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Journal articles on the topic 'Novel Molecules'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Yu, Chang Feng. "A Novel High Precision Analytic Potential Function for Diatomic Molecules." Key Engineering Materials 645-646 (May 2015): 313–18. http://dx.doi.org/10.4028/www.scientific.net/kem.645-646.313.

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A new analytical potential energy functions is presented, the potential energy function is examined by 13 examples of different diatomic molecules or ions——homonuclear ground-state for neutral diatomic molecules, heternuclear ground-state for charged diatomic molecular ion, heternuclear excitation-state neutral diatomic molecules ,heternuclear excited-state for charged diatomic molecular ion, homonuclear excited-state for neutral diatomic molecule , homonuclear excited-state for charged diatomic moleculeetc.. as a consequence, the theoretical values of the vibrational energy level of molecules calculated by the potential energy function are in high-precision consistent with RKR data (Rydberg-Klein-Rees) or experimental data.

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2

Walker, Michael A. "Novel antiviral molecules." Drug Discovery Today 7, no. 20 (October 2002): 1065–66. http://dx.doi.org/10.1016/s1359-6446(02)02471-6.

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3

Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 8, no. 1 (January 2003): 47–50. http://dx.doi.org/10.1016/s1359-6446(02)02551-5.

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4

Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 8, no. 5 (March 2003): 229–31. http://dx.doi.org/10.1016/s1359-6446(03)02622-9.

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Westwell, A. "Novel antitumour molecules." Drug Discovery Today 8, no. 9 (May 1, 2003): 421–22. http://dx.doi.org/10.1016/s1359-6446(03)02676-x.

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Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 8, no. 15 (August 2003): 718–19. http://dx.doi.org/10.1016/s1359-6446(03)02776-4.

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Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 8, no. 20 (October 2003): 955–57. http://dx.doi.org/10.1016/s1359-6446(03)02834-4.

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Westwell, Andrew. "Novel antitumour molecules." Drug Discovery Today 6, no. 4 (February 2001): 215–16. http://dx.doi.org/10.1016/s1359-6446(00)01619-6.

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Westwell, Andrew. "Novel antitumour molecules." Drug Discovery Today 6, no. 9 (May 2001): 489–91. http://dx.doi.org/10.1016/s1359-6446(01)01755-x.

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Westwell, Andrew. "Novel antitumour molecules." Drug Discovery Today 6, no. 12 (June 2001): 648–49. http://dx.doi.org/10.1016/s1359-6446(01)01829-3.

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Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 6, no. 13 (July 2001): 699–701. http://dx.doi.org/10.1016/s1359-6446(01)01836-0.

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Walker, Michael A. "Novel antiviral molecules." Drug Discovery Today 6, no. 14 (July 2001): 747–49. http://dx.doi.org/10.1016/s1359-6446(01)01860-8.

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Westwell, Andrew. "Novel antitumour molecules." Drug Discovery Today 6, no. 17 (September 2001): 916–18. http://dx.doi.org/10.1016/s1359-6446(01)01915-8.

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Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 7, no. 4 (February 2002): 269–72. http://dx.doi.org/10.1016/s1359-6446(01)02141-9.

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Walker, Michael A. "Novel antiviral molecules." Drug Discovery Today 7, no. 11 (May 2002): 630–31. http://dx.doi.org/10.1016/s1359-6446(02)02285-7.

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Walker, Michael A. "Novel antiviral molecules." Drug Discovery Today 7, no. 10 (May 2002): 581–82. http://dx.doi.org/10.1016/s1359-6446(02)02287-0.

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Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 7, no. 13 (July 2002): 739–40. http://dx.doi.org/10.1016/s1359-6446(02)02311-5.

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Walker, Michael A. "Novel antiviral molecules." Drug Discovery Today 7, no. 14 (July 2002): 779–80. http://dx.doi.org/10.1016/s1359-6446(02)02330-9.

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Westwell, Andrew D. "Novel antitumour molecules." Drug Discovery Today 7, no. 14 (July 2002): 780–83. http://dx.doi.org/10.1016/s1359-6446(02)02331-0.

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20

Allaka, Tejeswara Rao, Naresh Kumar Katari, Venkataramireddy Veeramreddy, and Jaya Shree Anireddy. "Molecular Modeling Studies of Novel Fluoroquinolone Molecules." Current Drug Discovery Technologies 15, no. 2 (April 26, 2018): 109–22. http://dx.doi.org/10.2174/1570163814666170829142044.

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21

McKinnon, Joshua J., Mark A. Spackman, and Anthony S. Mitchell. "Novel tools for visualizing and exploring intermolecular interactions in molecular crystals." Acta Crystallographica Section B Structural Science 60, no. 6 (November 11, 2004): 627–68. http://dx.doi.org/10.1107/s0108768104020300.

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A new way of exploring packing modes and intermolecular interactions in molecular crystals is described, using Hirshfeld surfaces to partition crystal space. These molecular Hirshfeld surfaces, so named because they derive from Hirshfeld's stockholder partitioning, divide the crystal into regions where the electron distribution of a sum of spherical atoms for the molecule (the promolecule) dominates the corresponding sum over the crystal (the procrystal). These surfaces reflect intermolecular interactions in a novel visual manner, offering a previously unseen picture of molecular shape in a crystalline environment. Surface features characteristic of different types of intermolecular interactions can be identified, and such features can be revealed by colour coding distances from the surface to the nearest atom exterior or interior to the surface, or by functions of the principal surface curvatures. These simple devices provide a striking and immediate picture of the types of interactions present, and even reflect their relative strengths from molecule to molecule. A complementary two-dimensional mapping is also presented, which summarizes quantitatively the types of intermolecular contacts experienced by molecules in the bulk and presents this information in a convenient colour plot. This paper describes the use of these tools in the compilation of a pictorial glossary of intermolecular interactions, using identifiable patterns of interaction between small molecules to rationalize the often complex mix of interactions displayed by large molecules.

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22

Banjare, Laxmi, Sant Kumar Verma, Akhlesh Kumar Jain, and Suresh Thareja. "Lead Molecules as Novel Aromatase Inhibitors: In Silico De Novo Designing and Binding Affinity Studies." Letters in Drug Design & Discovery 17, no. 5 (May 18, 2020): 655–65. http://dx.doi.org/10.2174/1570180816666190703152659.

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Background:Aromatase inhibitors emerged as a pivotal moiety to selectively block estrogen production, prevention and treatment of tumour growth in breast cancer. De novo drug design is an alternative approach to blind virtual screening for successful designing of the novel molecule against various therapeutic targets.Objective:In the present study, we have explored the de novo approach to design novel aromatase inhibitors.Method:The e-LEA3D, a computational-aided drug design web server was used to design novel drug-like candidates against the target aromatase. For drug-likeness ADME parameters (molecular weight, H-bond acceptors, H-bond donors, LogP and number of rotatable bonds) of designed molecules were calculated in TSAR software package, geometry optimization and energy minimization was accomplished using Chem Office. Further, molecular docking study was performed in Molegro Virtual Docker (MVD).Results:Among 17 generated molecules using the de novo pathway, 13 molecules passed the Lipinski filter pertaining to their bioavailability characteristics. De novo designed molecules with drug-likeness were further docked into the mapped active site of aromatase to scale up their affinity and binding fitness with the target. Among de novo fabricated drug like candidates (1-13), two molecules (5, 6) exhibited higher affinity with aromatase in terms of MolDock score (-150.650, -172.680 Kcal/mol, respectively) while molecule 8 showed lowest target affinity (-85.588 Kcal/mol).Conclusion:The binding patterns of lead molecules (5, 6) could be used as a pharmacophore for medicinal chemists to explore these molecules for their aromatase inhibitory potential.

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23

Tirosh, Oren, Yehoshua Katzhendler, Yechezkel Barenholz, Isaac Ginsburg, and Ron Kohen. "Amidothionophosphates: Novel Antioxidant Molecules." Phosphorus, Sulfur, and Silicon and the Related Elements 111, no. 1 (April 1, 1996): 75. http://dx.doi.org/10.1080/10426509608054704.

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24

Bermudez, V., T. Gase, F. Kajzar, N. Capron, F. Zerbetto, F. G. Gatti, D. A. Leigh, and S. Zhang. "Rotaxanes––novel photonic molecules." Optical Materials 21, no. 1-3 (January 2003): 39–44. http://dx.doi.org/10.1016/s0925-3467(02)00109-x.

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25

Pignatelli, Massimo, and Carina J. Vessey BM. "Adhesion molecules: Novel molecular tools in tumor pathology." Human Pathology 25, no. 9 (September 1994): 849–56. http://dx.doi.org/10.1016/0046-8177(94)90002-7.

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26

Nordon, Galia, Aviram Magen, Ido Guy, and Kira Radinsky. "Learning to Rank Articles for Molecular Queries." Proceedings of the AAAI Conference on Artificial Intelligence 36, no. 11 (June 28, 2022): 12594–600. http://dx.doi.org/10.1609/aaai.v36i11.21532.

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The cost of developing new drugs is estimated at billions of dollars per year. Identification of new molecules for drugs involves scanning existing bio-medical literature for relevant information. As the potential drug molecule is novel, retrieval of relevant information using a simple direct search is less likely to be productive. Identifying relevant papers is therefore a more complex and challenging task, which requires searching for information on molecules with similar characteristics to the novel drug. In this paper, we present the novel task of ranking documents based on novel molecule queries. Given a chemical molecular structure, we wish to rank medical papers that will contribute to a researcher's understanding of the novel molecule drug potential. We present a set of ranking algorithms and molecular embeddings to address the task. An extensive evaluation of the algorithms is performed over the molecular embeddings, studying their performance on a benchmark retrieval corpus, which we share with the community. Additionally, we introduce a heterogeneous edge-labeled graph embedding approach to address the molecule ranking task. Our evaluation shows that the proposed embedding model can significantly improve molecule ranking methods. The system is currently deployed in a targeted drug delivery and personalized medicine research laboratory.

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27

Xiao, Shu Juan, Shou Wu Yu, and Hong Xia Li. "Synthesis of Novel Separation Materials Based on Molecular Imprinting Technology." Advanced Materials Research 535-537 (June 2012): 1441–45. http://dx.doi.org/10.4028/www.scientific.net/amr.535-537.1441.

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Molecular imprinting technology is a kind of new-emerging polymerizing technology, which produces molecule recognition materials with high selectivity an affinity. MIPs were synthesized using acrylic amide as functional monomers, azodiisobutyronitrile as initiator, and lutelin as template molecules. The absorption capability of MIPs wans studied. The results showed that the imprinting efficiency is 97.9%.

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Albelda, S. M., P. D. Oliver, L. H. Romer, and C. A. Buck. "EndoCAM: a novel endothelial cell-cell adhesion molecule." Journal of Cell Biology 110, no. 4 (April 1, 1990): 1227–37. http://dx.doi.org/10.1083/jcb.110.4.1227.

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Cell-cell adhesion is controlled by many molecules found on the cell surface. In addition to the constituents of well-defined junctional structures, there are the molecules that are thought to play a role in the initial interactions of cells and that appear at precise times during development. These include the cadherins and cell adhesion molecules (CAMs). Representatives of these families of adhesion molecules have been isolated from most of the major tissues. The notable exception is the vascular endothelium. Here we report the identification of a cell surface molecule designated "endoCAM" (endothelial Cell Adhesion Molecule), which may function as an endothelial cell-cell adhesion molecule. EndoCAM is a 130-kD glycoprotein expressed on the surface of endothelial cells both in culture and in situ. It is localized to the borders of contiguous endothelial cells. It is also present on platelets and white blood cells. Antibodies against endoCAM prevent the initial formation of endothelial cell-cell contacts. Despite similarities in size and intercellular location, endoCAM does not appear to be a member of the cadherin family of adhesion receptors. The serologic and protease susceptibility characteristics of endoCAM are different from those of the known cadherins, including an endogenous endothelial cadherin. Although the precise biologic function of endoCAM has not been determined, it appears to be one of the molecules responsible for regulating endothelial cell-cell adhesion processes and may be involved in platelet and white blood cell interactions with the endothelium.

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29

Nagamalla, Lavanya, J. V. Shanmukha Kumar, Mohammed Rafi Shaik, Chintakindi Sanjay, Ali M. Alsamhan, Mohsin Ahmed Kasim, and Abdulrahman Alwarthan. "Identification of Novel AXL Kinase Inhibitors Using Ligand-Based Pharmacophore Screening and Molecular Dynamics Simulations." Crystals 12, no. 8 (August 17, 2022): 1158. http://dx.doi.org/10.3390/cryst12081158.

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AXL kinase is a promising target in novel drug discovery for cancer. A ligand-based pharmacophore model was generated with the Pharmit web server. Its inbuilt PubChem molecule database was screened and led to 408 candidate molecules. Docking of the AXL kinase active sites with the identified list of candidate molecules was carried out with Autodock Vina docking software. This resulted in four compounds selected for further investigation. Molecular dynamics simulation of two ligands (PubChem-122421875 and PubChem-78160848) showed considerable binding with AXL kinase. From the MM-PBSA binding free energies investigation, the PubChem-122421875 (G = −179.3 kJ/mol) and PubChem-78160848 (G = −208.3 kJ/mol) ligands had favorable protein-ligand complex stability and binding free energy. Hence, PubChem-122421875 and PubChem-78160848 molecules identified in this work could be a potent starting point for developing novel AXL kinase inhibitor molecules.

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30

Choi, Jieun, and Juyong Lee. "V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization." International Journal of Molecular Sciences 22, no. 21 (October 27, 2021): 11635. http://dx.doi.org/10.3390/ijms222111635.

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We propose a computational workflow to design novel drug-like molecules by combining the global optimization of molecular properties and protein-ligand docking with machine learning. However, most existing methods depend heavily on experimental data, and many targets do not have sufficient data to train reliable activity prediction models. To overcome this limitation, protein-ligand docking calculations must be performed using the limited data available. Such docking calculations during molecular generation require considerable computational time, preventing extensive exploration of the chemical space. To address this problem, we trained a machine-learning-based model that predicted the docking energy using SMILES to accelerate the molecular generation process. Docking scores could be accurately predicted using only a SMILES string. We combined this docking score prediction model with the global molecular property optimization approach, MolFinder, to find novel molecules exhibiting the desired properties with high values of predicted docking scores. We named this design approach V-dock. Using V-dock, we efficiently generated many novel molecules with high docking scores for a target protein, a similarity to the reference molecule, and desirable drug-like and bespoke properties, such as QED. The predicted docking scores of the generated molecules were verified by correlating them with the actual docking scores.

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de Coupade, Catherine, Antonio Fittipaldi, Vanessa Chagnas, Matthieu Michel, Sophie Carlier, Ennio Tasciotti, Audrey Darmon, et al. "Novel human-derived cell-penetrating peptides for specific subcellular delivery of therapeutic biomolecules." Biochemical Journal 390, no. 2 (August 23, 2005): 407–18. http://dx.doi.org/10.1042/bj20050401.

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Short peptide sequences that are able to transport molecules across the cell membrane have been developed as tools for intracellular delivery of therapeutic molecules. This work describes a novel family of cell-penetrating peptides named Vectocell® peptides [also termed DPVs (Diatos peptide vectors)]. These peptides, originating from human heparin binding proteins and/or anti-DNA antibodies, once conjugated to a therapeutic molecule, can deliver the molecule to either the cytoplasm or the nucleus of mammalian cells. Vectocell® peptides can drive intracellular delivery of molecules of varying molecular mass, including full-length active immunoglobulins, with efficiency often greater than that of the well-characterized cell-penetrating peptide Tat. The internalization of Vectocell® peptides has been demonstrated to occur in both adherent and suspension cell lines as well as in primary cells through an energy-dependent endocytosis process, involving cell-membrane lipid rafts. This endocytosis occurs after binding of the cell-penetrating peptides to extracellular heparan sulphate proteoglycans, except for one particular peptide (DPV1047) that partially originates from an anti-DNA antibody and is internalized in a caveolar independent manner. These new therapeutic tools are currently being developed for intracellular delivery of a number of active molecules and their potentiality for in vivo transduction investigated.

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Pang, Suna, and Feng Wang. "Novel All-Nitrogen Molecular Crystals Composed of Tetragonal N4 Molecules." International Journal of Molecular Sciences 23, no. 10 (May 14, 2022): 5503. http://dx.doi.org/10.3390/ijms23105503.

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A computational study promises insight into molecular crystals consisting of the tetrahedral form of N4 molecules (Td-N4). Here, our efforts are focused on theoretically predicting the existence of the molecular crystals consisting of Td-N4 molecules. On the basis of the first principles of Born–Oppenheimer molecular dynamics under constant temperature and pressure, and geometry optimizations under hydrostatic pressures without any constrained parameters, molecular crystals consisting of Td-N4 molecules were confirmed to be dynamically and thermally metastable. Our analysis shows that, with high detonation performance and high stability, these Td-N4 molecular crystals can indeed be potential candidates as high-energy density explosives.

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Feng, Simin, Maria Cristina dos Santos, Bruno R. Carvalho, Ruitao Lv, Qing Li, Kazunori Fujisawa, Ana Laura Elías, et al. "Ultrasensitive molecular sensor using N-doped graphene through enhanced Raman scattering." Science Advances 2, no. 7 (July 2016): e1600322. http://dx.doi.org/10.1126/sciadv.1600322.

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As a novel and efficient surface analysis technique, graphene-enhanced Raman scattering (GERS) has attracted increasing research attention in recent years. In particular, chemically doped graphene exhibits improved GERS effects when compared with pristine graphene for certain dyes, and it can be used to efficiently detect trace amounts of molecules. However, the GERS mechanism remains an open question. We present a comprehensive study on the GERS effect of pristine graphene and nitrogen-doped graphene. By controlling nitrogen doping, the Fermi level (EF) of graphene shifts, and if this shift aligns with the lowest unoccupied molecular orbital (LUMO) of a molecule, charge transfer is enhanced, thus significantly amplifying the molecule’s vibrational Raman modes. We confirmed these findings using different organic fluorescent molecules: rhodamine B, crystal violet, and methylene blue. The Raman signals from these dye molecules can be detected even for concentrations as low as 10−11M, thus providing outstanding molecular sensing capabilities. To explain our results, these nitrogen-doped graphene-molecule systems were modeled using dispersion-corrected density functional theory. Furthermore, we demonstrated that it is possible to determine the gaps between the highest occupied and the lowest unoccupied molecular orbitals (HOMO-LUMO) of different molecules when different laser excitations are used. Our simulated Raman spectra of the molecules also suggest that the measured Raman shifts come from the dyes that have an extra electron. This work demonstrates that nitrogen-doped graphene has enormous potential as a substrate when detecting low concentrations of molecules and could also allow for an effective identification of their HOMO-LUMO gaps.

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Kurt, Barış, and Hamdi Temel. "Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation." Molecules 25, no. 9 (May 8, 2020): 2196. http://dx.doi.org/10.3390/molecules25092196.

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Boric acid, borate esters, and hydroxy derivatives are biologically active molecules. Thus, performing molecular dynamics simulations of these molecules is vital in terms of drug design, but it is difficult to find directly generated Amber parameters based on an ab initio method for these kinds of molecules in the literature. In this study, Amber parameters for such molecules containing boron were generated based on ab initio calculations using the paramfit program, which applies a combination of genetic and simplex algorithms, and the Visual Force Field Derivation Toolkit (VFFDT) program containing the Seminario method. The minimized structure, after obtaining novel parameters and using the sander program, was compared with the experimental crystallographic structures, and it was observed that the root-mean-square deviation (RMSD) value between the experimental structure and minimized structure agreed reasonably well. In addition, the molecule was heated, and the molecular dynamics simulation was successfully obtained with the novel parameters.

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35

UEDA, Mitsuyoshi. "Molecular Tool Creating Novel and Functional Bio-active Molecules." Kobunshi 50, no. 4 (2001): 254. http://dx.doi.org/10.1295/kobunshi.50.254.

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36

Vinay, Dass S., Manoj Raje, Rakesh K. Verma, and Gyan C. Mishra. "Characterization of Novel Costimulatory Molecules." Journal of Biological Chemistry 270, no. 40 (October 6, 1995): 23429–36. http://dx.doi.org/10.1074/jbc.270.40.23429.

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37

Wada, Tatsuo, Yadong Zhang, Liming Wang, and Hiroyuki Sasabe. "Novel Molecules for Photorefractive Application." Molecular Crystals and Liquid Crystals Science and Technology. Section A. Molecular Crystals and Liquid Crystals 280, no. 1 (April 1996): 71–78. http://dx.doi.org/10.1080/10587259608040312.

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38

Saitoh, Ken-ichi, Yoshihiro Takai, Tomohiro Sato, Masanori Takuma, and Yoshimasa Takahashi. "Optimization of LIB Electrolyte and Exploration of Novel Compounds via the Molecular Dynamics Method." Batteries 8, no. 3 (March 21, 2022): 27. http://dx.doi.org/10.3390/batteries8030027.

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Due to great interest in the development of electric vehicles and other applications, improving the performances of lithium-ion batteries (LIBs) is crucial. Specifically, components of electrolytes for LIBs should be adequately chosen from hundreds of thousands of candidate compounds. In this study, we aimed to evaluate some physical properties expected for combinations of molecules for electrolytes by microscopic simulations. That is, the viscosity, ionic conductivity, degree of dissociation, diffusion coefficient, and conformation of each molecule were analyzed via molecular dynamics (MD) simulations. We aimed to understand how molecular-sized structures and properties collaboratively affect the behavior of electrolytes. The practical models of molecules we used were ethylene carbonate (EC), fluoroethylene carbonate (FEC), propylene carbonate (PC), butylene carbonate (BC), γ-butyrolactone (GBL), γ-valerolactone (GVL), dimethyl carbonate (DMC), ethyl-methyl carbonate (EMC), diethyl carbonate (DEC), and lithium hexafluorophosphate (LiPF6). Many molecular systems of electrolytes were simulated, in which one molar LiPF6 was mixed into a single or combined solvent. It was found that small solvent molecules diffused with relative ease, and they contributed to the higher ionic conductivity of electrolytes. It was clarified that the diffusion coefficient of lithium (Li) ions is greatly affected by the surrounding solvent molecules. We can conclude that high-permittivity solvents can be selectively coordinated around Li ions, and Li salts are sufficiently dissociated, even when there is only a small content of high-permittivity solvent. Thus, we can confirm solely by MD simulation that one of the better candidates for solvent molecules, formamide (F), will exhibit higher performance than the current solvents.

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39

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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40

Wan, Yichao, Chunxing Yan, Han Gao, and Tingting Liu. "Small-molecule PROTACs: novel agents for cancer therapy." Future Medicinal Chemistry 12, no. 10 (May 2020): 915–38. http://dx.doi.org/10.4155/fmc-2019-0340.

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Proteolysis-targeting chimera (PROTAC) is a new technology to selectively degrade target proteins via ubiquitin-proteasome system. PROTAC molecules (PROTACs) are a class of heterobifunctional molecules, which contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. They provide several advantages over traditional inhibitors in potency, selectivity and drug resistance. Thus, many promising PROTACs have been developed in the recent two decades, especially small-molecule PROTACs. In this review, we briefly introduce the mechanism of PROTACs and focus on the progress of small-molecule PROTACs based on different E3 ligases. In addition, we also introduce the opportunities and challenges of small-molecule PROTACs for cancer therapy.

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Inoue, Kazushi, and Elizabeth A. Fry. "Novel Molecular Markers for Breast Cancer." Biomarkers in Cancer 8 (January 2016): BIC.S38394. http://dx.doi.org/10.4137/bic.s38394.

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The use of molecular biomarkers assures that breast cancer (BC) patients receive optimal treatment. Established biomarkers, such as estrogen receptor, progesterone receptor, HER2, and Ki67, have been playing significant roles in the subcategorization of BC to predict the prognosis and decide the specific therapy to each patient. Antihormonal therapy using 4-hydroxytamoxifen or aromatase inhibitors have been employed in patients whose tumor cells express hormone receptors, while monoclonal antibody to HER2 has been administered to HER2-positive BCs. Although new therapeutic agents have been developed in the past few decades, many patients still die of the disease due to relapse; thus, novel molecular markers that predict therapeutic failure and those that can be targets for specific therapy are expected. We have chosen four of such molecules by reviewing recent publications, which are cyclin E, B-Myb, Twist, and DMP1β. The oncogenicity of these molecules has been demonstrated in vivo and/or in vitro through studies using transgenic mice or siRNAs, and their expressions have been shown to be associated with shortened overall or disease-free survival of BC patients. The former three molecules have been shown to accelerate epithelial-mesenchymal transition that is often associated with cancer stem cell-ness and metastasis; all these four can be novel therapeutic targets as well. Thus, large prospective studies employing immunohistochemistry will be needed to establish the predictive values of these molecules in patients with BC.

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42

Miao, Zongcheng, Yaqin Chu, Lei Wang, Wenqing Zhu, and Dong Wang. "Nonlinear Optical and Ion Sensor Properties of Novel Molecules Conjugated by Click Chemistry." Polymers 14, no. 8 (April 8, 2022): 1516. http://dx.doi.org/10.3390/polym14081516.

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The molecular structure, luminescence behavior, and electronic energy level of an organic optoelectronic materials are important parameters for its synthesis. The electro-optical properties can be changed by modifying the structure of the molecule to make the electronic energy level adjustable. In this article, a series of organic conjugated micro-molecules are successfully synthesized by linking small compound units. This metal-free [2 + 2] click chemistry process generates donor–acceptor chromophore substances with high yield, high solubility, and adjustable energy levels, which can be widely used for sensors and nonlinear optics in different fields. A-TCNE, A-TCNQ, and A-F4-TCNQ molecules are characterized comprehensively via UV-Vis-NIR spectra, 1H NMR spectra, infrared spectroscopy, and mass spectrometry. The unique nonlinear optical phenomena and powerful intra-molecular charge–transfer interactions of these new materials give them fascinating potential for application as optoelectronic materials.

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Tanaka, Koichi, Naoki Daikawa, and Shigeru Ohba. "Novel Bisurea Host Compounds." Journal of Chemical Research 2002, no. 11 (November 2002): 579–81. http://dx.doi.org/10.3184/030823402103170853.

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New host molecules, 4,4′-bis(dimethylamino-urea)diphenylmethane (1) and its derivatives (2 and 3), are reported. These hosts are shown to give inclusion complex crystals with a wide variety of organic guest molecules with high selectivity. The crystal structure of 1:2 inclusion complex of 1 with THF has been determined from X-ray crystal structure analysis. The cyclic N–H...O intermolecular hydrogen bonds between host molecules were found to form columns for accommodation of the guest molecules.

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Li, Minghao, and Yu Li. "A Vector Normalized Method-Assisted 3D-QSA2R Model and Its Application in the Molecular Modification of PCBs with Higher Flame Retardancy and Lower Toxicity." Science of Advanced Materials 13, no. 1 (January 1, 2021): 80–87. http://dx.doi.org/10.1166/sam.2021.3836.

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Flame retardants are widely used in many materials and products, and there is a pressing need to enhance the performance of flame retardants while lowering their toxicity. In this paper, using polychlorinated biphenyl flame retardants as an example, a three-dimensional quantitative structure-double-activity relationship (3D-QSA2R) model, with the double activities of flame retardancy and toxicity, was constructed by introducing a vector normalized method to achieve the goal of environmental risk management and control the sources of chemicals. The results showed that the 3D-QSA2R model has good robustness and strong predictive ability. PCB-209 was used as a target molecule for the contour map analysis and molecular modification. The comprehensive values (C) of six novel PCB-209 molecules were increased by up to 53.61%. The physical and chemical parameters (frequency and Gibbs free energy), functional properties (stability and insulation) and the other three POP properties of the novel PCB-209 molecules showed that the Cl atom substitution reaction of PCB209 molecules could occur and exist stably in the environment. With improvement in stability, the insulation of six novel PCB-209 molecules was not influenced after modification, and the environmental persistence, bioconcentration and long-distance migration of six novel PCB-209 molecules were increased up to 99.47%, 15.29% and 100.9%, respectively. The flame retardancy and toxicity of the new molecules were verified by Gaussian software and the EPI database, respectively. The single activity verification values of flame retardancy and toxicity followed the trend of C values predicted by the double-activity 3D-QSA2R model established in this paper. The ratio between the two single activities of the new PCB-209 molecule generally conformed to the weight setting, which satisfies the purpose of setting the weight as the main way to improve the efficacy of flame retardants.

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Ostrov, David A., José A. Hernández Prada, Patrick E. Corsino, Kathryn A. Finton, Nhan Le, and Thomas C. Rowe. "Discovery of Novel DNA Gyrase Inhibitors by High-Throughput Virtual Screening." Antimicrobial Agents and Chemotherapy 51, no. 10 (August 6, 2007): 3688–98. http://dx.doi.org/10.1128/aac.00392-07.

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ABSTRACT The bacterial type II topoisomerases DNA gyrase and topoisomerase IV are validated targets for clinically useful quinolone antimicrobial drugs. A significant limitation to widely utilized quinolone inhibitors is the emergence of drug-resistant bacteria due to an altered DNA gyrase. To address this problem, we have used structure-based molecular docking to identify novel drug-like small molecules that target sites distinct from those targeted by quinolone inhibitors. A chemical ligand database containing approximately 140,000 small molecules (molecular weight, <500) was molecularly docked onto two sites of Escherichia coli DNA gyrase targeting (i) a previously unexplored structural pocket formed at the dimer interface of subunit A and (ii) a small region of the ATP binding pocket on subunit B overlapping the site targeted by coumarin and cyclothialidine drugs. This approach identified several small-molecule compounds that inhibited the DNA supercoiling activity of purified E. coli DNA gyrase. These compounds are structurally unrelated to previously identified gyrase inhibitors and represent potential scaffolds for the optimization of novel antibacterial agents that act on fluoroquinolone-resistant strains.

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Zhu, Hao, and Qiliang Li. "Novel Molecular Non-Volatile Memory: Application of Redox-Active Molecules." Applied Sciences 6, no. 1 (December 26, 2015): 7. http://dx.doi.org/10.3390/app6010007.

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Jian, WANG, ZHANG Qing-Hua, LIU Li, and CHEN Shu-Hua. "Recognition of Neutral Molecules by Novel Schiff Base Molecular Tweezers." Acta Physico-Chimica Sinica 21, no. 01 (2005): 22–27. http://dx.doi.org/10.3866/pku.whxb20050105.

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Tzarum, Netanel, Yael Eisenberg-Domovich, Joell J. Gills, Phillip A. Dennis, and Oded Livnah. "Lipid Molecules Induce p38α Activation via a Novel Molecular Switch." Journal of Molecular Biology 424, no. 5 (December 2012): 339–53. http://dx.doi.org/10.1016/j.jmb.2012.10.007.

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Liu, Yu-Li, Hsiang-Wei Kuo, Chiu-Ping Fang, Jieh-Hen Tsung, and Andrew C. H. Chen. "Adhesion Molecules as Potential Novel Biomarkers for Opioid Dependence." Current Pharmaceutical Design 26, no. 2 (March 4, 2020): 253–59. http://dx.doi.org/10.2174/1381612826666200116144147.

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Background: Cell-cell adhesion is essential in maintaining the structure and function of an organ. Several adhesion molecules have recently been identified as associated with heroin dependence in both genetic and peripheral plasma studies. Methods and Results: We reviewed literature concerning studies on adhesion molecules in opioid addictions in rodents and human, including human genetic associations in different ethnic groups, and treatment responses to methadone maintenance treatment in heroin-dependent patients. Conclusion: Some important and novel findings were summarized and discussed. Adhesion molecules in the peripheral plasma, e.g., cadherin-2 (CDH2), may be biomarkers for both methadone treatment outcome and nectin 4 may be an indicator for continued opioid use. Neural cell adhesion molecule (NCAM) in the central nervous system may regulate opioid withdrawal and analgesic responses. Future studies to uncover the mechanisms underlying the involvement of adhesion molecules in the pathological process of addictions will be an important research direction in the field.

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Krishnan, Keerthi, Ryan Kassab, Steve Agajanian, and Gennady Verkhivker. "Interpretable Machine Learning Models for Molecular Design of Tyrosine Kinase Inhibitors Using Variational Autoencoders and Perturbation-Based Approach of Chemical Space Exploration." International Journal of Molecular Sciences 23, no. 19 (September 24, 2022): 11262. http://dx.doi.org/10.3390/ijms231911262.

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In the current study, we introduce an integrative machine learning strategy for the autonomous molecular design of protein kinase inhibitors using variational autoencoders and a novel cluster-based perturbation approach for exploration of the chemical latent space. The proposed strategy combines autoencoder-based embedding of small molecules with a cluster-based perturbation approach for efficient navigation of the latent space and a feature-based kinase inhibition likelihood classifier that guides optimization of the molecular properties and targeted molecular design. In the proposed generative approach, molecules sharing similar structures tend to cluster in the latent space, and interpolating between two molecules in the latent space enables smooth changes in the molecular structures and properties. The results demonstrated that the proposed strategy can efficiently explore the latent space of small molecules and kinase inhibitors along interpretable directions to guide the generation of novel family-specific kinase molecules that display a significant scaffold diversity and optimal biochemical properties. Through assessment of the latent-based and chemical feature-based binary and multiclass classifiers, we developed a robust probabilistic evaluator of kinase inhibition likelihood that is specifically tailored to guide the molecular design of novel SRC kinase molecules. The generated molecules originating from LCK and ABL1 kinase inhibitors yielded ~40% of novel and valid SRC kinase compounds with high kinase inhibition likelihood probability values (p > 0.75) and high similarity (Tanimoto coefficient > 0.6) to the known SRC inhibitors. By combining the molecular perturbation design with the kinase inhibition likelihood analysis and similarity assessments, we showed that the proposed molecular design strategy can produce novel valid molecules and transform known inhibitors of different kinase families into potential chemical probes of the SRC kinase with excellent physicochemical profiles and high similarity to the known SRC kinase drugs. The results of our study suggest that task-specific manipulation of a biased latent space may be an important direction for more effective task-oriented and target-specific autonomous chemical design models.

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