v—vi. http://dx.doi.org/10.1016/s0300-9084(10)00275-0.

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Mistry, Shailesh N., Pascal Marchand, and Barrie Kellam. "27th Annual GP2A Medicinal Chemistry Conference." Pharmaceuticals 12, no. 4 (December 6, 2019): 179. http://dx.doi.org/10.3390/ph12040179.

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The 27th annual GP2A (Groupement des Pharmacochimistes de l′Arc Atlantique/Group of Medicinal Chemists in the Atlantic Arc) conference took place from 21 to 23 August 2019, at the East Midlands Conference Centre (University Park, Nottingham, United Kingdom) and was hosted by the Division of Biomolecular Science and Medicinal Chemistry (BSMC), within the School of Pharmacy at the University of Nottingham. The event brought together an international delegation of researchers with interests in medicinal chemistry and interfacing disciplines. In addition, a pre-conference workshop provided an opportunity for younger researchers to develop their theoretical knowledge in quantitative pharmacology. Abstracts of presentations by the 14 invited speakers and 6 young researchers, in addition to 41 posters, are included in this report.

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Takahata, Hiroki. "Synthetic Medicinal Chemistry of the Biomolecular Components Mimics." YAKUGAKU ZASSHI 133, no. 5 (2013): 575–85. http://dx.doi.org/10.1248/yakushi.13-00054.

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Rowe, Rhianon K., and P. Shing Ho. "Relationships between hydrogen bonds and halogen bonds in biological systems." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, no. 2 (March 29, 2017): 255–64. http://dx.doi.org/10.1107/s2052520617003109.

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The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.

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Pandit, Upendra K. "Biomolecular approach to the design of potential drugs." Pure and Applied Chemistry 79, no. 12 (January 1, 2007): 2119–27. http://dx.doi.org/10.1351/pac200779122119.

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The approach to drug design on the basis of molecular-level information on biological processes is being driven by the expanding knowledge of the details of molecular events in biological systems. We have directed attention to the design of potentially active compounds based on the aforementioned "biomolecular" concepts. Selected examples from our studies are discussed. This paper presents three case studies of approaches to the development of potential medicinal agents whose design has evolved from considerations of molecular mechanisms of processes in selected biological systems.

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Gambari, Roberto. "Predictive Analyses of Biological Effects of Natural Products: From Plant Extracts to Biomolecular Laboratory and Computer Modeling." Evidence-Based Complementary and Alternative Medicine 2011 (2011): 1–4. http://dx.doi.org/10.1093/ecam/nep096.

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Year by year, the characterization of the biological activity of natural products is becoming more competitive and complex, with the involvement in this research area of experts belonging to different scientific fields, including chemistry, biochemistry, molecular biology, immunology and bioinformatics. These fields are becoming of great interest for several high-impact scientific journals, includingeCAM. The available literature in general, and a survey of reviews and original articles recently published, establishes that natural products, including extracts from medicinal plants and essential oils, retain interesting therapeutic activities, including antitumor, antiviral, anti-inflammatory, pro-apoptotic and differentiating properties. In this commentary, we focus attention on interest in networks based on complementary activation and comparative evaluation of different experimental strategies applied to the discovery and characterization of bioactive natural products. A representative flow chart is shown in the paper.

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Takayama, Kentaro. "Medicinal Chemistry Focused on Mid-sized Peptides Derived from Biomolecules." YAKUGAKU ZASSHI 139, no. 11 (November 1, 2019): 1377–84. http://dx.doi.org/10.1248/yakushi.19-00149.

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Fujisaki, Hiroshi, Kei Moritsugu, and Yasuhiro Matsunaga. "Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions." International Journal of Molecular Sciences 19, no. 10 (October 15, 2018): 3177. http://dx.doi.org/10.3390/ijms19103177.

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To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager–Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.

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Vacchini, Mattia, Rana Edwards, Roberto Guizzardi, Alessandro Palmioli, Carlotta Ciaramelli, Alice Paiotta, Cristina Airoldi, Barbara La Ferla, and Laura Cipolla. "Glycan Carriers As Glycotools for Medicinal Chemistry Applications." Current Medicinal Chemistry 26, no. 35 (December 13, 2019): 6349–98. http://dx.doi.org/10.2174/0929867326666190104164653.

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Carbohydrates are one of the most powerful and versatile classes of biomolecules that nature uses to regulate organisms’ biochemistry, modulating plenty of signaling events within cells, triggering a plethora of physiological and pathological cellular behaviors. In this framework, glycan carrier systems or carbohydrate-decorated materials constitute interesting and relevant tools for medicinal chemistry applications. In the last few decades, efforts have been focused, among others, on the development of multivalent glycoconjugates, biosensors, glycoarrays, carbohydrate-decorated biomaterials for regenerative medicine, and glyconanoparticles. This review aims to provide the reader with a general overview of the different carbohydrate carrier systems that have been developed as tools in different medicinal chemistry approaches relying on carbohydrate-protein interactions. Given the extent of this topic, the present review will focus on selected examples that highlight the advancements and potentialities offered by this specific area of research, rather than being an exhaustive literature survey of any specific glyco-functionalized system.

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Pattan, S. R., S. B. Pawar, S. S. Vetal, U. D. Gharate, and S. B. Bhawar. "THE SCOPE OF METAL COMPLEXES IN DRUG DESIGN - A REVIEW." INDIAN DRUGS 49, no. 11 (November 28, 2012): 5–12. http://dx.doi.org/10.53879/id.49.11.p0005.

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A significantly rising interest in the design of metal compounds as drugs and diagnostic agents is currently observed in the area of scientific inquiry, appropriately termed medicinal inorganic chemistry. Investigations in this area focus mostly on the speciation of metal species in biological media based on possible interactions of these metal ions with diverse biomolecules, in an effort to contribute to future development of new therapeutics or diagnostic agents. Metallopharmaceuticals used as anticancer agents, metal-mediated antibiotics, antibacterials, antivirals, antiparasitics, antiarthritics, antidiabetics and radio-sensitizing agents appear in therapeutic medicinal inorganic chemistry. The medicinal uses and applications of metals and metal complexes are of increasing clinical and commercial importance.

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Pattiya Arachchillage, Keshani G. Gunasinghe, Subrata Chandra, Angela Piso, Tiba Qattan, and Juan M. Artes Vivancos. "RNA BioMolecular Electronics: towards new tools for biophysics and biomedicine." Journal of Materials Chemistry B 9, no. 35 (2021): 6994–7006. http://dx.doi.org/10.1039/d1tb01141c.

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Nanoscience has enabled the electrical study of individual biomolecules. This perspective presents the nascent field of RNA BioMolecular Electronics, overviewing the main developments and exploring recent and future potential applications.

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Metzler-Nolte, Nils. "Labeling of Biomolecules for Medicinal Applications—Bioorganometallic Chemistry at Its Best." Angewandte Chemie International Edition 40, no. 6 (March 16, 2001): 1040–43. http://dx.doi.org/10.1002/1521-3773(20010316)40:6<1040::aid-anie10400>3.0.co;2-p.

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Milaeva, Elena R., and Vladimir Yu Tyurin. "Hybrid metal complexes with opposed biological modes of action – promising selective drug candidates." Pure and Applied Chemistry 89, no. 8 (July 26, 2017): 1065–88. http://dx.doi.org/10.1515/pac-2016-1130.

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AbstractThe oxidative stress is considered to be involved in the pathogenesis of many diseases. The antioxidative defense system in the living organism regulates the toxic impact of ROS and there is strong evidence that the antioxidants prevent some pathologies including cancer. The specific chemical properties of metal-based drugs impart innovative pharmacological profiles to this type of therapeutic agents, most likely in relation to novel biomolecular mechanisms. This review will focus on a novel approach to design polyfunctional metal-based physiollogically active compounds with opposed modes of action – prooxidant metal center and antioxidant 2,6-dialkylphenol group. The synthesis and anti/prooxidant activity and cytotoxicity studies of novel organometallic/coordination compounds (ferrocenes, complexes with di-(2-picolyl)amine ligand, porphyrins, pyridines, thiols, carboxylates) based on either biogenic metals (Fe, Mn, Co, Cu, Zn, Ni) or exogenic metals (Sn, Au, Rh) are presented and discussed. The results allow us to conclude that combining in one molecule a redox active metal center and cytoprotective functional organic moiety with antioxidative function is a promising way to rational metallodrug design in modern medicinal chemistry.

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Picci, Giacomo, Silvia Marchesan, and Claudia Caltagirone. "Ion Channels and Transporters as Therapeutic Agents: From Biomolecules to Supramolecular Medicinal Chemistry." Biomedicines 10, no. 4 (April 12, 2022): 885. http://dx.doi.org/10.3390/biomedicines10040885.

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Ion channels and transporters typically consist of biomolecules that play key roles in a large variety of physiological and pathological processes. Traditional therapies include many ion-channel blockers, and some activators, although the exact biochemical pathways and mechanisms that regulate ion homeostasis are yet to be fully elucidated. An emerging area of research with great innovative potential in biomedicine pertains the design and development of synthetic ion channels and transporters, which may provide unexplored therapeutic opportunities. However, most studies in this challenging and multidisciplinary area are still at a fundamental level. In this review, we discuss the progress that has been made over the last five years on ion channels and transporters, touching upon biomolecules and synthetic supramolecules that are relevant to biological use. We conclude with the identification of therapeutic opportunities for future exploration.

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Engeloch, Caroline, Ulrich Schopfer, Ingo Muckenschnabel, Francois Le Goff, Hervé Mees, Karoline Boesch, and Maxim Popov. "Stability of Screening Compounds in Wet DMSO." Journal of Biomolecular Screening 13, no. 10 (November 21, 2008): 999–1006. http://dx.doi.org/10.1177/1087057108326536.

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The impact of storage conditions on compound stability and compound solubility has been debated intensely over the past 5 years. At Novartis, the authors decided to opt for a storage concept that can be considered controversial because they are using a DMSO/water (90/10) mixture as standard solvent. To assess the effect of water in DMSO stocks on compound stability, the authors monitored the purity of a subset of 1404 compounds from ongoing medicinal chemistry projects over several months. The study demonstrated that 85% of the compounds were stable in wet DMSO over a 2-year period at 4 °C. This result validates the storage concept developed at Novartis as a pragmatic approach that takes advantage of the benefits of DMSO/water mixtures while mediating the disadvantages. In addition, the authors describe how purity data collected over the course of the chemical validation of high-throughput screening actives are used to improve the analytical quality of the Novartis screening deck. ( Journal of Biomolecular Screening 2008:999-1006)

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Hess, Henry, and Gadiel Saper. "Engineering with Biomolecular Motors." Accounts of Chemical Research 51, no. 12 (October 30, 2018): 3015–22. http://dx.doi.org/10.1021/acs.accounts.8b00296.

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Moragrega, Inés, and José Luis Ríos. "Medicinal Plants in the Treatment of Depression: Evidence from Preclinical Studies." Planta Medica 87, no. 09 (January 12, 2021): 656–85. http://dx.doi.org/10.1055/a-1338-1011.

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AbstractMedicinal plants and their extracts are natural remedies with enormous potential for treating various diseases, including depression and anxiety. In the case of depression, hundreds of plants have traditionally been used in folk medicine for generations. Different plant extracts and natural products have been analyzed as potential antidepressant agents with validated models to test for antidepressant-like effects in animals, although other complementary studies have also been employed. Most of these studies focus on the possible mediators implicated in these potential effects, with dopamine, serotonin, and noradrenaline being the principal neurotransmitters implicated, both through interference with receptors and with their metabolism by monoamino oxidases, as well as through neuro-endocrine and neuroprotective effects. There are approximately 650 reports of antidepressant-like medicinal plants in PubMed; 155 of them have been compiled in this review, with a relevant group yielding positive results. Saffron and turmeric are the most relevant species studied in both preclinical and clinical studies; St. Johnʼs wort or kava have also been tested extensively. To the best of our knowledge, no review to date has provided a comprehensive understanding of the biomolecular mechanisms of action of these herbs or of whether their potential effects could have real benefits. The purpose of this narrative review is to provide an update regarding medicinal plants from the year 2000 to the present to examine the therapeutic potential of these antidepressant-like plants in order to contribute to the development of new therapeutic methods to alleviate the tremendous burden that depression causes worldwide.

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Tiwari, Prince. "Fluorescence-based Techniques to Study the Structure and Dynamics of Mass-selected Biomolecular Ions." CHIMIA International Journal for Chemistry 75, no. 4 (April 28, 2021): 252–56. http://dx.doi.org/10.2533/chimia.2021.252.

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Laser-induced fluorescence studies on mass-selected biomolecules are a promising route to understand their properties in the gas phase and probe their intrinsic properties in a solvent-free environment. Fluorescence has been used to investigate the conformation and dynamics of gaseous biomolecular ions. With Förster Resonance Energy Transfer (FRET), it is now possible to obtain sensitive intramolecular distance information from large biomolecules, like proteins, with high chemical specificity. With growing interest and applications, gas-phase fluorescence measurements can shed greater light on the characteristics of proteins in the gas phase. Compared to the solution phase measurements, gas-phase fluorescence can also help understand the influence of solvent interactions on the protein structure and function.

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Li, Qian, Xi Wang, Zhihui Dou, Weishan Yang, Beifang Huang, Jizhong Lou, and Zhuqing Zhang. "Protein Databases Related to Liquid–Liquid Phase Separation." International Journal of Molecular Sciences 21, no. 18 (September 16, 2020): 6796. http://dx.doi.org/10.3390/ijms21186796.

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Liquid−liquid phase separation (LLPS) of biomolecules, which underlies the formation of membraneless organelles (MLOs) or biomolecular condensates, has been investigated intensively in recent years. It contributes to the regulation of various physiological processes and related disease development. A rapidly increasing number of studies have recently focused on the biological functions, driving, and regulating mechanisms of LLPS in cells. Based on the mounting data generated in the investigations, six databases (LLPSDB, PhaSePro, PhaSepDB, DrLLPS, RNAgranuleDB, HUMAN CELL MAP) have been developed, which are designed directly based on LLPS studies or the component identification of MLOs. These resources are invaluable for a deeper understanding of the cellular function of biomolecular phase separation, as well as the development of phase-separating protein prediction and design. In this review, we compare the data contents, annotations, and organization of these databases, highlight their unique features, overlaps, and fundamental differences, and discuss their suitable applications.

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Ogiso, Hideo, Ryoji Suno, Takuya Kobayashi, Masashi Kawami, Mikihisa Takano, and Masaru Ogasawara. "A Liquid Chromatography-Mass Spectrometry Method to Study the Interaction between Membrane Proteins and Low-Molecular-Weight Compound Mixtures." Molecules 27, no. 15 (July 30, 2022): 4889. http://dx.doi.org/10.3390/molecules27154889.

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Molecular interaction analysis is an essential technique for the study of biomolecular functions and the development of new drugs. Most current methods generally require manipulation to immobilize or label molecules, and require advance identification of at least one of the two molecules in the reaction. In this study, we succeeded in detecting the interaction of low-molecular-weight (LMW) compounds with a membrane protein mixture derived from cultured cells expressing target membrane proteins by using the size exclusion chromatography-mass spectrometry (SEC-MS) method under the condition of 0.001% lauryl maltose neopentyl glycol as detergent and atmospheric pressure chemical ionization. This method allowed us to analyze the interaction of a mixture of medicinal herbal ingredients with a mixture of membrane proteins to identify the two interacting ingredients. As it does not require specialized equipment (e.g., a two-dimensional liquid chromatography system), this SEC-MS method enables the analysis of interactions between LMW compounds and relatively high-expressed membrane proteins without immobilization or derivatization of the molecules.

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Metzler-Nolte, Nils. "ChemInform Abstract: Labeling of Biomolecules for Medicinal Applications - Bioorganometallic Chemistry at Its Best." ChemInform 32, no. 21 (May 26, 2010): no. http://dx.doi.org/10.1002/chin.200121277.

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Nair, Vishnu H., Philippe Schwaller, and Teodoro Laino. "Data-driven Chemical Reaction Prediction and Retrosynthesis." CHIMIA International Journal for Chemistry 73, no. 12 (December 18, 2019): 997–1000. http://dx.doi.org/10.2533/chimia.2019.997.

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The synthesis of organic compounds, which is central to many areas such as drug discovery, material synthesis and biomolecular chemistry, requires chemists to have years of knowledge and experience. The development of technologies with the potential to learn and support experts in the design of synthetic routes is a half-century-old challenge with an interesting revival in the last decade. In fact, the renewed interest in artificial intelligence (AI), driven mainly by data availability, is profoundly changing the landscape of computer-aided chemical reaction prediction and retrosynthetic analysis. In this article, we briefly review different approaches to predict forward reactions and retrosynthesis, with a strong focus on data-driven ones. While data-driven technologies still need to demonstrate their full potential compared to expert rule-based systems in synthetic chemistry, the acceleration experienced in the last decade is a convincing sign that where we use software today, there will be AI tomorrow. This revolution will help and empower bench chemists, driving the transformation of chemistry towards a high-tech business over the next decades.

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Selenko, Philipp. "Quo Vadis Biomolecular NMR Spectroscopy?" International Journal of Molecular Sciences 20, no. 6 (March 14, 2019): 1278. http://dx.doi.org/10.3390/ijms20061278.

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In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.

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Lu, Kai, Cong Quang Vu, Tomoki Matsuda, and Takeharu Nagai. "Fluorescent Protein-Based Indicators for Functional Super-Resolution Imaging of Biomolecular Activities in Living Cells." International Journal of Molecular Sciences 20, no. 22 (November 17, 2019): 5784. http://dx.doi.org/10.3390/ijms20225784.

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Super-resolution light microscopy (SRM) offers a unique opportunity for diffraction-unlimited imaging of biomolecular activities in living cells. To realize such potential, genetically encoded indicators were developed recently from fluorescent proteins (FPs) that exhibit phototransformation behaviors including photoactivation, photoconversion, and photoswitching, etc. Super-resolution observations of biomolecule interactions and biochemical activities have been demonstrated by exploiting the principles of bimolecular fluorescence complementation (BiFC), points accumulation for imaging nanoscale topography (PAINT), and fluorescence fluctuation increase by contact (FLINC), etc. To improve functional nanoscopy with the technology of genetically encoded indicators, it is essential to fully decipher the photo-induced chemistry of FPs and opt for innovative indicator designs that utilize not only fluorescence intensity but also multi-parametric readouts such as phototransformation kinetics. In parallel, technical improvements to both the microscopy optics and image analysis pipeline are promising avenues to increase the sensitivity and versatility of functional SRM.

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Zhang, Haofan, Fengming He, Guiping Gao, Sheng Lu, Qiaochu Wei, Hongyu Hu, Zhen Wu, Meijuan Fang, and Xiumin Wang. "Approved Small-Molecule ATP-Competitive Kinases Drugs Containing Indole/Azaindole/Oxindole Scaffolds: R&D and Binding Patterns Profiling." Molecules 28, no. 3 (January 17, 2023): 943. http://dx.doi.org/10.3390/molecules28030943.

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Kinases are among the most important families of biomolecules and play an essential role in the regulation of cell proliferation, apoptosis, metabolism, and other critical physiological processes. The dysregulation and gene mutation of kinases are linked to the occurrence and development of various human diseases, especially cancer. As a result, a growing number of small-molecule drugs based on kinase targets are being successfully developed and approved for the treatment of many diseases. The indole/azaindole/oxindole moieties are important key pharmacophores of many bioactive compounds and are generally used as excellent scaffolds for drug discovery in medicinal chemistry. To date, 30 ATP-competitive kinase inhibitors bearing the indole/azaindole/oxindole scaffold have been approved for the treatment of diseases. Herein, we summarize their research and development (R&D) process and describe their binding models to the ATP-binding sites of the target kinases. Moreover, we discuss the significant role of the indole/azaindole/oxindole skeletons in the interaction of their parent drug and target kinases, providing new medicinal chemistry inspiration and ideas for the subsequent development and optimization of kinase inhibitors.

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Ludeña Huaman, Michael Azael, Reneé Isabel Huamán Quispe, Ana Luz Tupa Quispe, and Carlos Alberto Serrano Flores. "Ursolic acid: an overview including research performed in Peru." Revista Bases de la Ciencia. e-ISSN 2588-0764 6, no. 1 (April 30, 2021): 19. http://dx.doi.org/10.33936/rev_bas_de_la_ciencia.v6i1.3097.

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Ursolic acid (3β-3-hydroxy-urs-12-en-28-oic-acid) is a pentacyclic triterpenoid compound present in many medicinal herbs and edible fruits of different species of plants. Ursolic acid is now considered an important biomolecule due to its pharmacological activity and much of the research has focused on anticancer activity. To achieve the clinical application of ursolic acid, delivery nanosystems have been developed and the synthesis of its derivatives has also been carried out. In this review, we address different aspects of the chemistry of ursolic acid. Furthermore, we highlight the investigations that were carried out in Peru concerning ursolic acid. Palavras-chave: Ursolic acid, Triterpenoid, Lamiaceae, Medicinal plants. Abstract El ácido ursólico (ácido 3β-hidroxi-urs-12-en-28-óico) es un triterpenoide pentacíclico presente en varias hierbas medicinales y frutos comestibles de diferentes especies de plantas, es considerado una importante biomolécula debido a su actividad farmacológica y gran parte de las investigaciones se han enfocado en su actividad anticancerígena. Para lograr la aplicación clínica del ácido ursólico, se han desarrollado nanosistemas para su administración y también se han sintetizado gran cantidad de derivados. En esta revisión abordamos diferentes aspectos de la química del ácido ursólico, y además, destacamos las investigaciones que se llevaron a cabo en el Perú. Keywords: Ácido ursólico, Triterpenoide, Lamiaceae, Plantas medicinales.

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Malhotra, B. D., and H. H. Weetall. "Special Issue on Biomolecular Electronics - Interfacing Physics and Chemistry with Biology." Applied Biochemistry and Biotechnology 96, no. 1-3 (2001): 001–2. http://dx.doi.org/10.1385/abab:96:1-3:001.

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Malhotra, B. D. "National Symposium on Biomolecular Electronics - Interfacing Physics and Chemistry with Biology." Applied Biochemistry and Biotechnology 96, no. 1-3 (2001): 003–8. http://dx.doi.org/10.1385/abab:96:1-3:003.

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Ryu, Je-Kyung, Da-Eun Hwang, and Jeong-Mo Choi. "Current Understanding of Molecular Phase Separation in Chromosomes." International Journal of Molecular Sciences 22, no. 19 (October 4, 2021): 10736. http://dx.doi.org/10.3390/ijms221910736.

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Biomolecular phase separation denotes the demixing of a specific set of intracellular components without membrane encapsulation. Recent studies have found that biomolecular phase separation is involved in a wide range of cellular processes. In particular, phase separation is involved in the formation and regulation of chromosome structures at various levels. Here, we review the current understanding of biomolecular phase separation related to chromosomes. First, we discuss the fundamental principles of phase separation and introduce several examples of nuclear/chromosomal biomolecular assemblies formed by phase separation. We also briefly explain the experimental and computational methods used to study phase separation in chromosomes. Finally, we discuss a recent phase separation model, termed bridging-induced phase separation (BIPS), which can explain the formation of local chromosome structures.

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Lajoie, C. A., G. S. Sayler, and C. J. Kelly. "The Activated Sludge Biomolecular Database." Water Environment Research 74, no. 5 (September 2002): 480–87. http://dx.doi.org/10.2175/106143002x140279.

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Shafiei, Mojtaba, Mohamed Nainar Mohamed Ansari, Saiful Izwan Abd Razak, and Muhammad Umar Aslam Khan. "A Comprehensive Review on the Applications of Exosomes and Liposomes in Regenerative Medicine and Tissue Engineering." Polymers 13, no. 15 (July 30, 2021): 2529. http://dx.doi.org/10.3390/polym13152529.

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Tissue engineering and regenerative medicine are generally concerned with reconstructing cells, tissues, or organs to restore typical biological characteristics. Liposomes are round vesicles with a hydrophilic center and bilayers of amphiphiles which are the most influential family of nanomedicine. Liposomes have extensive research, engineering, and medicine uses, particularly in a drug delivery system, genes, and vaccines for treatments. Exosomes are extracellular vesicles (EVs) that carry various biomolecular cargos such as miRNA, mRNA, DNA, and proteins. As exosomal cargo changes with adjustments in parent cells and position, research of exosomal cargo constituents provides a rare chance for sicknesses prognosis and care. Exosomes have a more substantial degree of bioactivity and immunogenicity than liposomes as they are distinctly chiefly formed by cells, which improves their steadiness in the bloodstream, and enhances their absorption potential and medicinal effectiveness in vitro and in vivo. In this review, the crucial challenges of exosome and liposome science and their functions in disease improvement and therapeutic applications in tissue engineering and regenerative medicine strategies are prominently highlighted.

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Hemmerová, Erika, Tomáš Špringer, Zdeňka Krištofiková, and Jiří Homola. "Ionic Environment Affects Biomolecular Interactions of Amyloid-β: SPR Biosensor Study." International Journal of Molecular Sciences 21, no. 24 (December 20, 2020): 9727. http://dx.doi.org/10.3390/ijms21249727.

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In early stages of Alzheimer’s disease (AD), amyloid beta (Aβ) accumulates in the mitochondrial matrix and interacts with mitochondrial proteins, such as cyclophilin D (cypD) and 17β-hydroxysteroid dehydrogenase 10 (17β-HSD10). Multiple processes associated with AD such as increased production or oligomerization of Aβ affect these interactions and disbalance the equilibrium between the biomolecules, which contributes to mitochondrial dysfunction. Here, we investigate the effect of the ionic environment on the interactions of Aβ (Aβ1–40, Aβ1–42) with cypD and 17β-HSD10 using a surface plasmon resonance (SPR) biosensor. We show that changes in concentrations of K+ and Mg2+ significantly affect the interactions and may increase the binding efficiency between the biomolecules by up to 35% and 65% for the interactions with Aβ1–40 and Aβ1–42, respectively, in comparison with the physiological state. We also demonstrate that while the binding of Aβ1–40 to cypD and 17β-HSD10 takes place preferentially around the physiological concentrations of ions, decreased concentrations of K+ and increased concentrations of Mg2+ promote the interaction of both mitochondrial proteins with Aβ1–42. These results suggest that the ionic environment represents an important factor that should be considered in the investigation of biomolecular interactions taking place in the mitochondrial matrix under physiological as well as AD-associated conditions.

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Chopra, Pratiksha N., and Jagdish K. Sahu. "Biological Significance of Imidazole-based Analogues in New Drug Development." Current Drug Discovery Technologies 17, no. 5 (December 23, 2020): 574–84. http://dx.doi.org/10.2174/1570163816666190320123340.

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In the field of heterocyclic medicinal chemistry, especially five-membered ring structures containing a nitrogen atom, imidazole core is an imperative aromatic heterocycle which is usually present in naturally occurring products and synthetic bioactive molecules. The occurrence of imidazole moiety in therapeutic compounds may be beneficial in terms of improving water-soluble properties due to its two nitrogen atoms which leads to the creation of hydrogen bonds. The imidazole nucleus has also been recognized as an important isostere of triazole, pyrazole, thiazole, tetrazole, oxazole, amide etc. for the purpose of designing and development of various biologically active molecules. Moreover, imidazole core as an attractive binding site could interact with diverse cations and anions as well as biomolecules through different reactions in the human biological system thus displaying extensive biological activities. This effort thoroughly provides a wide-ranging assessment in current drug discovery and developments of imidazolebased analogues in the entire series of synthetic medicinal chemistry as antibacterial and antifungal, anticancer, anti-tubercular, analgesic and anti-inflammatory, anti-neuropathic, antihypertensive, anti-allergic, anti-parasitic, antiviral, antidepressant, anti-obesity and so on, altogether with their prospective approaches in diagnostic and pathological field. It is expected that the present review will be supportive on behalf of new opinions in the search for rational strategies of more efficacious and less toxic medicinal agents and drugs containing imidazole core.

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Mathai, Bincy Mariyam, Manu M. Joseph, Santhi Maniganda, Jyothi B. Nair, J. S. Arya, Varsha Karunakaran, K. V. Radhakrishnan, and Kaustabh Kumar Maiti. "Guanidinium rich dendron-appended hydnocarpin exhibits superior anti-neoplastic effects through caspase mediated apoptosis." RSC Advances 6, no. 58 (2016): 52772–80. http://dx.doi.org/10.1039/c6ra08724h.

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Medicinal plants have truly demonstrated their potential as a repository of active biomolecules with promising therapeutic potential and represent an important source for the identification of novel drug leads.

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Ritsch, Irina, Daniel Klose, Henrik Hintz, Adelheid Godt, Gunnar Jeschke, and Maxim Yulikov. "Pulsed EPR Methods to Study Biomolecular Interactions." CHIMIA International Journal for Chemistry 73, no. 4 (April 24, 2019): 268–76. http://dx.doi.org/10.2533/chimia.2019.268.

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Sage, Andrew T., Justin D. Besant, Brian Lam, Edward H. Sargent, and Shana O. Kelley. "Ultrasensitive Electrochemical Biomolecular Detection Using Nanostructured Microelectrodes." Accounts of Chemical Research 47, no. 8 (June 25, 2014): 2417–25. http://dx.doi.org/10.1021/ar500130m.

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Li, Tao, Dawei Shang, Shouwu Gao, Bo Wang, Hao Kong, Guozheng Yang, Weidong Shu, Peilong Xu, and Gang Wei. "Two-Dimensional Material-Based Electrochemical Sensors/Biosensors for Food Safety and Biomolecular Detection." Biosensors 12, no. 5 (May 9, 2022): 314. http://dx.doi.org/10.3390/bios12050314.

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Two-dimensional materials (2DMs) exhibited great potential for applications in materials science, energy storage, environmental science, biomedicine, sensors/biosensors, and others due to their unique physical, chemical, and biological properties. In this review, we present recent advances in the fabrication of 2DM-based electrochemical sensors and biosensors for applications in food safety and biomolecular detection that are related to human health. For this aim, firstly, we introduced the bottom-up and top-down synthesis methods of various 2DMs, such as graphene, transition metal oxides, transition metal dichalcogenides, MXenes, and several other graphene-like materials, and then we demonstrated the structure and surface chemistry of these 2DMs, which play a crucial role in the functionalization of 2DMs and subsequent composition with other nanoscale building blocks such as nanoparticles, biomolecules, and polymers. Then, the 2DM-based electrochemical sensors/biosensors for the detection of nitrite, heavy metal ions, antibiotics, and pesticides in foods and drinks are introduced. Meanwhile, the 2DM-based sensors for the determination and monitoring of key small molecules that are related to diseases and human health are presented and commented on. We believe that this review will be helpful for promoting 2DMs to construct novel electronic sensors and nanodevices for food safety and health monitoring.

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Hippchen, Hendrik, Wiebke H. Pohl, and Peter J. Walla. "Single-Particle Identification of Encoded Nanospheres." Journal of Biomolecular Screening 15, no. 2 (January 19, 2010): 218–23. http://dx.doi.org/10.1177/1087057109356806.

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Recently, it has been shown that 2-photon fluorescence correlation spectroscopy of single glycosylated 20-nm fluorescent spheres allows measurement of the relative carbohydrate binding affinities of unlabeled proteins and that these modified spheres can mimic the glycocalix of cell or virus surfaces. An especially useful extension would be the analysis of mixtures of nanospheres that each contain different fluorescent labels and are thus differentially “encoded.” If the surfaces of these encoded nanospheres are modified with various receptors, many different biomolecule-surface interactions and concurrent reactions can be measured quickly and simultaneously in a single-reaction vessel. An essential prerequisite for this general assay principle is the ability to identify with an accuracy of nearly 100% any encoded nanosphere present in a mixture on a single-particle level. Here the authors present a method that indeed allows certain identification of differently encoded nanospheres during single transits through the focal volume of a microscope objective (ø~200-500 nm) in aqueous solution. This opens the way for using the encoded nanospheres in 1-well measurements of a large variety of biomolecular receptor-ligand interactions, inhibition and concurrent reactions, and thus either for testing the behavior of ligands in a mimicked complex biomolecular environment or for a fast simultaneous measurement of a multitude of receptor-ligand interactions.

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Zhao, Yuhai, Aileen I. Pogue, Peter N. Alexandrov, Leslie G. Butler, Wenhong Li, Vivian R. Jaber, and Walter J. Lukiw. "Alteration of Biomolecular Conformation by Aluminum—Implications for Protein Misfolding Disease." Molecules 27, no. 16 (August 11, 2022): 5123. http://dx.doi.org/10.3390/molecules27165123.

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The natural element aluminum possesses a number of unique biochemical and biophysical properties that make this highly neurotoxic species deleterious towards the structural integrity, conformation, reactivity and stability of several important biomolecules. These include aluminum’s (i) small ionic size and highly electrophilic nature, having the highest charge density of any metallic cation with a Z2/r of 18 (ionic charge +3, radius 0.5 nm); (ii) inclination to form extremely stable electrostatic bonds with a tendency towards covalency; (iii) ability to interact irreversibly and/or significantly slow down the exchange-rates of complex aluminum–biomolecular interactions; (iv) extremely dense electropositive charge with one of the highest known affinities for oxygen-donor ligands such as phosphate; (v) presence as the most abundant metal in the Earth’s biosphere and general bioavailability in drinking water, food, medicines, consumer products, groundwater and atmospheric dust; and (vi) abundance as one of the most commonly encountered intracellular and extracellular metallotoxins. Despite aluminum’s prevalence and abundance in the biosphere it is remarkably well-tolerated by all plant and animal species; no organism is known to utilize aluminum metabolically; however, a biological role for aluminum has been assigned in the compaction of chromatin. In this Communication, several examples are given where aluminum has been shown to irreversibly perturb and/or stabilize the natural conformation of biomolecules known to be important in energy metabolism, gene expression, cellular homeostasis and pathological signaling in neurological disease. Several neurodegenerative disorders that include the tauopathies, Alzheimer’s disease and multiple prion disorders involve the altered conformation of naturally occurring cellular proteins. Based on the data currently available we speculate that one way aluminum contributes to neurological disease is to induce the misfolding of naturally occurring proteins into altered pathological configurations that contribute to the neurodegenerative disease process.

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Marya, Anand, Dinesh Rokaya, Artak Heboyan, and Gustavo Vicentis de Oliveira Fernandes. "Biomolecular and Biochemical Aspects of the Oral Cavity." Molecules 27, no. 24 (December 8, 2022): 8676. http://dx.doi.org/10.3390/molecules27248676.

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Recent advances in science, especially innovations in the field of biochemistry and materials science, greatly contribute to improvements in the prevention, diagnosis, and treatment of oral diseases [...]

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41

Romesberg, Floyd E. "Multidisciplinary Experimental Approaches to Characterizing Biomolecular Dynamics." ChemBioChem 4, no. 7 (June 27, 2003): 563–71. http://dx.doi.org/10.1002/cbic.200300572.

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Renaudet, Olivier, Didier Boturyn, and Pascal Dumy. "Biomolecular assembly by iterative oxime ligations." Bioorganic & Medicinal Chemistry Letters 19, no. 14 (July 2009): 3880–83. http://dx.doi.org/10.1016/j.bmcl.2009.03.119.

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Takahashi, Shunsuke, Masahiko Oshige, and Shinji Katsura. "DNA Manipulation and Single-Molecule Imaging." Molecules 26, no. 4 (February 17, 2021): 1050. http://dx.doi.org/10.3390/molecules26041050.

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DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

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Vellore, Nadeem A., and Riccardo Baron. "Epigenetic Molecular Recognition: A Biomolecular Modeling Perspective." ChemMedChem 9, no. 3 (February 12, 2014): 484–94. http://dx.doi.org/10.1002/cmdc.201300510.

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Baluška, František, William B. Miller, and Arthur S. Reber. "Biomolecular Basis of Cellular Consciousness via Subcellular Nanobrains." International Journal of Molecular Sciences 22, no. 5 (March 3, 2021): 2545. http://dx.doi.org/10.3390/ijms22052545.

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Cells emerged at the very beginning of life on Earth and, in fact, are coterminous with life. They are enclosed within an excitable plasma membrane, which defines the outside and inside domains via their specific biophysical properties. Unicellular organisms, such as diverse protists and algae, still live a cellular life. However, fungi, plants, and animals evolved a multicellular existence. Recently, we have developed the cellular basis of consciousness (CBC) model, which proposes that all biological awareness, sentience and consciousness are grounded in general cell biology. Here we discuss the biomolecular structures and processes that allow for and maintain this cellular consciousness from an evolutionary perspective.

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Mrozikiewicz, Aleksandra E., Marcin Ożarowski, and Piotr Jędrzejczak. "Biomolecular Markers of Recurrent Implantation Failure—A Review." International Journal of Molecular Sciences 22, no. 18 (September 18, 2021): 10082. http://dx.doi.org/10.3390/ijms221810082.

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Currently, infertility affects 8–12% of reproductive age couples worldwide, a problem that also affects women suffering from recurrent implantation failure (RIF). RIF is a complex condition resulting from many physiological and molecular mechanisms involving dynamic endometrium–blastocyst interaction. The most important are the endometrial receptivity process, decidualization, trophoblast invasion, and blastocyst nesting. Although the exact multifactorial pathogenesis of RIF remains unclear, many studies have suggested the association between hormone level imbalance, disturbances of angiogenic and immunomodulatory factors, certain genetic polymorphisms, and occurrence of RIF. These studies were performed in quite small groups. Additionally, the results are inconsistent between ethnicities. The present review briefly summarizes the importance of factors involved in RIF development that could also serve as diagnostic determinants. Moreover, our review could constitute part of a new platform for discovery of novel diagnostic and therapeutic solutions for RIF.

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Porzberg, Miriam R. B., Laust Moesgaard, Catrine Johansson, Udo Oppermann, Jacob Kongsted, and Jasmin Mecinović. "Recognition of Dimethylarginine Analogues by Tandem Tudor Domain Protein Spindlin1." Molecules 27, no. 3 (February 1, 2022): 983. http://dx.doi.org/10.3390/molecules27030983.

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Epigenetic readout of the combinatorial posttranslational modification comprised of trimethyllysine and asymmetric dimethylarginine (H3K4me3R8me2a) takes place via biomolecular recognition of tandem Tudor-domain-containing protein Spindlin1. Through comparative thermodynamic data and molecular dynamics simulations, we sought to explore the binding scope of asymmetric dimethylarginine mimics by Spindlin1. Herein, we provide evidence that the biomolecular recognition of H3K4me2R8me2a is not significantly affected when R8me2a is replaced by dimethylarginine analogues, implying that the binding of K4me3 provides the major binding contribution. High-energy water molecules inside both aromatic cages of the ligand binding sites contribute to the reader–histone association upon displacement by histone peptide, with the K4me3 hydration site being lower in free energy due to a flip of Trp151.

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Fernandes, Henrique S., Nuno M. F. S. A. Cerqueira, Sérgio F. Sousa, and André Melo. "A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems." Molecules 27, no. 17 (August 27, 2022): 5524. http://dx.doi.org/10.3390/molecules27175524.

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The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand–protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store.

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O'Hara, Patricia B. "LANTHANIDE IONS AS LUMINESCENT PROBES OF BIOMOLECULAR STRUCTURE." Photochemistry and Photobiology 46, no. 6 (December 1987): 1067–70. http://dx.doi.org/10.1111/j.1751-1097.1987.tb04894.x.

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Krylov, Sergey N. "Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM): A Novel Method for Biomolecular Screening." Journal of Biomolecular Screening 11, no. 2 (December 16, 2005): 115–22. http://dx.doi.org/10.1177/1087057105284339.

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Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a new separation-based affinity method. It has kinetic capabilities exceeding those of surface plasmon resonance (SPR) and does not require immobilization of molecules on the surface. Another distinctive feature of NECEEM is that—if it is combined with an advanced method for the mixing solutions inside a capillary, termed transverse diffusion of laminar flow profiles (TDLFP)—it requires only nanoliter volumes of solutions. The proven applications of NECEEM to biomolecular screening include 1) measuring kinetic and thermodynamic parameters of protein-ligand interactions, 2) quantitative affinity analyses of proteins and hybridization analyses of DNA and RNA, and 3) selection of binding ligands from combinatorial libraries. NECEEM is easy to automate and parallelize. Because of its simplicity and analytical power, NECEEM has the potential to become a workhorse in studies of biomolecular interactions. The author reviews theoretical bases of NECEEM and its applications to biomolecular screening.

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Journal articles on the topic 'Biomolecular and medicinal chemistry'

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