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Kapuścińska K, Dukała Z, Doha M, Ansari E, Wang J, Brudvig GW, Brooks B, Amin M. Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. J Chem Inf Model 2024; 64:2586-2593. [PMID: 38054243 DOI: 10.1021/acs.jcim.3c01564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the biochemical reactions. Cryogenic electron microscopy, X-ray, and X-ray free electron laser (XFEL) crystallography are used to image metalloproteins to understand the reaction mechanisms. However, radiation damage in cryoEM and X-ray crystallography, and the challenge of generating homogeneous crystals and keeping the appropriate experimental conditions for all the crystals in XFEL crystallography, may alter the oxidation states. Here, we build machine learning models trained on a large data set from the Cambridge Crystallographic Data Center to evaluate the metal oxidation states. The models yield high accuracy scores (from 82% to 94%) for all metals in the small molecules. Then, they were used to predict the oxidation states of more than 30 000 metal clusters in metalloproteins with Fe, Mn, Co, and Cu in their active sites. We found that most of the metals exist in the lower oxidation states (Fe2+ 77%, Mn2+ 85%, Co2+ 65%, and Cu+ 64%), and these populations correlate with the standard reduction potentials of the metal ions. Furthermore, we found no clear correlation between these populations and the resolution of the structures, which suggests no significant dependence of these predictions on the resolution. Our models represent a valuable tool for evaluating the oxidation states of the metals in metalloproteins imaged with different techniques. The data files and the machine learning code are available in a public GitHub repository: https://github.com/mamin03/OxitationStatesMetalloprotein.git.
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Affiliation(s)
- Katarzyna Kapuścińska
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Zofia Dukała
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Mekhola Doha
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Eman Ansari
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
| | - Jimin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Gary W Brudvig
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Bernand Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Muhamed Amin
- Department of Sciences, University College Groningen, University of Groningen, 9718 BG Groningen, The Netherlands
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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2
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Lozano-Juste J, Infantes L, Garcia-Maquilon I, Ruiz-Partida R, Merilo E, Benavente JL, Velazquez-Campoy A, Coego A, Bono M, Forment J, Pampín B, Destito P, Monteiro A, Rodríguez R, Cruces J, Rodriguez PL, Albert A. Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought. SCIENCE ADVANCES 2023; 9:eade9948. [PMID: 36897942 PMCID: PMC10005185 DOI: 10.1126/sciadv.ade9948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/08/2023] [Indexed: 06/01/2023]
Abstract
Strategies to activate abscisic acid (ABA) receptors and boost ABA signaling by small molecules that act as ABA receptor agonists are promising biotechnological tools to enhance plant drought tolerance. Protein structures of crop ABA receptors might require modifications to improve recognition of chemical ligands, which in turn can be optimized by structural information. Through structure-based targeted design, we have combined chemical and genetic approaches to generate an ABA receptor agonist molecule (iSB09) and engineer a CsPYL1 ABA receptor, named CsPYL15m, which efficiently binds iSB09. This optimized receptor-agonist pair leads to activation of ABA signaling and marked drought tolerance. No constitutive activation of ABA signaling and hence growth penalty was observed in transformed Arabidopsis thaliana plants. Therefore, conditional and efficient activation of ABA signaling was achieved through a chemical-genetic orthogonal approach based on iterative cycles of ligand and receptor optimization driven by the structure of ternary receptor-ligand-phosphatase complexes.
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Affiliation(s)
- Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Lourdes Infantes
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Irene Garcia-Maquilon
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Rafael Ruiz-Partida
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Ebe Merilo
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Juan Luis Benavente
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units GBsC-CSIC-BIFI and ICVV-CSIC-BIFI, Universidad de Zaragoza, Mariano Esquillor s/n, 50018 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), Avenida de San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Avenida de Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Mar Bono
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Begoña Pampín
- GalChimia S.A., Parque Empresarial de Touro, Parcelas 26-27, Fonte Díaz, 15822 Touro, A Coruña, Spain
| | - Paolo Destito
- GalChimia S.A., Parque Empresarial de Touro, Parcelas 26-27, Fonte Díaz, 15822 Touro, A Coruña, Spain
| | - Adrián Monteiro
- GalChimia S.A., Parque Empresarial de Touro, Parcelas 26-27, Fonte Díaz, 15822 Touro, A Coruña, Spain
| | - Ramón Rodríguez
- GalChimia S.A., Parque Empresarial de Touro, Parcelas 26-27, Fonte Díaz, 15822 Touro, A Coruña, Spain
| | - Jacobo Cruces
- GalChimia S.A., Parque Empresarial de Touro, Parcelas 26-27, Fonte Díaz, 15822 Touro, A Coruña, Spain
| | - Pedro L. Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Armando Albert
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
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3
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Raush E, Abagyan R, Totrov M. Graph-Convolutional Neural Net Model of the Statistical Torsion Profiles for Small Organic Molecules. J Chem Inf Model 2022; 62:5896-5906. [PMID: 36456533 DOI: 10.1021/acs.jcim.2c00790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
We present a graph-convolutional neural network (GCNN)-based method for learning and prediction of statistical torsional profiles (STP) in small organic molecules based on the experimental X-ray structure data. A specialized GCNN torsion profile model is trained using the structures in the Crystallography Open Database (COD). The GCNN-STP model captures torsional preferences over a wide range of torsion rotor chemotypes and correctly predicts a variety of effects from the vicinal atoms and moieties. GCNN-STP statistical profiles also show good agreement with quantum chemically (DFT) calculated torsion energy profiles. Furthermore, we demonstrate the application of the GCNN-STP statistical profiles for conformer generation. A web server that allows interactive profile prediction and viewing is made freely available at https://www.molsoft.com/tortool.html.
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Affiliation(s)
- Eugene Raush
- Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, California92121, United States
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California92093, United States
| | - Maxim Totrov
- Molsoft L.L.C., 11199 Sorrento Valley Road, S209, San Diego, California92121, United States
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4
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Koehl A, Jagota M, Erdmann-Pham DD, Fung A, Song YS. Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2022; 27:22-33. [PMID: 34890133 PMCID: PMC8669734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There is significant interest in developing machine learning methods to model protein-ligand interactions but a scarcity of experimentally resolved protein-ligand structures to learn from. Protein self-contacts are a much larger source of structural data that could be leveraged, but currently it is not well understood how this data source differs from the target domain. Here, we characterize the 3D geometric patterns of protein self-contacts as probability distributions. We then present a flexible statistical framework to assess the transferability of these patterns to protein-ligand contacts. We observe that the level of transferability from protein self-contacts to protein-ligand contacts depends on contact type, with many contact types exhibiting high transferability. We then demonstrate the potential of leveraging information from these geometric patterns to aid in ligand pose-selection problems in protein-ligand docking. We publicly release our extracted data on geometric interaction patterns to enable further exploration of this problem.
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Affiliation(s)
- Antoine Koehl
- Department of Statistics, University of California, Berkeley, CA 94720, USA
| | - Milind Jagota
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
| | | | - Alexander Fung
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
| | - Yun S. Song
- Department of Statistics, University of California, Berkeley, CA 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158
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5
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Bojarska J, New R, Borowiecki P, Remko M, Breza M, Madura ID, Fruziński A, Pietrzak A, Wolf WM. The First Insight Into the Supramolecular System of D,L-α-Difluoromethylornithine: A New Antiviral Perspective. Front Chem 2021; 9:679776. [PMID: 34055746 PMCID: PMC8155678 DOI: 10.3389/fchem.2021.679776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/26/2021] [Indexed: 12/28/2022] Open
Abstract
Targeting the polyamine biosynthetic pathway by inhibiting ornithine decarboxylase (ODC) is a powerful approach in the fight against diverse viruses, including SARS-CoV-2. Difluoromethylornithine (DFMO, eflornithine) is the best-known inhibitor of ODC and a broad-spectrum, unique therapeutical agent. Nevertheless, its pharmacokinetic profile is not perfect, especially when large doses are required in antiviral treatment. This article presents a holistic study focusing on the molecular and supramolecular structure of DFMO and the design of its analogues toward the development of safer and more effective formulations. In this context, we provide the first deep insight into the supramolecular system of DFMO supplemented by a comprehensive, qualitative and quantitative survey of non-covalent interactions via Hirshfeld surface, molecular electrostatic potential, enrichment ratio and energy frameworks analysis visualizing 3-D topology of interactions in order to understand the differences in the cooperativity of interactions involved in the formation of either basic or large synthons (Long-range Synthon Aufbau Modules, LSAM) at the subsequent levels of well-organized supramolecular self-assembly, in comparison with the ornithine structure. In the light of the drug discovery, supramolecular studies of amino acids, essential constituents of proteins, are of prime importance. In brief, the same amino-carboxy synthons are observed in the bio-system containing DFMO. DFT calculations revealed that the biological environment changes the molecular structure of DFMO only slightly. The ADMET profile of structural modifications of DFMO and optimization of its analogue as a new promising drug via molecular docking are discussed in detail.
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Affiliation(s)
- Joanna Bojarska
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Roger New
- Faculty of Science & Technology, Middlesex University, London, United Kingdom
| | - Paweł Borowiecki
- Faculty of Chemistry, Department of Drugs Technology and Biotechnology, Laboratory of Biocatalysis and Biotransformation, Warsaw University of Technology, Warsaw, Poland
| | | | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Bratislava, Slovakia
| | - Izabela D. Madura
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Andrzej Fruziński
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Anna Pietrzak
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Wojciech M. Wolf
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
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6
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Bojarska J, Remko M, Breza M, Madura I, Fruziński A, Wolf WM. A Proline-Based Tectons and Supramolecular Synthons for Drug Design 2.0: A Case Study of ACEI. Pharmaceuticals (Basel) 2020; 13:E338. [PMID: 33114370 PMCID: PMC7692516 DOI: 10.3390/ph13110338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 11/16/2022] Open
Abstract
Proline is a unique, endogenous amino acid, prevalent in proteins and essential for living organisms. It is appreciated as a tecton for the rational design of new bio-active substances. Herein, we present a short overview of the subject. We analyzed 2366 proline-derived structures deposited in the Cambridge Structure Database, with emphasis on the angiotensin-converting enzyme inhibitors. The latter are the first-line antihypertensive and cardiological drugs. Their side effects prompt a search for improved pharmaceuticals. Characterization of tectons (molecular building blocks) and the resulting supramolecular synthons (patterns of intermolecular interactions) involving proline derivatives, as presented in this study, may be useful for in silico molecular docking and macromolecular modeling studies. The DFT, Hirshfeld surface and energy framework methods gave considerable insight into the nature of close inter-contacts and supramolecular topology. Substituents of proline entity are important for the formation and cooperation of synthons. Tectonic subunits contain proline moieties characterized by diverse ionization states: -N and -COOH(-COO-), -N+ and -COOH(-COO-), -NH and -COOH(-COO-), -NH+ and -COOH(-COO-), and -NH2+ and -COOH(-COO-). Furthermore, pharmacological profiles of ACE inhibitors and their impurities were determined via an in silico approach. The above data were used to develop comprehensive classification, which may be useful in further drug design studies.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Milan Remko
- Remedika, Luzna 9, 85104 Bratislava, Slovakia;
| | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia;
| | - Izabela Madura
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland;
| | - Andrzej Fruziński
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General and Ecological Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland; (A.F.); (W.M.W.)
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7
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Cabaj MK, Dominiak PM. Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. Nucleic Acids Res 2020; 48:8302-8319. [PMID: 32725210 PMCID: PMC7470937 DOI: 10.1093/nar/gkaa629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/10/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022] Open
Abstract
We used the high resolution and accuracy of the Cambridge Structural Database (CSD) to provide detailed information regarding base pairing interactions of selected nucleobases. We searched for base pairs in which nucleobases interact with each other through two or more hydrogen bonds and form more or less planar structures. The investigated compounds were either free forms or derivatives of adenine, guanine, hypoxanthine, thymine, uracil and cytosine. We divided our findings into categories including types of pairs, protonation patterns and whether they are formed by free bases or substituted ones. We found base pair types that are exclusive to small molecule crystal structures, some that can be found only in RNA containing crystal structures and many that are native to both environments. With a few exceptions, nucleobase protonation generally followed a standard pattern governed by pKa values. The lengths of hydrogen bonds did not depend on whether the nucleobases forming a base pair were charged or not. The reasons why particular nucleobases formed base pairs in a certain way varied significantly.
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Affiliation(s)
- Małgorzata Katarzyna Cabaj
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
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8
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Bojarska J, Remko M, Breza M, Madura ID, Kaczmarek K, Zabrocki J, Wolf WM. A Supramolecular Approach to Structure-Based Design with A Focus on Synthons Hierarchy in Ornithine-Derived Ligands: Review, Synthesis, Experimental and in Silico Studies. Molecules 2020; 25:E1135. [PMID: 32138329 PMCID: PMC7179192 DOI: 10.3390/molecules25051135] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 12/24/2022] Open
Abstract
The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H…O, O…H, C…H, Cl (Br, F)…H and O…O interactions. Additionally, π…π, C-H…π and N-O…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity.
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Affiliation(s)
- Joanna Bojarska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland;
| | - Milan Remko
- Remedika, Sustekova, 1 85104 Bratislava, Slovakia;
| | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Radlinskeho 9, SK-81237 Bratislava, Slovakia;
| | - Izabela D. Madura
- Warsaw University of Technology, Faculty of Chemistry, Noakowskiego 3, 00-664 Warszawa, Poland;
| | - Krzysztof Kaczmarek
- Institute of Organic Chemistry, Lodz University of Technology, Faculty of Chemistry, Żeromskiego 116, 90-924 Lodz, Poland; (K.K.); (J.Z.)
| | - Janusz Zabrocki
- Institute of Organic Chemistry, Lodz University of Technology, Faculty of Chemistry, Żeromskiego 116, 90-924 Lodz, Poland; (K.K.); (J.Z.)
| | - Wojciech M. Wolf
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland;
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9
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Spackman PR, Yu L, Morton CJ, Parker MW, Bond CS, Spackman MA, Jayatilaka D, Thomas SP. Bridging Crystal Engineering and Drug Discovery by Utilizing Intermolecular Interactions and Molecular Shapes in Crystals. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906602] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Peter R. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - Li‐Juan Yu
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Research School of Chemistry Australian National University Canberra Australia
| | - Craig J. Morton
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
- St Vincent's Institute of Medical Research Fitz-roy VIC 3065 Australia
| | - Charles S. Bond
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Mark A. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Sajesh P. Thomas
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Department of Chemistry and iNano Aarhus University Langelandsgade 140 Aarhus 8000 Denmark
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10
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Brink A, Helliwell JR. Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? IUCRJ 2019; 6:788-793. [PMID: 31576212 PMCID: PMC6760442 DOI: 10.1107/s2052252519010972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, Free State 9301, South Africa
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
- Correspondence e-mail:
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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11
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Spackman PR, Yu L, Morton CJ, Parker MW, Bond CS, Spackman MA, Jayatilaka D, Thomas SP. Bridging Crystal Engineering and Drug Discovery by Utilizing Intermolecular Interactions and Molecular Shapes in Crystals. Angew Chem Int Ed Engl 2019; 58:16780-16784. [DOI: 10.1002/anie.201906602] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Peter R. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- School of Chemistry University of Southampton Highfield Southampton SO17 1BJ UK
| | - Li‐Juan Yu
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Research School of Chemistry Australian National University Canberra Australia
| | - Craig J. Morton
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
| | - Michael W. Parker
- Department of Biochemistry and Molecular Biology University of Melbourne Parkville VIC 3010 Australia
- St Vincent's Institute of Medical Research Fitz-roy VIC 3065 Australia
| | - Charles S. Bond
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Mark A. Spackman
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Dylan Jayatilaka
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
| | - Sajesh P. Thomas
- School of Molecular Sciences University of Western Australia Perth WA 6009 Australia
- Department of Chemistry and iNano Aarhus University Langelandsgade 140 Aarhus 8000 Denmark
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12
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Taylor R, Wood PA. A Million Crystal Structures: The Whole Is Greater than the Sum of Its Parts. Chem Rev 2019; 119:9427-9477. [PMID: 31244003 DOI: 10.1021/acs.chemrev.9b00155] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The founding in 1965 of what is now called the Cambridge Structural Database (CSD) has reaped dividends in numerous and diverse areas of chemical research. Each of the million or so crystal structures in the database was solved for its own particular reason, but collected together, the structures can be reused to address a multitude of new problems. In this Review, which is focused mainly on the last 10 years, we chronicle the contribution of the CSD to research into molecular geometries, molecular interactions, and molecular assemblies and demonstrate its value in the design of biologically active molecules and the solid forms in which they are delivered. Its potential in other commercially relevant areas is described, including gas storage and delivery, thin films, and (opto)electronics. The CSD also aids the solution of new crystal structures. Because no scientific instrument is without shortcomings, the limitations of CSD research are assessed. We emphasize the importance of maintaining database quality: notwithstanding the arrival of big data and machine learning, it remains perilous to ignore the principle of garbage in, garbage out. Finally, we explain why the CSD must evolve with the world around it to ensure it remains fit for purpose in the years ahead.
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Affiliation(s)
- Robin Taylor
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
| | - Peter A Wood
- Cambridge Crystallographic Data Centre , 12 Union Road , Cambridge CB2 1EZ , United Kingdom
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13
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Tesch R, Becker C, Müller MP, Beck ME, Quambusch L, Getlik M, Lategahn J, Uhlenbrock N, Costa FN, Polêto MD, Pinheiro PDSM, Rodrigues DA, Sant'Anna CMR, Ferreira FF, Verli H, Fraga CAM, Rauh D. Eine ungewöhnliche intramolekulare Halogenbindung führt zu konformationeller Selektion. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Roberta Tesch
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Christian Becker
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Matthias Philipp Müller
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Michael Edmund Beck
- Bayer AG; division Crop Science; Alfred-Nobel-Straße 50 40789 Monheim am Rhein Deutschland
| | - Lena Quambusch
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Matthäus Getlik
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Jonas Lategahn
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | - Niklas Uhlenbrock
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
| | | | - Marcelo D. Polêto
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brasilien
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Carlos Mauricio R. Sant'Anna
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
- Departamento de Química; Instituto de Ciências Exatas Universidade Federal Rural do Rio de Janeiro; Seropédica Brasilien
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; São Paulo Brasilien
| | - Hugo Verli
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brasilien
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas, (LASSBio); Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brasilien
| | - Daniel Rauh
- Fakultät für Chemie und Chemische Biologie; Technische Universität Dortmund; Otto-Hahn-Straße 4a 44227 Dortmund Deutschland
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14
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Tesch R, Becker C, Müller MP, Beck ME, Quambusch L, Getlik M, Lategahn J, Uhlenbrock N, Costa FN, Polêto MD, Pinheiro PDSM, Rodrigues DA, Sant'Anna CMR, Ferreira FF, Verli H, Fraga CAM, Rauh D. An Unusual Intramolecular Halogen Bond Guides Conformational Selection. Angew Chem Int Ed Engl 2018; 57:9970-9975. [DOI: 10.1002/anie.201804917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/01/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Roberta Tesch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Christian Becker
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Matthias Philipp Müller
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Michael Edmund Beck
- Bayer AG; division Crop Science; Alfred-Nobel-Strasse 50 40789 Monheim am Rhein Germany
| | - Lena Quambusch
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Matthäus Getlik
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jonas Lategahn
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Niklas Uhlenbrock
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | | | - Marcelo D. Polêto
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brazil
| | - Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Daniel Alencar Rodrigues
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Carlos Mauricio R. Sant'Anna
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
- Departamento de Química; Instituto de Ciências Exatas Universidade Federal Rural do Rio de Janeiro; Seropédica Brazil
| | - Fabio Furlan Ferreira
- Centro de Ciências Naturais e Humanas; Universidade Federal do ABC; São Paulo Brazil
| | - Hugo Verli
- Centro de Biotecnologia; Universidade Federal do Rio Grande do Sul; Av. Bento Gonçalves 9500 Porto Alegre Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas; Universidade Federal do Rio de Janeiro; Av. Carlos Chagas Filho, 373, CEP 21941-902 Rio de Janeiro Brazil
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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15
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Helliwell JR. New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences. Biosci Rep 2017; 37:BSR20170204. [PMID: 28572170 PMCID: PMC6434086 DOI: 10.1042/bsr20170204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.
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