Journal articles: 'Natural molecules'

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Chen, Ya, Conrad Stork, Steffen Hirte, and Johannes Kirchmair. "NP-Scout: Machine Learning Approach for the Quantification and Visualization of the Natural Product-Likeness of Small Molecules." Biomolecules 9, no. 2 (January 24, 2019): 43. http://dx.doi.org/10.3390/biom9020043.

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Natural products (NPs) remain the most prolific resource for the development of small-molecule drugs. Here we report a new machine learning approach that allows the identification of natural products with high accuracy. The method also generates similarity maps, which highlight atoms that contribute significantly to the classification of small molecules as a natural product or synthetic molecule. The method can hence be utilized to (i) identify natural products in large molecular libraries, (ii) quantify the natural product-likeness of small molecules, and (iii) visualize atoms in small molecules that are characteristic of natural products or synthetic molecules. The models are based on random forest classifiers trained on data sets consisting of more than 265,000 to 322,000 natural products and synthetic molecules. Two-dimensional molecular descriptors, MACCS keys and Morgan2 fingerprints were explored. On an independent test set the models reached areas under the receiver operating characteristic curve (AUC) of 0.997 and Matthews correlation coefficients (MCCs) of 0.954 and higher. The method was further tested on data from the Dictionary of Natural Products, ChEMBL and other resources. The best-performing models are accessible as a free web service at http://npscout.zbh.uni-hamburg.de/npscout.

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Clardy, Jon, and Christopher Walsh. "Lessons from natural molecules." Nature 432, no. 7019 (December 2004): 829–37. http://dx.doi.org/10.1038/nature03194.

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Reisberg, Solomon H., Yang Gao, Allison S. Walker, Eric J. N. Helfrich, Jon Clardy, and Phil S. Baran. "Total synthesis reveals atypical atropisomerism in a small-molecule natural product, tryptorubin A." Science 367, no. 6476 (January 2, 2020): 458–63. http://dx.doi.org/10.1126/science.aay9981.

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Molecular shape defines function in both biological and material settings, and chemists have developed an ever-increasing vernacular to describe these shapes. Noncanonical atropisomers—shape-defined molecules that are formally topologically trivial but are interconvertible only by complex, nonphysical multibond torsions—form a unique subset of atropisomers that differ from both canonical atropisomers (e.g., binaphthyls) and topoisomers (i.e., molecules that have identical connectivity but nonidentical molecular graphs). Small molecules, in contrast to biomacromolecules, are not expected to exhibit such ambiguous shapes. Using total synthesis, we found that the peptidic alkaloid tryptorubin A can be one of two noncanonical atropisomers. We then devised a synthetic strategy that drives the atropospecific synthesis of a noncanonical atrop-defined small molecule.

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Saikin, Semion K., Alexander Eisfeld, Stéphanie Valleau, and Alán Aspuru-Guzik. "Photonics meets excitonics: natural and artificial molecular aggregates." Nanophotonics 2, no. 1 (February 1, 2013): 21–38. http://dx.doi.org/10.1515/nanoph-2012-0025.

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AbstractOrganic molecules store the energy of absorbed light in the form of charge-neutral molecular excitations – Frenkel excitons. Usually, in amorphous organic materials, excitons are viewed as quasiparticles, localized on single molecules, which diffuse randomly through the structure. However, the picture of incoherent hopping is not applicable to some classes of molecular aggregates – assemblies of molecules that have strong near-field interaction between electronic excitations in the individual subunits. Molecular aggregates can be found in nature, in photosynthetic complexes of plants and bacteria, and they can also be produced artificially in various forms including quasi-one dimensional chains, two-dimensional films, tubes, etc. In these structures light is absorbed collectively by many molecules and the following dynamics of molecular excitation possesses coherent properties. This energy transfer mechanism, mediated by the coherent exciton dynamics, resembles the propagation of electromagnetic waves through a structured medium on the nanometer scale. The absorbed energy can be transferred resonantly over distances of hundreds of nanometers before exciton relaxation occurs. Furthermore, the spatial and energetic landscape of molecular aggregates can enable the funneling of the exciton energy to a small number of molecules either within or outside the aggregate. In this review we establish a bridge between the fields of photonics and excitonics by describing the present understanding of exciton dynamics in molecular aggregates.

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Espinosa Aguirre, J. J. "Natural molecules as quimiopreventive agents." Toxicology Letters 259 (October 2016): S14—S15. http://dx.doi.org/10.1016/j.toxlet.2016.07.072.

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Gottlieb, Alex D., John D. Head, and Dennis Perusse. "Natural molecular shells as open subsystems of small molecules." International Journal of Quantum Chemistry 111, no. 15 (January 19, 2011): 4158–73. http://dx.doi.org/10.1002/qua.22980.

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Bai, Wen-Ju, and Xiqing Wang. "Appreciation of symmetry in natural product synthesis." Natural Product Reports 34, no. 12 (2017): 1345–58. http://dx.doi.org/10.1039/c7np00045f.

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Molteni, Monica, Annalisa Bosi, and Carlo Rossetti. "Natural Products with Toll-Like Receptor 4 Antagonist Activity." International Journal of Inflammation 2018 (2018): 1–9. http://dx.doi.org/10.1155/2018/2859135.

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Toll-Like Receptors (TLRs) are the innate immunity receptors that play an activating role when interacting with molecules released by bacteria and viruses (PAMPs, pathogen-associated molecular patterns) or with molecules released by injured cells and tissues (DAMPs, danger-associated molecular patterns). TLR triggering leads to the induction of proinflammatory cytokines and chemokines, driving the activation of both innate and adaptive immunity. In particular, Toll-Like Receptor 4 (TLR4) has been described to be involved in the inflammatory processes observed in several pathologies (such as ischemia/reperfusion injury, neuropathic pain, neurodegenerative diseases, and cancer). Molecules obtained by natural sources have been discovered to exert an anti-inflammatory action by targeting TLR4 activation pathways. This review focuses on TLR4 antagonists obtained from bacteria, cyanobacteria, and plants.

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W.J.O.-T. "Molecules in Natural Science and Medicine." Journal of Molecular Structure 271, no. 1-2 (August 1992): 155–56. http://dx.doi.org/10.1016/0022-2860(92)80218-7.

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BENDER, CHARLIE. "Natural orbitals, diatomic molecules and ERD." Molecular Physics 100, no. 3 (February 10, 2002): 335–36. http://dx.doi.org/10.1080/00268970110095642.

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Ahmed, Mukhtiar, and Muhammad Moazzam Naseer. "Organolithium-mediated cyclization reactions: a practical way to access hetero- and carbocycles." New Journal of Chemistry 41, no. 16 (2017): 7824–35. http://dx.doi.org/10.1039/c7nj01763d.

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Cyclization reactions are considered as one of the most important reactions in organic synthesis due to the fact that natural molecules contain cyclic components either as part of the molecule or molecular skeleton.

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Walker, Mark C., and Michelle C. Y. Chang. "Natural and engineered biosynthesis of fluorinated natural products." Chem. Soc. Rev. 43, no. 18 (2014): 6527–36. http://dx.doi.org/10.1039/c4cs00027g.

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Gaudreault, Roger, and Normand Mousseau. "Mitigating Alzheimer’s Disease with Natural Polyphenols: A Review." Current Alzheimer Research 16, no. 6 (July 23, 2019): 529–43. http://dx.doi.org/10.2174/1567205016666190315093520.

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:According to Alzheimer’s Disease International (ADI), nearly 50 million people worldwide were living with dementia in 2017, and this number is expected to triple by 2050. Despite years of research in this field, the root cause and mechanisms responsible for Alzheimer’s disease (AD) have not been fully elucidated yet. Moreover, promising preclinical results have repeatedly failed to translate into patient treatments. Until now, none of the molecules targeting AD has successfully passed the Phase III trial. Although natural molecules have been extensively studied, they normally require high concentrations to be effective; alternately, they are too large to cross the blood-brain barrier (BBB).:In this review, we report AD treatment strategies, with a virtually exclusive focus on green chemistry (natural phenolic molecules). These include therapeutic strategies for decreasing amyloid-β (Aβ) production, preventing and/or altering Aβ aggregation, and reducing oligomers cytotoxicity such as curcumin, (-)-epigallocatechin-3-gallate (EGCG), morin, resveratrol, tannic acid, and other natural green molecules. We also examine whether consideration should be given to potential candidates used outside of medicine and nutrition, through a discussion of two intermediate-sized green molecules, with very similar molecular structures and key properties, which exhibit potential in mitigating Alzheimer’s disease.

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Demay, Justine, Cécile Bernard, Anita Reinhardt, and Benjamin Marie. "Natural Products from Cyanobacteria: Focus on Beneficial Activities." Marine Drugs 17, no. 6 (May 30, 2019): 320. http://dx.doi.org/10.3390/md17060320.

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Cyanobacteria are photosynthetic microorganisms that colonize diverse environments worldwide, ranging from ocean to freshwaters, soils, and extreme environments. Their adaptation capacities and the diversity of natural products that they synthesize, support cyanobacterial success in colonization of their respective ecological niches. Although cyanobacteria are well-known for their toxin production and their relative deleterious consequences, they also produce a large variety of molecules that exhibit beneficial properties with high potential in various fields (e.g., a synthetic analog of dolastatin 10 is used against Hodgkin’s lymphoma). The present review focuses on the beneficial activities of cyanobacterial molecules described so far. Based on an analysis of 670 papers, it appears that more than 90 genera of cyanobacteria have been observed to produce compounds with potentially beneficial activities in which most of them belong to the orders Oscillatoriales, Nostocales, Chroococcales, and Synechococcales. The rest of the cyanobacterial orders (i.e., Pleurocapsales, Chroococcidiopsales, and Gloeobacterales) remain poorly explored in terms of their molecular diversity and relative bioactivity. The diverse cyanobacterial metabolites possessing beneficial bioactivities belong to 10 different chemical classes (alkaloids, depsipeptides, lipopeptides, macrolides/lactones, peptides, terpenes, polysaccharides, lipids, polyketides, and others) that exhibit 14 major kinds of bioactivity. However, no direct relationship between the chemical class and the respective bioactivity of these molecules has been demonstrated. We further selected and specifically described 47 molecule families according to their respective bioactivities and their potential uses in pharmacology, cosmetology, agriculture, or other specific fields of interest. With this up-to-date review, we attempt to present new perspectives for the rational discovery of novel cyanobacterial metabolites with beneficial bioactivity.

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Ye, Wenyu, Jian Hao, Yufeng Chen, Mengzhao Zhu, Zhen Pan, and Fei Hou. "Difference Analysis of Gas Molecules Diffusion Behavior in Natural Ester and Mineral Oil Based on Molecular Dynamic Simulation." Molecules 24, no. 24 (December 5, 2019): 4463. http://dx.doi.org/10.3390/molecules24244463.

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Natural ester, as a new environmentally green insulating oil, has been widely used in transformer. In an oil-immersed transformer, the normal aging, thermal failure, and discharge failure could easily lead to the decomposition of the oil-paper insulation system and produce different kinds of gases. Studying gas dissolution in natural ester and mineral oil could provide assistance in applying criteria to make a diagnosis of different kinds of faults in the transformer. In this paper, the molecular dynamics method was used to investigate the diffusion behavior of seven fault characteristic gases (including H2, CO, CH4, C2H2, CO2, C2H4, C2H6) in natural ester and mineral oil. The simulation parameters of free volume, interaction energy, mean square displacement, and diffusion coefficient were compared between the natural ester and mineral oil. Meanwhile, the influence of temperature on the diffusion of gas molecules in two kinds of oils was also analyzed. Results showed that the free volume, the interaction energy, and the relative molecular mass of gas molecules were the factors influenced by the diffusion of gas molecules in natural ester and mineral oil. The order of the diffusion coefficients of gas molecules in natural ester was as follows: H2 > CH4 > CO > C2H2 > C2H4 > CO2 > C2H6 and that in mineral oil was as follows: H2 > CH4 > CO> C2H2 > C2 H4 > C2H6 > CO2. By comparing the diffusion behavior of gas molecules in natural ester and mineral oil, it was found that the smaller free volume and higher interaction energy of gas molecules in natural ester were the major reasons for the gas molecules to be more difficult to diffuse in natural ester. The rising temperature could enhance the free volume and reduce the interaction energy between gas molecules and oil. The diffusion coefficient of gas molecules increased exponentially with the follow of temperature. However, the temperature didn’t affect the ordering of diffusion coefficient, free volume, and interaction energy of gas molecules in natural ester and mineral oil.

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Kowalak, S., and A. Jankowska. "Natural zeolites for styrene oligomerization." Clay Minerals 46, no. 2 (June 2011): 189–95. http://dx.doi.org/10.1180/claymin.2011.046.2.189.

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AbstractHydrogen forms of natural mordenite and clinoptilolite were used as catalysts for styrene oligomerization and as matrices to hold the resultant oligomers in order to prepare intense and light-resistant pigments. In contrast to synthetic zeolites of similar pore sizes (mainly H-ZSM-5, H-mordenite), the natural zeolites did not form products with an intense (pink) colouration. H-mordenite samples treated with styrene developed some colour due to styrene oligomers (the chromophore) whereas, in treated clinoptilolites, colour formation was negligible due to the lack of access of styrene molecules into the elliptical channels. The results of catalytic tests for cracking of cumene (cumene and styrene have similar molecular sizes) were consistent with the styrene oligomerization results. They indicate a noticeable catalytic activity with natural H-mordenite and a lack of activity with clinoptilolite. On the other hand, catalytic tests for propan-2-ol decomposition indicate a high activity with both natural zeolites, which confirms the presence of acid sites and their accessibility to small alcohol molecules.

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Laurent, Gabin, Luca Peliti, and David Lacoste. "Survival of Self-Replicating Molecules under Transient Compartmentalization with Natural Selection." Life 9, no. 4 (October 3, 2019): 78. http://dx.doi.org/10.3390/life9040078.

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The problem of the emergence and survival of self-replicating molecules in origin-of-life scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple system composed of a self-replicating molecule (a replicase) and a parasite molecule that needs the replicase for copying itself, we show that transient (rather than permanent) compartmentalization is sufficient to the task. We also exhibit a regime in which the concentrations of the two kinds of molecules undergo sustained oscillations. Our model should be relevant not only for origin-of-life scenarios but also for describing directed evolution experiments, which increasingly rely on transient compartmentalization with pooling and natural selection.

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Ridzwan, Wan Mohd Faruq Wan Mohd, Dzaraini Kamarun, Azemi Samsuri, Ahmad Faiza Mohd, and Che Mohd Som Said. "Blending of Polyvulcanize Natural Rubber." Advanced Materials Research 879 (January 2014): 224–29. http://dx.doi.org/10.4028/www.scientific.net/amr.879.224.

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Natural rubber (NR) latex is widely used in the manufacture of thin film barrier products such as gloves and condom. However, due to its low Tg, film casted from NR latex is soft and tacky, and needed to be strengthened to produced high performance products. Films of prevulcanized natural rubber latex (PVNR) blended with nanosized copolymer of n-butyl acrylate/butyl methacrylate (BA/BMA) were prepared at three different ratios of acrylate copolymer: PVNR. The tensile strength and elongation at break of films prepared decreased with increasing ratios of acrylate copolymer:PVNR. FESEM images showed the occurrence of agglomeration of the acrylate copolymers with PVNR molecules. The degree of agglomeration of the blended molecules increased with percentages of copolymer added. The decrease in the tensile strength and elongation at break may due to the agglomeration of the blended molecules suggesting poor dispersion and/or destabilization of PVNR molecules.

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Buyukbingol. "Natural Products for Anti-Cancer Progress: The Impact of Artificial Intelligence." Proceedings 40, no. 1 (December 30, 2019): 37. http://dx.doi.org/10.3390/proceedings2019040037.

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Finding for more effective anticancer drugs on almost different types of cancer, a huge number of molecules is still under evaluation and barely many more than 100,000 compounds have been tested with researchers and several institutions since recent decades. The fact that plant-derived molecules are treated at various levels against cancer is based on a very long history. This has enabled many molecules derived from plant sources to be used in cancer treatment. With the introduction of artificial intelligence, studies on the discovery of new molecules that may be effective in the etiology of various diseases have gained weight as in every field. Artificial intelligence learns the relationship between molecular structure and biological components in certain mathematical algorithms with the obtained in vitro and in vivo values and helps to create new molecular patterns as a result of certain validations. In fact, the artificial intelligence, is now able to develop novel algorithms over the initially defined and further realization might proceed new designs with advanced programming by self-settings new routes through the improvement of desired targets. The introduction of the genetic profile and consequently the discovery of new drug molecules will be one of the most important fields of study of the future. Molecules to be obtained from plant sources will also have very important roles in this direction. Drug therapy for patients with the same disease but with a different genetic profile does not give the same treatment success in every patient. The reason for this is that due to the different mutations in DNA, the protein structures encoded by the genes show differences and the interaction pattern of molecules on the proteins responsible for diseases, could be different. Therefore, for each patient, due to the mutation, diverse molecules that can interact with mutated proteins should be required. This issue is becoming increasingly important all over the world, especially under the name of precision medicine and in the form of personalized drug administration, and demonstrates the importance of drug treatment depending on the individual's genetic profile. It is then useful to treat anticancer molecules of plant origin in this direction. For this purpose, gene rearrangements and gene editing procedures can be applied in plants by using CRISPR technology to improve several factors through leading to design and develop new plant origin molecules for the intended purpose with the assistance of artificial intelligence algorithms.

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Li, Zi Jian, Yan Ping Ding, Su Lin Zhang, Yan Ling Wu, and Wen Zhang. "Small Natural Molecules Targeting DNA G-Quadruplexes." Advanced Materials Research 955-959 (June 2014): 423–26. http://dx.doi.org/10.4028/www.scientific.net/amr.955-959.423.

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DNA G-quadruplex (G4-DNA) has emerged as a new drug target for anti-tumor. The small compounds can induce the formation of G4-DNA and stabilize its structures, which is of potential significance for the tumor treatment. This paper focuses on our current understanding about the structure of G4-DNA, the binding mode between G4-DNA and small molecular ligands, and natural products targeting G4-DNA.

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Lemanek, Kamil. "Issues with molecules in Natural Semantic Metalanguage." Language Sciences 77 (January 2020): 101239. http://dx.doi.org/10.1016/j.langsci.2019.101239.

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Stone, Marcia. "Natural Antibiotics — Small Molecules with Large Repertoires." Microbe Magazine 4, no. 10 (October 1, 2009): 442–43. http://dx.doi.org/10.1128/microbe.4.442.1.

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Holdener, Stephanie L. "Natural Flexibility of Type I Collagen Molecules." Biophysical Journal 102, no. 3 (January 2012): 579a. http://dx.doi.org/10.1016/j.bpj.2011.11.3154.

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Tarasov, Egor A. "Interaction Potential of Open Carbon Nanotube with Natural Gas Molecular Components." Key Engineering Materials 685 (February 2016): 534–38. http://dx.doi.org/10.4028/www.scientific.net/kem.685.534.

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In this paper presents the study of the process of interaction between helium (He) and methane (СH4) molecules and the energy barrier created by a single-layer carbon nanotube. The interaction potential fields for the case of a tube as a nano-scale object interacting with single molecules or atoms were determined. Calculations show the dependence of molecular velocity within the symmetry axis of a single-layer carbon nanotube on the axial coordinate. The influence of the tube radius on the character of molecular passage through the open tube is considered.

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Novak, Jurica, Hrvoje Rimac, Shivananda Kandagalla, Maria A. Grishina, and Vladimir A. Potemkin. "Can natural products stop the SARS-CoV-2 virus? A docking and molecular dynamics study of a natural product database." Future Medicinal Chemistry 13, no. 4 (February 2021): 363–78. http://dx.doi.org/10.4155/fmc-2020-0248.

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Background: The SARS-CoV-2 3CLpro is one of the primary targets for designing new and repurposing known drugs. Methodology: A virtual screening of molecules from the Natural Product Atlas was performed, followed by molecular dynamics simulations of the most potent inhibitor bound to two conformations of the protease and into two binding sites. Conclusion: Eight molecules with appropriate ADMET properties are suggested as potential inhibitors. The greatest benefit of this study is the demonstration that these ligands can bind in the catalytic site but also to the groove between domains II and III, where they interact with a series of residues which have an important role in the dimerization and the maturation process of the enzyme.

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Arouche, Tiago S., Júlio C. N. Aires, Tais S. S. Pereira, Abel F. G. Neto, José F. S. Costa, Mozaniel S. Oliveira, and Antonio M. J. C. Neto. "Trapping Using Molecular Dynamics of Natural Gas in Carbon Nanotubes Under the External Uniform Electric Field." Advanced Science, Engineering and Medicine 12, no. 6 (June 1, 2020): 711–18. http://dx.doi.org/10.1166/asem.2020.2641.

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We perform behavioral analysis of natural gas and SYNGAS molecules interacting with a carbon nanotube at an initial simulation temperature of 300 K, and under a uniform electric field, as a gas sensor system using molecular dynamics. Each gas molecule was relaxed for 50 ps outside the carbon nanotube, describing each possible arrangement. A constant external electric field was applied longitudinally to this system, along the length of the carbon nanotube, promoting an evanescent effect, capable of trapping each gas molecule by spinning around it. The electric field intensities were from a range of 10–8 a.u. to 10–1 a.u. were performed, and mean orbit radii and thermodynamic properties were estimated. The results indicate that an external uniform electric field and van der Waals interactions in a carbon-derived nanotube are sufficient to create an evanescent field of attractive potential, presenting it as a practical system for detecting through temperature and ray analysis, of the GN molecules and the SYNGAS.

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Karlhofer, F. M., M. M. Orihuela, and W. M. Yokoyama. "Ly-49-independent natural killer (NK) cell specificity revealed by NK cell clones derived from p53-deficient mice." Journal of Experimental Medicine 181, no. 5 (May 1, 1995): 1785–95. http://dx.doi.org/10.1084/jem.181.5.1785.

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Natural killer (NK) cells are heterogeneous in their specificity and expression of cell surface molecules. In the mouse, the Ly-49A molecule is a primary determinant of NK cell specificity because of its ability to downregulate NK cell activation after physical interaction with target cell MHC class I molecules. Ly-49A is expressed on an NK cell subset, and it belongs to a family of highly related molecules that may similarly dictate major histocompatibility complex (MHC) class I-associated specificity of Ly-49A- NK cells. It is not known, however, whether murine NK cell specificity may occur independently of the Ly-49 family and target cell MHC class I molecules. Similar to the impact of cloned murine T cell lines on molecular description of T cell recognition, derivation of cloned murine NK cells should permit dissection of NK cell specificity but, to date, it has not been possible to produce such effector cells. In this study, we derived NK cell clones from mice that were homozygous for a mutation in the p53 tumor suppressor gene. The cloned cells displayed the molecular, cell surface, and functional phenotype of NK cells. Significantly, the NK cell clones displayed clonal differences in ability to kill a panel of murine tumor targets and did not lyse normal cells. Target lysis was unaffected by target cell MHC class I expression, and none of the clones expressed Ly-49A on the cell surface or transcripts for Ly-49 isoforms. Although consistent with the possibility that NK cell specificity for MHC class I molecules is mediated by the Ly-49 family of molecules, the results indicate that NK cell specificity also is regulated by a mechanism independent of target cell MHC class I and the Ly-49 family.

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Petrescu, Florian Ion Tiberiu, Relly Victoria Virgil Petrescu, and Eleni Mimi Buzea. "New natural antioxidants." Independent Journal of Management & Production 11, no. 3 (June 1, 2020): 967. http://dx.doi.org/10.14807/ijmp.v11i3.938.

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Antioxidants are, no doubt, an essential part of an optimal health and even traditional doctors support the importance of an appropriate contribution of antioxidants taken through food. Antioxidants are a category of molecules able to inhibit the oxidation of other molecules. The body distributes various nutrients in the body due to their antioxidant properties and also factory antioxidant enzymes to keep under control the reaction in the chain of free radicals. Some antioxidants are produced by the body, but others don't. In addition, the body's natural ability to produce antioxidants decreases with age. Antioxidants play a significant role for health as it may influence the aging by fighting free radicals. There are antioxidants which can’t be produced in the human body, and to be taken through antioxidant-rich foods, or supplements powerful antioxidant. The paper aims to present some natural sources of oxidants that can be obtained through diet.

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Yazaydin, A. Ozgur, Geoffrey M. Bowers, and R. James Kirkpatrick. "Molecular dynamics modeling of carbon dioxide, water and natural organic matter in Na-hectorite." Physical Chemistry Chemical Physics 17, no. 36 (2015): 23356–67. http://dx.doi.org/10.1039/c5cp03552j.

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Molecular dynamics modeling of systems containing a Na-exchanged hectorite and model natural organic matter molecules along with pure H₂O, pure CO₂, or a mixture of H₂O and CO₂ provides significant new insight into the molecular scale interactions among silicate surfaces, dissolved cations and organic molecules, H₂O and CO₂.

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Carotenuto, Gianfranco. "Isothermal Kinetic Investigation of the Water-Cations Interaction in Natural Clinoptilolite." European Journal of Engineering Research and Science 4, no. 5 (May 25, 2019): 119–25. http://dx.doi.org/10.24018/ejers.2019.4.5.1341.

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The kinetics of water adsorption by a natural zeolite (clinoptilolite) sample has been investigated by high-frequency AC current intensity measurements. According to the achieved kinetic results, cations should play a relevant role in the clinoptilolite hydration, in fact most of adsorbed water stay in the cationic sites. The water molecules associate withcation one-by-one. In particular, the forced adsorption of water molecules in a wet atmosphere is a quite slow process, while water desorption in air or dry atmosphere is a spontaneous and fast process. The observed increase of cation mobility could be adequately explained by assuming an arrangement of water molecules between the cation and the negatively charged oxygens contained in the cationic site. Such molecular arrangement could increase the strength of both dipole-cation and hydrogen bond interactions.

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LIEBOVITCH, LARRY S., NIKITA D. ARNOLD, and LEV Y. SELECTOR. "NEURAL NETWORKS TO COMPUTE MOLECULAR DYNAMICS." Journal of Biological Systems 02, no. 02 (June 1994): 193–228. http://dx.doi.org/10.1142/s0218339094000155.

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Large molecules such as proteins have many of the properties of neural networks. Hence, neural networks may serve as a natural and thus efficient method to compute the time dependent changes of the structure in large molecules. We describe how to encode the spatial conformation and energy structure of a molecule in a neural network. The dynamics of the molecule can then be computed from the dynamics of the corresponding neural network. As a detailed example, we formulated a Hopfield network to compute the molecular dynamics of a small molecule, cyclohexane. We used this network to determine the distribution of times spent in the twist and chair conformational states as the cyclohexane thermally switches between these two states.

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Zhang, Mei-Chen, Shu-Hui Gu, Guang-Pan Liu, Chen-Cheng Li, Han-Mei Xu, Zhong-Xi Wu, Bo-Ping Ye, et al. "Facile Synthesis and Cytotoxicity of Phenazine-Chromene Hybrid Molecules Derived from Phenazine Natural Product." Combinatorial Chemistry & High Throughput Screening 22, no. 1 (May 3, 2019): 35–40. http://dx.doi.org/10.2174/1386207322666190307125015.

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Aim and Objective: Small molecule targeted drugs can effectively reduce the toxicity and side effects of drugs, and improve the efficacy of drugs by their specific antitumor activity. Hence, the development of small molecular targeted drugs for cancer has important significance. This study was undertaken to design and synthesize novel phenazine-chromene hybrid molecules in order to optimize the structure and improve the efficacy of this kind of hybrids. Materials and Methods: O-diaminobenzene was used as starting material to synthesize twentyfour heterocyclic compounds designed as hybrid molecules of phenazine and 4H-chromene pharmacophores by facile methods. The structures of the compound were confirmed by 1H NMR, 13C NMR and HRMS. Furthermore, the synthesized compounds were evaluated for in vitro activity against four human cancer cell lines and two non-cancer cell lines by MTT test. Results: Some compounds showed strong cytotoxic activities against HepG2 and A549 cancer lines (IC50 = 5-10 µM). Comparing 2i with 2l, the introduction of hydrophilic groups on the phenazine core could not improve the antiproliferative activity significantly. Except 2d and 3c, compounds owning chlorine substituent on the 4H-chromene pharmacophore seemingly contribute to enhance the compounds’ antiproliferative activity. Specially, compound 3c showed highest cytotoxicity against A549 cells with IC50 values of 3.3±0.4 µM. Furthermore, all compounds showed low or no cytotoxicity against HUVEC and L02 non-cancer cells in vitro. Conclusion: Compound 3c may be used as potential lead molecule against A549 cancer cells.

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Gutiérrez-Arzaluz, Luis, Fatima López-Salazar, Bernardo Salcido-Santacruz, Beatriz Gonzalez-Cano, Rafael López-Arteaga, Rubén O. Torres-Ochoa, Nuria Esturau-Escofet, Fernando Cortés-Guzmán, Roberto Martinez, and Jorge Peon. "Bisindole caulerpin analogues as nature-inspired photoresponsive molecules." Journal of Materials Chemistry C 8, no. 20 (2020): 6680–88. http://dx.doi.org/10.1039/c9tc05889c.

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Tóth, Fanni, Edina Katalin Cseh, and László Vécsei. "Natural Molecules and Neuroprotection: Kynurenic Acid, Pantethine and α-Lipoic Acid." International Journal of Molecular Sciences 22, no. 1 (January 2, 2021): 403. http://dx.doi.org/10.3390/ijms22010403.

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The incidence of neurodegenerative diseases has increased greatly worldwide due to the rise in life expectancy. In spite of notable development in the understanding of these disorders, there has been limited success in the development of neuroprotective agents that can slow the progression of the disease and prevent neuronal death. Some natural products and molecules are very promising neuroprotective agents because of their structural diversity and wide variety of biological activities. In addition to their neuroprotective effect, they are known for their antioxidant, anti-inflammatory and antiapoptotic effects and often serve as a starting point for drug discovery. In this review, the following natural molecules are discussed: firstly, kynurenic acid, the main neuroprotective agent formed via the kynurenine pathway of tryptophan metabolism, as it is known mainly for its role in glutamate excitotoxicity, secondly, the dietary supplement pantethine, that is many sided, well tolerated and safe, and the third molecule, α-lipoic acid is a universal antioxidant. As a conclusion, because of their beneficial properties, these molecules are potential candidates for neuroprotective therapies suitable in managing neurodegenerative diseases.

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Ribó, Josep M. "Chirality: The Backbone of Chemistry as a Natural Science." Symmetry 12, no. 12 (November 30, 2020): 1982. http://dx.doi.org/10.3390/sym12121982.

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Chemistry as a natural science occupies the length and temporal scales ranging between the formation of atoms and molecules as quasi-classical objects, and the formation of proto-life systems showing catalytic synthesis, replication, and the capacity for Darwinian evolution. The role of chiral dissymmetry in the chemical evolution toward life is manifested in how the increase of chemical complexity, from atoms and molecules to complex open systems, accompanies the emergence of biological homochirality toward life. Chemistry should express chirality not only as molecular structural dissymmetry that at the present is described in chemical curricula by quite effective pedagogical arguments, but also as a cosmological phenomenon. This relates to a necessarily better understanding of the boundaries of chemistry with physics and biology.

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Veeramachaneni, Thunuguntla, Bhaswant, Mathai, and Bondili. "Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT2C Receptor." Biomolecules 9, no. 10 (October 1, 2019): 556. http://dx.doi.org/10.3390/biom9100556.

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Obesity prevalence continues to be a foremost health concern across the globe leading to the development of major health risk conditions like type II diabetes, hyperlipidemia, hypertension and even cancers. Because of the deprived drug-based management system, there is an urgent need for the development of new drugs aiming at satiety and appetite control targets. Among the reported satiety signaling targets, 5HT2C receptor plays a crucial role in decreasing appetite and has become a promising target for the development of anti-obesity drugs. Lorcaserin, a 5HT2C receptor agonist and the only drug available in the market, was designed based on the receptor mechanism of action. Due to limited drug options available and considering the adverse drug effects of Lorcaserin, the development of new drugs which are highly specific toward the 5HT2C target and with lesser side effects is essential. The present study is majorly focused on developing new 5HT2C agonists through computational approaches like screening, docking, and simulation using Phase, QikProp, Glide and Desmond applications of the Schrodinger suite. Screening protocols resulted in eight best hit molecules with affinity for the receptor and among them, five hits displayed binding affinity toward the conserved residue Asp 134 of the receptor. The stability of the five molecules in complex with the 5HT2C receptor was studied through molecular dynamic simulations. Three molecules, ZINC32123870, ZINC40312983 and ZINC32124535, maintained stable interactions with the Asp 134 residue throughout the 50 ns simulation run time. Further, due to the high sequence similarity seen among the receptors of 5HT2 family, the three potential hits were cross validated against other subtypes 5HT2A and 5HT2B of the 5HT2 family to determine the specificity of the molecules against the target. Among the three hits, ZINC32124535 was identified as the best potential hit based on the hydrogen bond interaction percentage with Asp residue [5HT2A (Asp 155:60%); 5HT2B (Asp155: No interaction); 5HT2C (Asp 134:86%)]. The ZINC32124535 molecule produced one salt bridge and hydrogen bond interactions with Asp 134, alike the known drug Lorcaserin. Based on the results, ZINC32124535 was identified as the best potential hit against the 5HT2C receptor.

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Manivannan, Jeganathan, Thangarasu Silambarasan, Rajendran Kadarkarairaj, and Boobalan Raja. "Systems pharmacology and molecular docking strategies prioritize natural molecules as cardioprotective agents." RSC Advances 5, no. 94 (2015): 77042–55. http://dx.doi.org/10.1039/c5ra10761j.

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Kikuchi, Asuka, and Tomonori Kawano. "Discrete Biochemistry of DNA: Arithmetic DNA Molecules for Binary Additions, Naturally Found Genetic Logic Circuits for Plant Sensing, and DNA-Based Animation." Journal of Advanced Computational Intelligence and Intelligent Informatics 20, no. 5 (September 20, 2016): 671–80. http://dx.doi.org/10.20965/jaciii.2016.p0671.

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To date, a number of researchers are seeking for and/or designing novel molecules which function as arithmetic molecular engines. Biomolecules such as deoxyribonucleic acid (DNA) and proteins are examples of promising candidate molecules. In the present article, we showed our view that DNA-based molecules could be used as a novel class of platforms for discrete mathematical operations or tools for natural computation. Here, we report on a novel molecular logic circuit combining exclusive disjunction (XOR) gate and conjunction (AND) gate implemented on a single DNA molecule performing arithmetic operations with simple binary numbers through polymerase chain reactions (PCR); which was inspired by previously developed protein-based computing model allowing simple polynomial algebra over fields through algebraic representation of cyclic inter-conversions in the catalytic modes of a plant enzyme as a cyclic additive group. In addition, we showed that DNA can be used as the platform for image coding and processing leading to DNA-coded animation by using novel PCR-based protocols. Lastly, we discussed the significance of recent attempts in the stream of natural computing and synthetic biological research, by handling DNA and related biomolecules as the media for discrete mathematical operations.

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Sephton, Mark A., Will Meredith, Cheng-Gong Sun, and Colin E. Snape. "Biomedical and Forensic Applications of Combined Catalytic Hydrogenation-Stable Isotope Ratio Analysis." Analytical Chemistry Insights 2 (January 2007): 117739010700200. http://dx.doi.org/10.4137/117739010700200013.

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Studies of biological molecules such as fatty acids and the steroid hormones have the potential to benefit enormously from stable carbon isotope ratio measurements of individual molecules. In their natural form, however, the body's molecules interact too readily with laboratory equipment designed to separate them for accurate measurements to be made. Some methods overcome this problem by adding carbon to the target molecule, but this can irreversibly overprint the carbon source ‘signal’. Hydropyrolysis is a newly-applied catalytic technique that delicately strips molecules of their functional groups but retains their carbon skeletons and stereochemistries intact, allowing precise determination of the carbon source. By solving analytical problems, the new technique is increasing the ability of scientists to pinpoint molecular indicators of disease, elucidate metabolic pathways and recognise administered substances in forensic investigations.

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Gu, Qiong, Xin Yan, and Jun Xu. "Drug Discovery Inspired by Mother Nature: Seeking Natural Biochemotypes and the Natural Assembly Rules of the Biochemome." Journal of Pharmacy & Pharmaceutical Sciences 16, no. 2 (August 2, 2013): 331. http://dx.doi.org/10.18433/j3c31s.

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Purpose. The Human Genome Project is producing a new biological ‘periodic table’, which defines all genes for making macromolecules (proteins, DNA, RNA, etc) and the relations between genes and their biological functions. We now need to consider whether to initiate a biochemome project aimed at discovering biochemistry’s ‘periodic table’, which would define all molecular parts for making small molecules (natural products) and the relations between the parts and their functions to regulate genes. By understanding the Biochemome, we might be able to design biofunctional molecules based upon a set of molecular parts for drug innovation. Methods. A number of algorithms for processing chemical structures are used to systematically derive chemoyls (natural building blocks) from a database of compounds identified in Traditional Chinese Medicine (TCM). The rules to combine chemoyls for biological activities are then deduced by mining an annotated TCM structure-activity database (ATCMD). Based upon the rules and the basic chemoyls, a chemical library can be biochemically profiled, virtual synthetic routes can be planned, and lead compounds can be identified for a specific drug target. Conclusions. The Biochemome is the complete set of molecular components (chemoyls) in an organism and Biochemomics studies the rules governing their assembly and their evolution, together with the relations between the Biochemome and drug targets. This approach provides a new paradigm for drug discovery that is based on a comprehensive knowledge of the synthetic origins of biochemical diversity, and helps to direct biomimetic syntheses aimed at assembling quasi-natural product libraries for drug screening. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.

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Lindner, Moshe, Guy Nir, Heidelinde��R C. Dietrich, Ian��T Young, Elad Tauber, I. Bronshtein, Liat Altman, and Yuval Garini. "Studies of Single Molecules in their Natural Form." Israel Journal of Chemistry 49, no. 3-4 (June 8, 2010): 283–91. http://dx.doi.org/10.1560/ijc.49.3-4.283.

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Gao, Yuxi, Jun Hu, and Yong Ju. "Supramolecular Self-Assembly Based on Natural Small Molecules." Acta Chimica Sinica 74, no. 4 (2016): 312. http://dx.doi.org/10.6023/a16010016.

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Robles-Fernandez, Inmaculada, Fernando Rodriguez-Serrano, Pablo Alvarez, Raul Ortiz, Ana Rama, Jose Prados, Consolacion Melguizo, Enrique Alvarez-Manzaneda, and Antonia Aranega. "Antitumor Properties of Natural Compounds and Related Molecules." Recent Patents on Anti-Cancer Drug Discovery 8, no. 3 (June 1, 2013): 203–15. http://dx.doi.org/10.2174/1574891x113089990034.

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Scior, T., and S. Garces-Eisele. "Epigenetic Control Using Natural Products and Synthetic Molecules." Current Medicinal Chemistry 13, no. 8 (April 1, 2006): 935–58. http://dx.doi.org/10.2174/092986706776361067.

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Zaid, Abdel Naser, and Rowa’ Al Ramahi. "Depigmentation and Anti-aging Treatment by Natural Molecules." Current Pharmaceutical Design 25, no. 20 (September 19, 2019): 2292–312. http://dx.doi.org/10.2174/1381612825666190703153730.

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Natural molecules are becoming more accepted choices as cosmetic agents, many products in the market today claim to include natural components. Plants include many substances that could be of a value in the whitening of the skin and working as anti-aging agents. A wide range of articles related to natural skin whitening and anti-aging agents have been reviewed. Many plant-derived and natural molecules have shown to affect melanin synthesis by different mechanisms, examples include Arbutin, Ramulus mori extract, Licorice extract, Glabridin, Liquiritin, Kojic acid, Methyl gentisate, Aloesin, Azelaic acid, Vitamin C, Thioctic acid, Soya bean extracts, Niacinamide, α and β-hydroxy acids, Lactic acid, Chamomile extract, and Ellagic acid. Some of the widely used natural anti-aging products as natural antioxidants, collagen, hyaluronic acid, and coenzyme Q can counteract the effects of reactive oxygen species in skin cells and have anti-aging properties on the skin. It was concluded that many natural products including antioxidants can prevent UV-induced skin damage and have whitening and anti-aging effects. It is very important to develop and stabilize appropriate methods for the evaluation of the whitening and anti-aging capacity of natural products and their exact mechanism of action to ensure real efficacy based on evidence-based studies. The attention should be oriented on the formulations and the development of an appropriate vehicle to ensure suitable absorption of these natural products in addition to evaluating the suitable concentration of these molecules required having the desired effects without causing harmful side effects.

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Esposito, Elisabetta, Claudio Nastruzzi, Maddalena Sguizzato, and Rita Cortesi. "Nanomedicines to Treat Skin Pathologies with Natural Molecules." Current Pharmaceutical Design 25, no. 21 (September 26, 2019): 2323–37. http://dx.doi.org/10.2174/1381612825666190709210703.

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The skin and mucous membranes are subjected to many disorders and pathological conditions. Nature offers a wide range of molecules with antioxidant activity able to neutralize, at least in part, the formation of free radicals and therefore to counteract the phenomena of cellular aging. Since synthetic drugs for the treatment of skin diseases can induce resistance, it is particularly interesting to use compounds of plant origin, transporting them in pharmaceutical forms capable of controlling their release and absorption. This review provides an overview of new findings about the use of lipid-based nanosystems for the delivery of natural molecules useful on the topical treatment of skin disorders. Several natural molecules encapsulated in lipid nanosystems have been considered in the treatment of some skin pathologies or diseases. Particularly, the use of rosemary and eucalyptus essential oil, saffron derivatives, curcumin, eugenol, capsaicin, thymol and lycopene has been reported. The molecules have been alternatively encapsulated in viscous systems, such as the organogels, or in liquid systems, such as ethosomes, transferosomes, solid lipid nanoparticles and monoolein based dispersions thickened by inclusion in carbomer gels. The nanostructured forms have been in vitro and in vivo investigated for the treatment of skin disorders due to dehydration, inflammation, melanoma, wound healing, fungal infections or psoriasis. The data reported in the different studies have suggested that the cutaneous application of lipid nanosystems allows a deep interaction between lipid matrix and skin strata, promoting a prolonged release and efficacy of the loaded natural molecules. This review suggests that the application of natural molecules onto the skin by lipid-based nanosystems can provide numerous clinician benefits in dermatology and cosmetics.

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Natsheh, Hiba, Elisa Vettorato, and Elka Touitou. "Ethosomes for Dermal Administration of Natural Active Molecules." Current Pharmaceutical Design 25, no. 21 (September 26, 2019): 2338–48. http://dx.doi.org/10.2174/1381612825666190716095826.

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: Ethosomes are nanovesicular carriers for dermal administration. Phospholipids, ethanol at relatively high concentrations (up to 50%) and water are their main components. Ethosomes are what we call “soft vesicles” with fluid bilayers due to the presence of ethanol. The composition and structure of the vesicles augment their ability to entrap molecules with various physicochemical properties and deliver them to the deep strata of skin. Since their first design, ethosomal systems have been extensively investigated for a wide range of applications. : This review focuses on work carried out in vitro, in vivo in animal models and in humans in clinical studies, with ethosomal formulations containing natural active molecules for the treatment of skin disorders. Skin bacterial and fungal infections, skin inflammation, acne vulgaris, arthritis, and skin cancer are examples of disorders managed successfully by ethosomal systems. Furthermore, Ethosomes loaded with a number of naturally occurring compounds for cosmetic applications are also reported. The efficient treatments together with a good safety profile and lack of toxicity or irritation paved the way towards the development of new dermal therapies.

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Das, Viswanath, and Juan Bautista De Sanctis. "Small Natural and Synthetic Molecules for Therapeutic Use." Current Pharmaceutical Design 26, no. 35 (October 16, 2020): 4349–50. http://dx.doi.org/10.2174/138161282635200910103400.

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Leonor Sánchez, Mercedes, Melina María Belén Martínez, and Paulo César Maffia. "Natural Antimicrobial Peptides: Pleiotropic Molecules in Host Defense." CellBio 02, no. 04 (2013): 200–210. http://dx.doi.org/10.4236/cellbio.2013.24023.

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Walsh, Christopher T., and Michael A. Fischbach. "Natural Products Version 2.0: Connecting Genes to Molecules." Journal of the American Chemical Society 132, no. 8 (March 3, 2010): 2469–93. http://dx.doi.org/10.1021/ja909118a.

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Journal articles on the topic 'Natural molecules'

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