Relevant bibliographies by topics / Protein-small molecule interactions

Academic literature on the topic 'Protein-small molecule interactions'

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Published: 6 September 2023

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Journal articles on the topic "Protein-small molecule interactions"

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Kuusk, Ave, Helen Boyd, Hongming Chen, and Christian Ottmann. "Small-molecule modulation of p53 protein-protein interactions." Biological Chemistry 401, no. 8 (July 28, 2020): 921–31. http://dx.doi.org/10.1515/hsz-2019-0405.

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AbstractSmall-molecule modulation of protein-protein interactions (PPIs) is a very promising but also challenging area in drug discovery. The tumor suppressor protein p53 is one of the most frequently altered proteins in human cancers, making it an attractive target in oncology. 14-3-3 proteins have been shown to bind to and positively regulate p53 activity by protecting it from MDM2-dependent degradation or activating its DNA binding affinity. PPIs can be modulated by inhibiting or stabilizing specific interactions by small molecules. Whereas inhibition has been widely explored by the pharmaceutical industry and academia, the opposite strategy of stabilizing PPIs still remains relatively underexploited. This is rather interesting considering the number of natural compounds like rapamycin, forskolin and fusicoccin that exert their activity by stabilizing specific PPIs. In this review, we give an overview of 14-3-3 interactions with p53, explain isoform specific stabilization of the tumor suppressor protein, explore the approach of stabilizing the 14-3-3σ-p53 complex and summarize some promising small molecules inhibiting the p53-MDM2 protein-protein interaction.
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Ottmann, Christian. "Small-molecule modulation of protein–protein interactions." Drug Discovery Today: Technologies 10, no. 4 (December 2013): e499-e500. http://dx.doi.org/10.1016/j.ddtec.2013.08.001.

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Pollock, Julie A., Courtney L. Labrecque, Cassidy N. Hilton, Justin Airas, Alexis Blake, Kristen J. Rubenstein, and Carol A. Parish. "Small Molecule Modulation of MEMO1 Protein-Protein Interactions." Journal of the Endocrine Society 5, Supplement_1 (May 1, 2021): A1031. http://dx.doi.org/10.1210/jendso/bvab048.2110.

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Abstract MEMO1 (mediator of ErbB2-driven cell motility) is upregulated in breast tumors and has been correlated with poor prognosis in patients. As a scaffolding protein that binds to phosphorylated-tyrosine residues on receptors such as estrogen receptor and ErbB2, MEMO1 levels can influence phosphorylation cascades. Using our previously developed fluorescence polarization assay, we have identified small molecules with the ability to disrupt the interactions of MEMO1. We have performed limited structure-activity-relationship studies and computational analyses to investigate the molecular requirements for MEMO1 inhibition. The most promising compounds exhibit slowed migration of breast cancer cell lines (T47D and SKBR3) in a wound-healing assay emulating results obtained from the knockdown of MEMO1 protein. To our knowledge, these are the first small molecules targeting the MEMO1 protein-protein interface and therefore, will be invaluable tools for the investigation of the role of the MEMO1 in breast cancer and other biological contexts.
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Linhares, Brian M., Jolanta Grembecka, and Tomasz Cierpicki. "Targeting epigenetic protein–protein interactions with small-molecule inhibitors." Future Medicinal Chemistry 12, no. 14 (July 2020): 1305–26. http://dx.doi.org/10.4155/fmc-2020-0082.

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Epigenetic protein–protein interactions (PPIs) play essential roles in regulating gene expression, and their dysregulations have been implicated in many diseases. These PPIs are comprised of reader domains recognizing post-translational modifications on histone proteins, and of scaffolding proteins that maintain integrities of epigenetic complexes. Targeting PPIs have become focuses for development of small-molecule inhibitors and anticancer therapeutics. Here we summarize efforts to develop small-molecule inhibitors targeting common epigenetic PPI domains. Potent small molecules have been reported for many domains, yet small domains that recognize methylated lysine side chains on histones are challenging in inhibitor development. We posit that the development of potent inhibitors for difficult-to-prosecute epigenetic PPIs may be achieved by interdisciplinary approaches and extensive explorations of chemical space.
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Guo, Z. "Designing Small-Molecule Switches for Protein-Protein Interactions." Science 288, no. 5473 (June 16, 2000): 2042–45. http://dx.doi.org/10.1126/science.288.5473.2042.

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Li, Xiyan, Xin Wang, and Michael Snyder. "Systematic investigation of protein-small molecule interactions." IUBMB Life 65, no. 1 (December 7, 2012): 2–8. http://dx.doi.org/10.1002/iub.1111.

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D’Abramo, C. M. "Small Molecule Inhibitors of Human Papillomavirus Protein - Protein Interactions." Open Virology Journal 5, no. 1 (July 4, 2011): 80–95. http://dx.doi.org/10.2174/1874357901105010080.

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Song, Yun, and Peter Buchwald. "TNF Superfamily Protein-Protein Interactions: Feasibility of Small- Molecule Modulation." Current Drug Targets 16, no. 4 (April 6, 2015): 393–408. http://dx.doi.org/10.2174/1389450116666150223115628.

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de Vink, Pim J., Sebastian A. Andrei, Yusuke Higuchi, Christian Ottmann, Lech-Gustav Milroy, and Luc Brunsveld. "Cooperativity basis for small-molecule stabilization of protein–protein interactions." Chemical Science 10, no. 10 (2019): 2869–74. http://dx.doi.org/10.1039/c8sc05242e.

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A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented, which allows elucidating structure–activity relationships regarding cooperativity and intrinsic affinity.
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Aeluri, Madhu, Srinivas Chamakuri, Bhanudas Dasari, Shiva Krishna Reddy Guduru, Ravikumar Jimmidi, Srinivas Jogula, and Prabhat Arya. "Small Molecule Modulators of Protein–Protein Interactions: Selected Case Studies." Chemical Reviews 114, no. 9 (March 27, 2014): 4640–94. http://dx.doi.org/10.1021/cr4004049.

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Dissertations / Theses on the topic "Protein-small molecule interactions"

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Napoleon, Raeanne L. "Understanding small molecule-protein interactions." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31592.

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Thesis (Ph.D.)--Boston University
PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
The binding of small molecules to a protein is among the most important phenomena in the chemistry of life; the activity and functionality of many proteins depend critically on binding small molecules. A deep understanding of protein-small molecule interactions and the interplay between ligation and function can give valuable insight into key systems of interest. The complete characterization of any small molecule-protein interaction requires quantification of many interactions and the pursuit of such information is the purpose of this body of work. The discovery of binding regions on proteins, or "hot spots," is an important step in drug development. To this end, a highly regarded and robust fragment-based protocol has been developed for the detection of hot spots. Firstly, we use this protocol in conjunction with other computation techniques, such as homology modeling, to locate the allosteric binding site of £-phenylalanine in Phenylalanine Hydroxylase. Secondly, computational fragment mapping was employed to locate the site of allostery for Ras, an important signaling protein. Lastly, the identification of hot spots for many unligated protein targets is presented highlighting the importance of a reliable way to predict druggability computationally. The second part of this dissertation shifts focus to the development of electrostatic models of small molecules. It is widely believed that classical potentials can describe neither vibrational frequency shifts in condensed phases nor the response of vibrational frequencies to an applied electric field, the vibrational Stark effect. In this work, an improved classical molecular electrostatic model for the CO ligand was developed to faithfully model these phenomena. This model is found to predict the vibrational Stark effect and Fe-CO binding energy with unprecedented accuracy for such a classical model. As an extension of this work, a geometrically dependent water potential was developed. This work has shown that comparison of results obtained from current water models against experimentally determined proton momentum distributions is an invaluable benchmark
2031-01-01
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Albertoni, Barbara [Verfasser]. "Biophysical analysis of protein-protein and protein-small molecule interactions / Barbara Albertoni." Bonn : Universitäts- und Landesbibliothek Bonn, 2011. http://d-nb.info/1044846909/34.

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Park, Chihyo. "Combinatorial design and synthesis of peptidomimics and small molecules for protein-protein interactions." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4692.

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The solid phase combinatorial method is an excellent tool for the modulation of protein-protein interactions through focused library generations. Nucleophilic aromatic substitution reactions with an iodinated template on solid phase has opened a door for easy and pure libraries of 13-22 membered medium and macrocyclic peptidomimetics. These peptide mimics showed promising activities for tyrosine kinase receptors. Iodine functionality can then be used to modify the products, on the resin, via Sonogashira and Suzuki couplings and presumably through other organometallic catalysis. The coupled products can have conformational biases that differ from the iodinated macrocycles. These coupling reactions also provide a means to introduce additional pharmacophores and to adjust the solubilities of the products. The fluorinated template also gave libraries of cyclic peptidomimetics on solid phase in good yields and purities. These libraries have improved water solubility over the iodinated libraries. The 3-fluorinated template yielded better results than the 5- fluorinated template. Some compounds showed biological activities in cell survival assays providing strong support of our approach to mimic external β-turn sequences in target proteins. Intrasite dimerization with 1,5-hexadiyne gave a homodimer as a byproduct. Solidphase synthesis of bivalent turn mimics with fluorescent tags has been demonstrated. The key feature of this synthetic route is that homo- and hetero-dimers can be formed chemoselectively from unprotected monomeric precursors. The dimerization reaction is very mild and versatile, as only potassium carbonate is required to affect the coupling. Solution phase library synthesis of small molecule mimics is presented. Some monomers of full sequence mimics have been prepared to afford dimer generations. Theses monomers were combined with linker handles to afford diverse length of dimers. Final combination of monomers to make bivalent compounds is in progress.
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Jackson, Matthew. "Assay development and investigation of small molecule and amyloid protein interactions." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6549/.

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Mittal, Sumit [Verfasser], Elsa [Gutachter] Sanchez-Garcia, and Simon [Gutachter] Ebbinghaus. "Small molecule modulation of protein-protein interactions / Sumit Mittal ; Gutachter: Elsa Sanchez-Garcia, Simon Ebbinghaus." Bochum : Ruhr-Universität Bochum, 2017. http://d-nb.info/1133361854/34.

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Nilsson, Jonas. "Design, Synthesis and Characterization of Small Molecule Inhibitors and Small Molecule : Peptide Conjugates as Protein Actors." Doctoral thesis, Linköpings universitet, Organisk Kemi, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-3943.

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This thesis describes different aspects of protein interactions. Initially the function of peptides and their conjugates with small molecule inhibitors on the surface of Human Carbonic Anhydrase isoenzyme II (HCAII) is evaluated. The affinities for HCAII of the flexible, synthetic helix-loop-helix motif conjugated with a series of spacered inhibitors were measured by fluorescence spectroscopy and found in the best cases to be in the low nM range. Dissociation constants show considerable dependence on linker length and vary from 3000 nM for the shortest spacer to 40 nM for the longest with a minimum of 5 nM for a spacer with an intermediate length. A rationale for binding differences based on cooperativity is presented and supported by affinities as determined by fluorescence spectroscopy. Heteronuclear Single Quantum Correlation Nuclear Magnetic Resonance (HSQC) spectroscopic experiments with 15N-labeled HCAII were used for the determination of the site of interaction. The influence of peptide charge and hydrophobicity was evaluated by surface plasmon resonance experiments. Hydrophobic sidechain branching and, more pronounced, peptide charge was demonstrated to modulate peptide – HCAII binding interactions in a cooperative manner, with affinities spanning almost two orders of magnitude. Detailed synthesis of small molecule inhibitors in a general lead discovery library as well as a targeted library for inhibition of α-thrombin is described. For the lead discovery library 160 members emanate from two N4-aryl-piperazine-2-carboxylic acid scaffolds derivatized in two dimensions employing a combinatorial approach on solid support. The targeted library was based on peptidomimetics of the D-Phe-Pro-Arg showing the scaffolds cyclopropane-1R,2R-dicarboxylic acid and (4-amino-3-oxo-morpholin-2-yl)- acetic acid as proline isosters. Employing 4-aminomethyl-benzamidine as arginine mimic and different hydrophobic amines and electrophiles as D-phenylalanine mimics resulted in 34 compounds showing IC50 values for α-thrombin ranging more than three orders of magnitude with the best inhibitor showing an IC50 of 130 nM. Interestingly, the best inhibitors showed reversed stereochemistry in comparison with a previously reported series employing a 3-oxo-morpholin-2-yl-acetic acid scaffold.
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Fagiewicz, Robert Mateusz. "Structural analysis of protein-small molecule interactions by a crystallographic and spectroscopic approach." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13892/.

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Modern spectroscopic techniques grant various methods for a protein structure determination among with a ligand interaction. This work aims at probing the structural insights of a protein-small molecule interaction with biocrystallography and optical spectroscopies. Two independent systems were investigated in the frame of this thesis. The first one involves flavoenzyme interaction with a natural nucleotide as a cofactor required for its catalytic activity and work was purely based on macromolecular crystallography. The second concerns incorporation of a synthetic fluorescent ligand into a model protein as a solution for hydrophobicity of the probe. Due to the nature of the probe optical spectroscopies (such as absorption, fluorescence lifetime, circular dichroism) were effectively employed together with the crystallographic methodology.
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Kung, Wei-Wei. "Protein-protein interactions and small molecule targeting of the multisubunit SOCS2-EloBC-Cul5-Rbx2 E3 ubiquitin ligase." Thesis, University of Dundee, 2018. https://discovery.dundee.ac.uk/en/studentTheses/b2dd4bc4-9a13-428b-a45a-bc46b1d9c116.

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The Cullin-RING E3 ligases (CRLs) are the largest subfamily of E3 ligases that participate in many biological processes determining the fate of proteins by catalysing ubiquitin transfer to specific substrates for proteasomal degradation. SOCS2 is a component of the multisubunit CRL E3 complex (CRL5SOCS2). SOCS2 plays important roles in several cancers and is involved in diabetes and inflammatory diseases. This work aims to understand the substrate recognition mechanism of SOCS2 at an atomic level and provides structural insights to guide the development of small-molecule tools and potential drug leads. Current structural information on SOCS2 is limited to apo form (no ligand bound). In the first part of the work, two novel SOCS2-ElonginB-ElonginC (SBC) structures in complex with substrate peptides of growth hormone receptor (GHR) and erythropoietin receptor (EpoR) were solved by X-ray crystallography with a goal to elucidate the SOCS2 recognition mechanism. Different interactions of the peptides were observed in the structures as a consequence of divergences in the peptide sequences, revealing residues required to catch specific interactions and a protein loop rearrangement as a result of the binding event. An alanine scanning of substrate peptides allowed cross-validation of the structures and identified critical interactions. Based on the crystal structure, five residues that interact with GHR were selected for which single-nucleotide polymorphisms (SNPs) are known in cancer. The results show that the SNPs mutants of SOCS2 located at the phosphotyrosine (pY) pocket are highly disruptive and abolish substrate recognition, suggesting a significant impact to SOCS2 mediated interactions. The second and third part of the work focused on the ligand development at the pY pocket of SOCS2 SH2 domain using a combination of X-ray crystallography and biophysical techniques. Novel crystal structures of SBC in complex with pY and pY analogues were obtained, providing a starting point for compound design. A screening cascade consisting of nuclear magnetic resonance (NMR), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) was established and validated by an in-house small library of pY analogues. This workflow will facilitate the process of ligand characterisation and design towards a potent binder. The findings of this work unravel interactions of SOCS2 with its substrates in mechanistic detail. Together with the small molecule bound structures and biophysical screening assays, this work provides insights and tools to assist future ligand discovery for CRL5SOCS2.
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Wang, Lin. "DEVELOPMENT OF A NEW SCREENING AND DETECTION METHOD FOR IDENTIFYING PROTEIN-SMALL MOLECULE INTERACTIONS." OpenSIUC, 2014. https://opensiuc.lib.siu.edu/dissertations/861.

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Small molecules are known to play critical role in understanding most biological mechanisms of cells and organisms. Some examples, such as RNAs, peptides and drug molecules, etc., work by modulating cellular function, but with unknown modes. In most cases, these actions involve the small molecule interacting with proteins serving various functions. In recent years, much effort has been made in the investigation of interactions between small molecules (ligands) and target proteins. In our laboratory, a new technique termed Dynamic Isoelectric focusing Anisotropy Binding Ligand Assay (DIABLA) is being in collaboration with the Tolley Laboratory (SIU) developed to fulfill this task. In this technique, a protein mixture is separated within the capillary using dynamic isoelectric focusing, while a specific small molecule is evenly distributed throughout the capillary. Fluorescence anisotropy is then used to identify target proteins that bind with the ligand. In our research, emphasis has been put on evaluating optimum detection conditions for the fluorescence anisotropy aspects of the measurement. Fluorescence anisotropy has been proven to be an effective and powerful tool in evaluating ligand-protein interactions. In our studies, various protein-ligand systems are investigated, especially inhibitor-cyclooxygenase (COX) systems which include naproxen-COX system, ibuprofen-COX system, resveratrol-COX system and COX inhibitor II-COX system. Other systems include biotin-streptavidin system and progesterone-progesterone receptor system. Several fundamental parameters (concentration, pH, etc.) that affect the detection of fluorescence anisotropy measurement are evaluated. In addition, non-specific binding of the ligands with BSA was also tested as a comparison to specific binding of ligand-COX. By optimizing the binding conditions, the detection limit of using fluorescence anisotropy technique was found to be as low as nanomolar concentrations, which is much improved compared to the current literature reported micromolar regime. A binding curve representing the anisotropy's value as a function of protein concentration was constructed experimentally for each study system. On another study, mathematical calculation of the binding curve was also carried out by Wolfram Mathematica for prediction of the binding curve as well as estimation of the dissociation constant (Kd). By simply curve fitting experimental data to our simulated binding curve, with known ligand concentration, the dissociation constant (Kd) can be obtained with very high accuracy relative to current reported value. Isoelectric focusing coupled fluorescence anisotropy was also performed on the laboratory built system to test the validation of DIABLA. Three standard dyes, rose bengal, erythrosin B and Ru(bpy)3 were used for calibration of the in-laboratory built instrument. Fluorescence measurements were performed in both Horiba Jobin Yvon fluorimeter and our in-laboratory built DIABLA equipment by Cecil Bailey. Good correspondence of data acquired by DIABLA equipment and Horiba fluoremeter was successfully obtained, which proves the validation of DIABLA. Ongoing research is focusing on investigation of the standard dyes as well as some protein mixtures in capillary using DIABLA equipment. In another study, in investigation of inhibitor-COX system, fluorescence properties of most inhibitors were tested for further applications. Fluorescence excitation and emission spectra, fluorescence quantum yield, as well as fluorescence lifetimes were tested with the inhibitors dissolved in both ethanol and water. The difference of fluorescence properties observed in different solvents revealed the solvent effects as well as some possible intramolecular transitions or intermolecular interactions, such as internal charge transfer (ICT) and molecule aggregations.
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Krumm, Stefanie A. [Verfasser], and Dieter [Akademischer Betreuer] Wolf. "Protein-protein and protein-small-molecule inhibitor interactions in the measles virus replication complex / Stefanie A. Krumm. Betreuer: Dieter Wolf." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1069815470/34.

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Books on the topic "Protein-small molecule interactions"

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Waldmann, H., and M. Koppitz, eds. Small Molecule — Protein Interactions. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0.

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name, No. Small molecule-protein interactions. Berlin: Springer, 2003.

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H, Waldmann, and Koppitz M. 1965-, eds. Small molecule--protein interactions. Berlin: Springer, 2003.

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Vassilev, Lyubomir, and David Fry, eds. Small-Molecule Inhibitors of Protein-Protein Interactions. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-17083-6.

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Byun, Wan Gi. Discovery of Small-Molecule Modulators of Protein–RNA Interactions for Treating Cancer and COVID-19. Singapore: Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-7814-2.

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Sheng, Chunquan, and Gunda I. Georg, eds. Targeting Protein-Protein Interactions by Small Molecules. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-0773-7.

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Waldmann, Herbert, and Marcus Koppitz. Small Molecule -- Protein Interactions. Springer London, Limited, 2013.

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Waldmann, Herbert. Small Molecule - Protein Interactions. Springer, 2012.

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Waldmann, Herbert, and Marcus Koppitz. Small Molecule - Protein Interactions. Springer, 2014.

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Fry, David, and Lyubomir Vassilev. Small-Molecule Inhibitors of Protein-Protein Interactions. Springer, 2011.

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Book chapters on the topic "Protein-small molecule interactions"

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Reinhard-Rupp, J., and G. Wess. "Drug Discovery Opportunities." In Small Molecule — Protein Interactions, 1–10. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_1.

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Briem, H. "De Novo Design Methods." In Small Molecule — Protein Interactions, 153–66. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_10.

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Breinbauer, R., I. R. Vetter, and H. Waldmann. "From Protein Domains to Drug Candidates — Natural Products as Guiding Principles in Compound Library Design and Synthesis." In Small Molecule — Protein Interactions, 167–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_11.

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Weber, L. "Discovery of New MCRs, Chemical Evolution and Lead Optimization." In Small Molecule — Protein Interactions, 189–99. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_12.

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Hermkens, P. H. H., and G. Müller. "The Impact of Combinatorial Chemistry on Drug Discovery." In Small Molecule — Protein Interactions, 201–20. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_13.

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Hopkins, A. L., and C. R. Groom. "Target Analysis: A Priori Assessment of Druggability." In Small Molecule — Protein Interactions, 11–17. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_2.

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Wells, J., M. Arkin, A. Braisted, W. DeLano, B. McDowell, J. Oslob, B. Raimundo, and M. Randal. "Drug Discovery at Signaling Interfaces." In Small Molecule — Protein Interactions, 19–27. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_3.

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Willson, T. "Chemical Genomics of Orphan Nuclear Receptors." In Small Molecule — Protein Interactions, 29–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_4.

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Jhoti, H. "High-Throughput X-Ray Techniques and Drug Discovery." In Small Molecule — Protein Interactions, 43–58. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_5.

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Kessler, H., M. Heller, G. Gemmecker, T. Diercks, E. Planker, and M. Coles. "NMR in Medicinal Chemistry." In Small Molecule — Protein Interactions, 59–85. Berlin, Heidelberg: Springer Berlin Heidelberg, 2003. http://dx.doi.org/10.1007/978-3-662-05314-0_6.

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Conference papers on the topic "Protein-small molecule interactions"

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Jongwan, Kim, Hocheol Lim, and K. T. No. "Abstract A45: In silico drug discovery targeting Hippo pathway and YAP-TEAD protein-protein interactions for small-molecule anticancer agent." In Abstracts: AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; May 8-11, 2019; San Diego, CA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1557-3125.hippo19-a45.

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Kabir, Abbas, and Aaron Muth. "Abstract 1311: Inhibition of gankyrin-tumor suppressor protein interactions due to small molecule induced conformational change." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1311.

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Kabir, Abbas, and Aaron Muth. "Abstract 1311: Inhibition of gankyrin-tumor suppressor protein interactions due to small molecule induced conformational change." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1311.

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Tseng, Fan-Gang. "From High Performance Protein Micro Chip Toward Ultra High Sensitive Single Molecule Nano Array." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82291.

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Protein microarrays have been employed to screen tens to thousands of proteins simultaneously for the observation of the biochemical activities in the protein-protein, protein-nucleic acid and small molecule interactions. This technology allows high throughput analysis and holds great potential for basic molecular biology research, disease marker identification, toxicological response profiling and pharmaceutical target screening. However, proteins easily malfunction in harsh environments so that they are hardly preserved before the application because of their complex and fragile structures. On the other hand, identify scarce amount of proteins less than fM range is very important and challenge for disease diagnosis at very early stage. As a result, the procedures for protein micro array formation are very important for preserving protein functionality to ensure useful protein assays, as well as the improvement of the detection sensitivity up to single molecule event but with high dynamic range for disease early detection. Therefore, this paper provides a novel view from the preparation of high efficient protein micro chip toward ultra high sensitive single protein nano array through the technology integration of BioMEMS and Bio-Nanotechnology.
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Toretsky, Jeffrey A., Hayriye V. Erkizan, Yali Kong, Melinda Merchant, Julie S. Barber-Rotenberg, Milton L. Brown, and Aykut Üren. "Abstract 3411: Targeting of EWS-FLI1 with small molecule YK-4-279 reduces xenograft growth by disruption of disordered protein-protein interactions." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-3411.

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Al Balushi, Ahmed A., and Reuven Gordon. "Real-Time Dynamics of Single Protein-Small Molecule Interactions with Label-Free, Free-Solution Double-Nanohole Optical Trapping." In Frontiers in Optics. Washington, D.C.: OSA, 2014. http://dx.doi.org/10.1364/fio.2014.fth1e.7.

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Huang, Cindy, Vivian Zhang, Ning Deng, Irene Yuan, Linda Pullan, C. Glenn Begley, and Ping Cao. "Abstract P098: A chemoproteomic platform for identifying small-molecule modulators of protein-protein interactions, discovering new cancer targets, and revealing previously unknown targets for well-known drugs." In Abstracts: AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; October 7-10, 2021. American Association for Cancer Research, 2021. http://dx.doi.org/10.1158/1535-7163.targ-21-p098.

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Tavousi, Pouya, Morad Behandish, Kazem Kazerounian, and Horea T. Ilieş. "An Improved Free Energy Formulation and Implementation for Kinetostatic Protein Folding Simulation." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-12671.

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Protein structure prediction remains one of the significant challenges in computational biology. We have previously shown that our kinetostatic compliance method can overcome some of the key difficulties faced by other de novo structural prediction methods, such as the very small time steps required by the molecular dynamics approaches, or the very large number of samples required by the sampling based techniques. In this paper we extend the previous free energy formulation by adding the solvent effects, which contribute predominantly to the folding phenomena. We show that the addition of the solvation effects, which complement the existing Coulombic and van der Waals interactions, lead to a physically effective energy function. Furthermore, we achieve significant computational speed-up by employing efficient algorithms and data structures that effectively reduce the time complexity from O(n2) to O(n), n being the number of atoms. Our simulations are consistent with the general behavior observed in protein folding, and show that the hydrophobic atoms tend to pack inside the core of the molecule in an aqueous solvent, while a vacuum environment produces no such effect.
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Liu, Yuanjie, Jeremy W. Prokop, Hongzhuang Peng, and Frank J. Rauscher. "Abstract 1061: High resolution DNA recognition by the Snail zinc finger protein: Testing of a molecular dynamics based model defines the atomic level interactions required for high affinity binding, E-box specificity and reveals potential strategies for small molecule control of EMT transcriptional programs." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-1061.

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Jewel, Yead, Prashanta Dutta, and Jin Liu. "Coarse-Grained Molecular Dynamics Simulations of Sugar Transport Across Lactose Permease." In ASME 2015 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/imece2015-52337.

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Sugar (one of the critical nutrition elements for all life forms) transport across the cell membranes play essential roles in a wide range of living organism. One of the most important active transport (against the sugar concentration) mechanisms is facilitated by the transmembrane transporter proteins, such as the Escherichia coli lactose permease (LacY) proteins. Active transport of sugar molecules with LacY proteins requires a proton gradient and a sequence of complicated protein conformational changes. However, the exact molecular mechanisms and the protein structural information involved in the transport process are largely unknown. All atom atomistic simulations are able to provide full details but are limited to relative small length and time scales due to the computational cost. The protein conformational changes during sugar transport across LacY are large scale structural reorganization and inaccessible to all atom simulations. In this work, we investigate the molecular mechanisms and conformational changes during sugar transport using coarse-grained molecular dynamics (CGMD) simulations. In our coarse-grained force field, we follow the procedures developed by Han et al. [1, 2], in which the protein model is united-atom based and each heavy atom together with the attached hydrogen atoms is represented by one site, then the protein force filed is coupled with the MARTINI [3] water and lipid force fields. This hybrid force field takes the advantage of the efficiency of MARTINI force field for the environment (water and lipid), while retaining the detailed conformational information for the proteins. Specifically, we develop the new force fields for interactions between sugar molecules and protein by matching the potential of mean force between all-atom and coarse-grained models. Then we validate our force field by comparing the potential of mean force for a glucose interaction with a carbohydrate binding protein from our new force field, with the results from all atom simulations. After validation, we implement the force field for sugar transport across LacY proteins. Through our simulations we are able to capture the formation/breakage of the important hydrogen bonds and salt bridges, which are crucial to the overall conformational changes of LacY.
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Reports on the topic "Protein-small molecule interactions"

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Chamovitz, Daniel A., and Zhenbiao Yang. Chemical Genetics of the COP9 Signalosome: Identification of Novel Regulators of Plant Development. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7699844.bard.

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This was an exploratory one-year study to identify chemical regulators of the COP9 signalosome. Chemical Genetics uses small molecules to modify or disrupt the function of specific genes/proteins. This is in contrast to classical genetics, in which mutations disrupt the function of genes. The underlying concept is that the functions of most proteins can be altered by the binding of a chemical, which can be found by screening large libraries for compounds that specifically affect a biological, molecular or biochemical process. In addition to screens for chemicals which inhibit specific biological processes, chemical genetics can also be employed to find inhibitors of specific protein-protein interactions. Small molecules altering protein-protein interactions are valuable tools in probing protein-protein interactions. In this project, we aimed to identify chemicals that disrupt the COP9 signalosome. The CSN is an evolutionarily conserved eight-subunit protein complex whose most studied role is regulation of E3 ubiquitinligase activity. Mutants in subunits of the CSN undergo photomorphogenesis in darkness and accumulate high levels of pigments in both dark- and light-grown seedlings, and are defective in a wide range of important developmental and environmental-response pathways. Our working hypothesis was that specific molecules will interact with the CSN7 protein such that binding to its various interacting proteins will be inhibited. Such a molecule would inhibit either CSN assembly, or binding of CSN-interacting proteins, and thus specifically inhibit CSN function. We used an advanced chemical genetic screen for small-molecule-inhibitors of CSN7 protein-protein interactions. In our pilot study, following the screening of ~1200 unique compounds, we isolated four chemicals which reproducibly interfere with CSN7 binding to either CSN8 or CSN6.
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McClure, Michael A., Yitzhak Spiegel, David M. Bird, R. Salomon, and R. H. C. Curtis. Functional Analysis of Root-Knot Nematode Surface Coat Proteins to Develop Rational Targets for Plantibodies. United States Department of Agriculture, October 2001. http://dx.doi.org/10.32747/2001.7575284.bard.

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The goal of this research was to provide a better understanding of the interface between root-knot nematodes, Meloidogyne spp., and their host in order to develop rational targets for plantibodies and other novel methods of nematode control directed against the nematode surface coat (SC). Specific objectives were: 1. To produce additional monoclonal SC antibodies for use in Objectives 2, 3, and 4 and as candidates for development of plantibodies. 2. To determine the production and distribution of SC proteins during the infection process. 3. To use biochemical and immunological methods to perturbate the root-knot nematode SC in order to identify SC components that will serve as targets for rationally designed plantibodies. 4. To develop SC-mutant nematodes as additional tools for defining the role of the SC during infection. The external cuticular layer of nematodes is the epicuticle. In many nematodes, it is covered by a fuzzy material termed "surface coat" (SC). Since the SC is the outermost layer, it may playa role in the interaction between the nematode and its surroundings during all life stages in soil and during pathogenesis. The SC is composed mainly of proteins, carbohydrates (which can be part of glycoproteins), and lipids. SC proteins and glycoproteins have been labeled and extracted from preparasitic second-stage juveniles and adult females of Meloidogyne and specific antibodies have been raised against surface antigens. Antibodies can be used to gain more information about surface function and to isolate genes encoding for surface antigens. Characterization of surface antigens and their roles in different life-stages may be an important step towards the development of alternative control. Nevertheless, the role of the plant- parasitic nematode's surface in plant-nematode interaction is still not understood. Carbohydrates or carbohydrate-recognition domains (CROs) on the nematode surface may interact with CROs or carbohydrate molecules, on root surfaces or exudates, or be active after the nematode has penetrated into the root. Surface antigens undoubtedly play an important role in interactions with microorganisms that adhere to the nematodes. Polyclonal (PC) and monoclonal (MC) antibodies raised against Meloidogyne javanica, M. incognita and other plant-parasitic nematodes, were used to characterize the surface coat and secreted-excreted products of M. javanica and M. incognita. Some of the MC and PC antibodies raised against M. incognita showed cross-reactivity with the surface coat of M. javanica. Further characterization, in planta, of the epitopes recognized by the antibodies, showed that they were present in the parasitic juvenile stages and that the surface coat is shed during root penetration by the nematode and its migration between root cells. At the molecular level, we have followed two lines of experimentation. The first has been to identify genes encoding surface coat (SC) molecules, and we have isolated and characterized a small family of mucin genes from M. incognita. Our second approach has been to study host genes that respond to the nematode, and in particular, to the SC. Our previous work has identified a large suite of genes expressed in Lycopersicon esculentum giant cells, including the partial cDNA clone DB#131, which encodes a serine/threonine protein kinase. Isolation and predicted translation of the mature cDNA revealed a frame shift mutation in the translated region of nematode sensitive plants. By using primers homologous to conserved region of DB#131 we have identified the orthologues from three (nematode-resistant) Lycopersicon peruvianum strains and found that these plants lacked the mutation.
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Horwitz, Benjamin, and Barbara Gillian Turgeon. Secondary Metabolites, Stress, and Signaling: Roles and Regulation of Peptides Produced by Non-ribosomal Peptide Synthetases. United States Department of Agriculture, 2005. http://dx.doi.org/10.32747/2005.7696522.bard.

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Fungal pathogens of plants produce a diverse array of small molecules. Often referred to as secondary metabolites because they were thought to be dispensable for basic functions, they may indeed have central roles as signals for the fungal cell, and in interactions with the host. We have identified more than a dozen genes encoding nonribosomal peptide synthetases (NPS) in Cochliobolusheterostrophus, the agent of southern corn leaf blight. The aim of this project was to identify roles of these genes in stress responses and signaling. The first objective was to test a complete collection of C. heterostrophus nonribosomal peptide synthetase (NRPS)-encoding gene deletion mutant and wildtype (WT) strains for sensitivity to various agents of oxidative (ROS) and nitrosative (RNOS) stress, in vitro. The second objective and next step in this part of the project was to study the relevance of sensitivity to ROS and RNOS in the host pathogen interaction, by measuring the production of ROS and RNOS in planta, when plants are inoculated with wild type and mutant strains. A third objective was to study expression of any genes shown to be involved in sensitivity to ROS or RNOS, in vitro and in planta. Another objective was to determine if any of the genes involved in oxidative or nitrosative stress responses are regulated by components of signal transduction pathways (STP) that we have identified and to determine where mechanisms overlap. Study of the collection of nps mutants identified phenotypes relevant for virulence, development and oxidative stress resistance for two of the genes, NPS2 and NPS6. Mutants in genes related to RNOS stress have no virulence phenotypes, while some of those related to ROS stress have reduced virulence as well as developmental phenotypes, so we focused primarily on ROS stress pathways. Furthermore, the identification of NPS2 and NPS6 as encoding for NRPS responsible for siderophore biosynthesis lent a new focus to the project, regulation by Fe. We have not yet developed good methods to image ROS in planta and work in this direction is continuing. We found that NPS6 expression is repressed by Fe, responding over the physiological Fe concentration range. Studying our collection of mutants, we found that conserved MAPK and G protein signal transduction pathways are dispensable for Fe regulation of NPS6, and initiated work to identify other pathways. The transcription factor SreA is one candidate, and is responsible for part, but not all, of the control of NPS6 expression. The results of this project show that the pathogen contends with oxidative stress through several signaling pathways. Loss of the siderophore produced by Nps6 makes the fungus sensitive to oxidative stress, and decreases virulence, suggesting a central role of the ability to sequester and take up extracellular iron in the host-pathogen interaction. Siderophores, and manipulation of Fe levels, could be targets for new strategies to deal with fungal pathogens of maize and other plants.
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Dickman, Martin B., and Oded Yarden. Characterization of the chorismate mutase effector (SsCm1) from Sclerotinia sclerotiorum. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600027.bard.

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Sclerotinia sclerotiorum is a filamentous fungus (mold) that causes plant disease. It has an extremely wide range of hosts (>400 species) and causes considerable damage (annual multimillion dollar losses) in economically important crops. It has proven difficult to control (culturally or chemically) and host resistance to this fungus has generally been inadequate. It is believed that this fungus occurs in almost every country. Virulence of this aggressive pathogen is bolstered by a wide array of plant cell wall degrading enzymes and various compounds (secondary metabolites) produced by the fungus. It is well established that plant pathogenic fungi secrete proteins and small molecules that interact with host cells and play a critical role in disease development. Such secreted proteins have been collectively designated as “effectors”. Plant resistance against some pathogens can be mediated by recognition of such effectors. Alternatively, effectors can interfere with plant defense. Some such effectors are recognized by the host plant and can culminate in a programmed cell death (PCD) resistant response. During the course of this study, we analyzed an effector in Sclerotiniasclerotiorum. This specific effector, SsCM1 is the protein chorismatemutase, which is an enzyme involved in a pathway which is important in the production of important amino acids, such a Tryptophan. We have characterized the Sclerotiniaeffector, SsCM1, and have shown that inactivation of Sscm1 does not affect fungal vegetative growth, development or production of oxalic acid (one of this fungus’ secondary metabolites associated with disease) production. However, yhis does result in reduced fungal virulence. We show that, unexpectedly, the SsCM1 protein translocates to the host chloroplast, and demonstrated that this process is required for full fungal virulence. We have also determined that the fungal SsCM1 protein can interact with similar proteins produced by the host. In addition, we have shown that the fungal SsCM1 is able to suppress at least some of the effects imposed by reactive oxygen species which are produced as a defense mechanism by the host. Last, but not least, the results of our studies have provided evidence contradicting the current dogma on at least some of the mechanist aspects of how this pathogen infects the host. Contrary to previousons, indicating that this pathogen kills its host by use of metabolites and enzymes that degrade the host tissue (a process called necrotrophy), we now know that at least in the early phases of infection, the fungus interacts with live host tissue (a phenomenon known as biotrophy). Taken together, the results of our studies provide novel insights concerning the mechanistic aspects of Sclerotinia-host interactions. We hope this information will be used to interfere with the disease cycle in a manner that will protect plants from this devastating fungus.
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