The Serpintine Solution
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Polygenic Risk Score of SERPINA6/SERPINA1 Associates with Diurnal and Stress-Induced HPA Axis Activity in Children
Edinburgh Research Explorer Polygenic risk score of SERPINA6/SERPINA1 associates with diurnal and stress-induced HPA axis activity in children Citation for published version: Utge, S, Räikkönen, K, Kajantie, E, Lipsanen, J, Andersson, S, Strandberg, T, Reynolds, R, Eriksson, JG & Lahti, J 2018, 'Polygenic risk score of SERPINA6/SERPINA1 associates with diurnal and stress-induced HPA axis activity in children', Psychoneuroendocrinology. https://doi.org/10.1016/j.psyneuen.2018.04.009 Digital Object Identifier (DOI): 10.1016/j.psyneuen.2018.04.009 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Psychoneuroendocrinology General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 29. Sep. 2021 Psychoneuroendocrinology 93 (2018) 1–7 Contents lists available at ScienceDirect Psychoneuroendocrinology journal homepage: www.elsevier.com/locate/psyneuen Polygenic risk score of SERPINA6/SERPINA1 associates with diurnal and T stress-induced HPA axis activity in children Siddheshwar Utgea,b, Katri Räikkönena, Eero Kajantiec,d,e, Jari Lipsanena, Sture Anderssond, ⁎ Timo Strandbergf,g, Rebecca M. -
Adaptive Evolution and Divergence of SERPINB3: a Young Duplicate in Great Apes
Adaptive Evolution and Divergence of SERPINB3: A Young Duplicate in Great Apes Sı´lvia Gomes1*, Patrı´cia I. Marques1,2, Rune Matthiesen3, Susana Seixas1* 1 Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal, 2 Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal, 3 National Health Institute Doutor Ricardo Jorge (INSA), Lisboa, Portugal Abstract A series of duplication events led to an expansion of clade B Serine Protease Inhibitors (SERPIN), currently displaying a large repertoire of functions in vertebrates. Accordingly, the recent duplicates SERPINB3 and B4 located in human 18q21.3 SERPIN cluster control the activity of different cysteine and serine proteases, respectively. Here, we aim to assess SERPINB3 and B4 coevolution with their target proteases in order to understand the evolutionary forces shaping the accelerated divergence of these duplicates. Phylogenetic analysis of primate sequences placed the duplication event in a Hominoidae ancestor (,30 Mya) and the emergence of SERPINB3 in Homininae (,9 Mya). We detected evidence of strong positive selection throughout SERPINB4/B3 primate tree and target proteases, cathepsin L2 (CTSL2) and G (CTSG) and chymase (CMA1). Specifically, in the Homininae clade a perfect match was observed between the adaptive evolution of SERPINB3 and cathepsin S (CTSS) and most of sites under positive selection were located at the inhibitor/protease interface. Altogether our results seem to favour a coevolution hypothesis for SERPINB3, CTSS and CTSL2 and for SERPINB4 and CTSG and CMA1.A scenario of an accelerated evolution driven by host-pathogen interactions is also possible since SERPINB3/B4 are potent inhibitors of exogenous proteases, released by infectious agents. -
Gene Symbol Category ACAN ECM ADAM10 ECM Remodeling-Related ADAM11 ECM Remodeling-Related ADAM12 ECM Remodeling-Related ADAM15 E
Supplementary Material (ESI) for Integrative Biology This journal is (c) The Royal Society of Chemistry 2010 Gene symbol Category ACAN ECM ADAM10 ECM remodeling-related ADAM11 ECM remodeling-related ADAM12 ECM remodeling-related ADAM15 ECM remodeling-related ADAM17 ECM remodeling-related ADAM18 ECM remodeling-related ADAM19 ECM remodeling-related ADAM2 ECM remodeling-related ADAM20 ECM remodeling-related ADAM21 ECM remodeling-related ADAM22 ECM remodeling-related ADAM23 ECM remodeling-related ADAM28 ECM remodeling-related ADAM29 ECM remodeling-related ADAM3 ECM remodeling-related ADAM30 ECM remodeling-related ADAM5 ECM remodeling-related ADAM7 ECM remodeling-related ADAM8 ECM remodeling-related ADAM9 ECM remodeling-related ADAMTS1 ECM remodeling-related ADAMTS10 ECM remodeling-related ADAMTS12 ECM remodeling-related ADAMTS13 ECM remodeling-related ADAMTS14 ECM remodeling-related ADAMTS15 ECM remodeling-related ADAMTS16 ECM remodeling-related ADAMTS17 ECM remodeling-related ADAMTS18 ECM remodeling-related ADAMTS19 ECM remodeling-related ADAMTS2 ECM remodeling-related ADAMTS20 ECM remodeling-related ADAMTS3 ECM remodeling-related ADAMTS4 ECM remodeling-related ADAMTS5 ECM remodeling-related ADAMTS6 ECM remodeling-related ADAMTS7 ECM remodeling-related ADAMTS8 ECM remodeling-related ADAMTS9 ECM remodeling-related ADAMTSL1 ECM remodeling-related ADAMTSL2 ECM remodeling-related ADAMTSL3 ECM remodeling-related ADAMTSL4 ECM remodeling-related ADAMTSL5 ECM remodeling-related AGRIN ECM ALCAM Cell-cell adhesion ANGPT1 Soluble factors and receptors -
Understanding Drug-Drug Interactions Due to Mechanism-Based Inhibition in Clinical Practice
pharmaceutics Review Mechanisms of CYP450 Inhibition: Understanding Drug-Drug Interactions Due to Mechanism-Based Inhibition in Clinical Practice Malavika Deodhar 1, Sweilem B Al Rihani 1 , Meghan J. Arwood 1, Lucy Darakjian 1, Pamela Dow 1 , Jacques Turgeon 1,2 and Veronique Michaud 1,2,* 1 Tabula Rasa HealthCare Precision Pharmacotherapy Research and Development Institute, Orlando, FL 32827, USA; [email protected] (M.D.); [email protected] (S.B.A.R.); [email protected] (M.J.A.); [email protected] (L.D.); [email protected] (P.D.); [email protected] (J.T.) 2 Faculty of Pharmacy, Université de Montréal, Montreal, QC H3C 3J7, Canada * Correspondence: [email protected]; Tel.: +1-856-938-8697 Received: 5 August 2020; Accepted: 31 August 2020; Published: 4 September 2020 Abstract: In an ageing society, polypharmacy has become a major public health and economic issue. Overuse of medications, especially in patients with chronic diseases, carries major health risks. One common consequence of polypharmacy is the increased emergence of adverse drug events, mainly from drug–drug interactions. The majority of currently available drugs are metabolized by CYP450 enzymes. Interactions due to shared CYP450-mediated metabolic pathways for two or more drugs are frequent, especially through reversible or irreversible CYP450 inhibition. The magnitude of these interactions depends on several factors, including varying affinity and concentration of substrates, time delay between the administration of the drugs, and mechanisms of CYP450 inhibition. Various types of CYP450 inhibition (competitive, non-competitive, mechanism-based) have been observed clinically, and interactions of these types require a distinct clinical management strategy. This review focuses on mechanism-based inhibition, which occurs when a substrate forms a reactive intermediate, creating a stable enzyme–intermediate complex that irreversibly reduces enzyme activity. -
Serpins—From Trap to Treatment
MINI REVIEW published: 12 February 2019 doi: 10.3389/fmed.2019.00025 SERPINs—From Trap to Treatment Wariya Sanrattana, Coen Maas and Steven de Maat* Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands Excessive enzyme activity often has pathological consequences. This for example is the case in thrombosis and hereditary angioedema, where serine proteases of the coagulation system and kallikrein-kinin system are excessively active. Serine proteases are controlled by SERPINs (serine protease inhibitors). We here describe the basic biochemical mechanisms behind SERPIN activity and identify key determinants that influence their function. We explore the clinical phenotypes of several SERPIN deficiencies and review studies where SERPINs are being used beyond replacement therapy. Excitingly, rare human SERPIN mutations have led us and others to believe that it is possible to refine SERPINs toward desired behavior for the treatment of enzyme-driven pathology. Keywords: SERPIN (serine proteinase inhibitor), protein engineering, bradykinin (BK), hemostasis, therapy Edited by: Marvin T. Nieman, Case Western Reserve University, United States INTRODUCTION Reviewed by: Serine proteases are the “workhorses” of the human body. This enzyme family is conserved Daniel A. Lawrence, throughout evolution. There are 1,121 putative proteases in the human body, and about 180 of University of Michigan, United States Thomas Renne, these are serine proteases (1, 2). They are involved in diverse physiological processes, ranging from University Medical Center blood coagulation, fibrinolysis, and inflammation to immunity (Figure 1A). The activity of serine Hamburg-Eppendorf, Germany proteases is amongst others regulated by a dedicated class of inhibitory proteins called SERPINs Paulo Antonio De Souza Mourão, (serine protease inhibitors). -
Insights Into the Role of Tick Salivary Protease Inhibitors During Ectoparasite–Host Crosstalk
International Journal of Molecular Sciences Review Insights into the Role of Tick Salivary Protease Inhibitors during Ectoparasite–Host Crosstalk Mohamed Amine Jmel 1,† , Hajer Aounallah 2,3,† , Chaima Bensaoud 1, Imen Mekki 1,4, JindˇrichChmelaˇr 4, Fernanda Faria 3 , Youmna M’ghirbi 2 and Michalis Kotsyfakis 1,* 1 Laboratory of Genomics and Proteomics of Disease Vectors, Biology Centre CAS, Institute of Parasitology, Branišovská 1160/31, 37005 Ceskˇ é Budˇejovice,Czech Republic; [email protected] (M.A.J.); [email protected] (C.B.); [email protected] (I.M.) 2 Institut Pasteur de Tunis, Université de Tunis El Manar, LR19IPTX, Service d’Entomologie Médicale, Tunis 1002, Tunisia; [email protected] (H.A.); [email protected] (Y.M.) 3 Innovation and Development Laboratory, Innovation and Development Center, Instituto Butantan, São Paulo 05503-900, Brazil; [email protected] 4 Faculty of Science, University of South Bohemia in Ceskˇ é Budˇejovice, 37005 Ceskˇ é Budˇejovice, Czech Republic; [email protected] * Correspondence: [email protected] † These authors contributed equally. Abstract: Protease inhibitors (PIs) are ubiquitous regulatory proteins present in all kingdoms. They play crucial tasks in controlling biological processes directed by proteases which, if not tightly regulated, can damage the host organism. PIs can be classified according to their targeted proteases or their mechanism of action. The functions of many PIs have now been characterized and are showing clinical relevance for the treatment of human diseases such as arthritis, hepatitis, cancer, AIDS, and cardiovascular diseases, amongst others. Other PIs have potential use in agriculture as insecticides, anti-fungal, and antibacterial agents. -
Competitive Inhibition That Barrier, As We Shall See
Chapter 4 Catalysis In living systems, speed is everything. Providing the reaction speeds necessary to support life are the catalysts, mostly in the form of enzymes. Catalysis Introduction Introduction Activation Energy General Mechanisms of Action If there is a magical component to life, an argument can surely be made for it Substrate Binding being catalysis. Thanks to catalysis, reactions that could take hundreds of years Enzyme Flexibility to complete in the “real world,” occur in seconds in the presence of a catalyst. Active Site Chymotrypsin Chemical catalysts, like platinum, speed reactions, but enzymes (which are simply Enzyme Parameters super-catalysts with a twist) put chemical catalysts to shame. To understand VMAX & KCAT enzymatic catalysis, we must first understand energy. In Chapter 2, we noted the KM tendency for processes to move in the direction of lower energy. Chemical Perfect Enzymes Lineweaver-Burk Plots reactions follow this universal trend, but they often have a barrier in place that Enzyme Inhibition must be overcome. The secret to catalytic action is reducing the magnitude of Competitive Inhibition that barrier, as we shall see. No Effect On VMAX Increased KM Non-Competitive Inhibition Uncompetitive Inhibition Suicide Inhibition Control of Enzymes Allosterism Covalent Control of Enzymes Other Controls of Enzymes Ribozymes Enzyme Rate Enhancements 81 Activation Energy Another feature to note about catalyzed reactions is Click HERE, HERE, and HERE for The figure below schematically depicts the energy changes that the reduced energy barrier Kevin’s Catalytic Mechanism occur during the progression of a simple reaction. In the figure, lectures on YouTube (also called the activation the energy differences during the reaction are compared for a energy or free energy of catalyzed (plot on the right) and an uncatalyzed reaction (plot on activation) to reach the transition state of the catalyzed reaction. -
Optimizing Defence, Counter-Defence and Counter-Counter Defence in Parasitic and Trophic Interactions – a Modelling Study
1 Optimizing defence, counter-defence and counter-counter defence in parasitic and trophic interactions – A modelling study Stefan Schuster1*, Jan Ewald1,2, Thomas Dandekar2, Sybille Dühring1 1Dept. of Bioinformatics, Friedrich Schiller University of Jena Ernst-Abbe-Platz 2, 07743 Jena, Germany 2Dept. of Bioinformatics, Biocenter Julius Maximilian University of Würzburg Am Hubland, 97074 Würzburg *Corresponding author, e-mail: [email protected] Abstract In host-pathogen interactions, often the host (attacked organism) defends itself by some toxic compound and the parasite, in turn, responds by producing an enzyme that inactivates that compound. In some cases, the host can respond by producing an inhibitor of that enzyme, which can be considered as a counter-counter defence. An example is provided by cephalosporins, β-lactamases and clavulanic acid (an inhibitor of β-lactamases). Here, we tackle the question under which conditions it pays, during evolution, to establish a counter- counter defence rather than to intensify or widen the defence mechanisms. We establish a mathematical model describing this phenomenon, based on enzyme kinetics for competitive inhibition. We use an objective function based on Haber’s rule, which says that the toxic effect is proportional to the time integral of toxin concentration. The optimal allocation of defence and counter-counter defence can be calculated in an analytical way despite the nonlinearity in the underlying differential equation. The calculation provides a threshold value for the dissociation constant of the inhibitor. Only if the inhibition constant is below that threshold, that is, in the case of strong binding of the inhibitor, it pays to have a counter-counter defence. -
Bsc Chemistry
Subject Chemistry Paper No and Title 16, Bio-organic and Biophysical Chemistry Module No and Title 30, Enzymes as targets or drug design Module Tag CHE_P16_M30 Chemistry PAPER No. : 16, Bioorganic and biophysical chemistry MODULE No. : 30, Enzymes as targets of drug design TABLE OF CONTENTS 1. Learning outcomes 2. Why Enzymes as Drug Targets? 3. Enzyme structure and Catalysis 4. Concept of Enzyme Inhibition 5. Types of Enzyme Inhibition 5.1. Nonspecific Inhibitors 5.2. Specific Inhibitors 6. Summary Chemistry PAPER No. : 16, Bioorganic and biophysical chemistry MODULE No. : 30, Enzymes as targets of drug design 1. Learning outcomes After studying this module you shall be able to: Know about enzymes as drug targets Learn about enzyme structure and catalysis Know the concept of enzyme inhibition Understand the different types of enzyme inhibition 2. Introduction 2.1 Why Enzymes as Drug Targets? Medicine in twenty first century has become a science in which drug molecules are directed against the macromolecules. Enzymes hold a prominent position among the biological macromolecules that can be used as drug targets. Some features of enzyme structures and reaction pathways which make them attractive and primary target for drug action are as follows They play an essential role in biological life processes and pathophysiology The structures of active sites of enzymes and the ligand binding pockets are highly amenable for high affinity interactions with small drug like molecules Presence of potential allosteric sites Conformational variations in the binding sites Can be directly used as a therapeutic agent 3. Enzyme structure and catalysis Enzymes are biological catalysts as well as can act as receptors by acting with the substrates. -
Imexon and Gemcitabine: Mechanisms of Synergy Against Human Pancreatic Cancer
Imexon and Gemcitabine: Mechanisms of Synergy against Human Pancreatic Cancer Item Type text; Electronic Dissertation Authors Roman, Nicholas Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 02/10/2021 18:39:06 Link to Item http://hdl.handle.net/10150/194494 IMEXON AND GEMCITABINE: MECHANISMS OF SYNERGY AGAINST HUMAN PANCREATIC CANCER by NICHOLAS ORDUÑO ROMÁN _________________________ A Dissertation Submitted to the Faculty of the COMMITTEE ON PHARMACOLOGY AND TOXICOLOGY (GRADUATE) In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2 0 0 5 2 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the disser tation prepared by Nicholas Ordu ño Rom án entitled Imexon and Gemcitabine: Mechanisms of Synergy against Human Pancreatic Cancer and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy _____________________________________ ___________________________ Date:_______________ Robert T. Dorr, Ph.D. 4/12/05 _________ _______________________________________________________ Date:_______________ Terrence J. Monks. Ph.D. 4/12/05 _____ ___________________________________________________________ Date:_______________ Nathan J. Cherrington, Ph.D. 4/12/05 __________________________________________ ______________________ Date:_______________ Garth Powis, D. Phil. 4/12/05 ________ __ ______________________________________________________ Date:_______________ Terry H. Landowski, Ph.D. 4/12/05 Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertatio n to the Graduate College. -
Identification of Regulatory Mechanisms of the Hepatic
Available online at www.sciencedirect.com Computers and Chemical Engineering 32 (2008) 356–369 Identification of regulatory mechanisms of the hepatic response to thermal injury E. Yang a, T.J. Maguire a, M.L. Yarmush a, F. Berthiaume b, I.P. Androulakis a,∗ a Biomedical Engineering Department, Rutgers University, Piscataway, NJ, USA b Center for Engineering in Medicine/Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, Boston, MA, USA Received 30 October 2006; received in revised form 11 February 2007; accepted 13 February 2007 Available online 25 February 2007 Abstract The purpose of this paper is to evaluate the hypothesis that a systems biology approach can be developed such that a set of transcription factors, relevant to burn-induced inflammatory response can be identified and modulated to control the host response. We explore a novel method for identifying coherent and informative expression motifs and we subsequently determine conserved transcription factor binding sites for the sub-sets of co-expressed genes. The responses are rationalized in the context of burn-induced inflammation and the putative transcription factors are rationalized in the context of intervention targets for controlling gene expression. © 2007 Published by Elsevier Ltd. Keywords: Gene expression; Burn; Inflammation; Transcritpion factors 1. Introduction to thermal injury predispose to the later hypermetabolic state would make it possible to define points of intervention by which Deep thermal injury over greater than 20 percent of the total such outcomes can be avoided. body surface area is one of the most severe forms of trauma. The response to burn injury and trauma results from a com- Following the early acute phase response dealing with the initial plex interplay between inflammation caused by the initial injury injury and shock (Carter, Tompkins, Yarmush, Walker, & Burke, and hypermetabolism. -
Reversible and Mechanism-Based Irreversible Inhibitor Studies on Human Steroid Sulfatase and Protein Tyrosine Phosphatase 1B
Reversible and Mechanism-Based Irreversible Inhibitor Studies on Human Steroid Sulfatase and Protein Tyrosine Phosphatase 1B by F. Vanessa Ahmed A thesis presented to the University of Waterloo in fulfilment of the thesis requirement for the degree of Doctor of Philosophy in Chemistry Waterloo, Ontario, Canada, 2009 © F. Vanessa Ahmed 2009 Author’s Declaration I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the public. ii Abstract The development of reversible and irreversible inhibitors of steroid sulfatase (STS) and protein tyrosine phosphatase 1B (PTP1B) is reported herein. STS belongs to to the aryl sulfatase family of enzymes that have roles in diverse processes such as hormone regulation, cellular degradation, bone and cartilage development, intracellular communication, and signalling pathways. STS catalyzes the desulfation of sulfated steroids which are the storage forms of many steroids such as the female hormone estrone. Its crucial role in the regulation of estrogen levels has made it a therapeutic target for the treatment of estrogen-dependent cancers. Estrone sulfate derivatives bearing 2- and 4- mono- and difluoromethyl substitutions were examined as quinone methide-generating suicide inhibitors of STS with the goal of developing these small molecules as activity- based probes for proteomic profiling of sulfatases. Kinetic studies suggest that inhibition by the monofluoro derivatives is a result of a quinone methide intermediate that reacts with active-site nucleophiles. However, the main inhibition pathway of the 4- difluoromethyl derivative involved an unexpected process in which initially formed quinone methide diffuses from the active site and decomposes to an aldehyde in solution which then acts as a potent, almost irreversible STS inhibitor.