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Ahmed A, Saeed A, Ejaz SA, Aziz M, Hashmi MZ, Channar PA, Abbas Q, Raza H, Shafiq Z, El-Seedi HR. Novel adamantyl clubbed iminothiazolidinones as promising elastase inhibitors: design, synthesis, molecular docking, ADMET and DFT studies. RSC Adv 2022; 12:11974-11991. [PMID: 35481107 PMCID: PMC9016748 DOI: 10.1039/d1ra09318e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Porcine Pancreatic Elastase (PPE) is a serine protease that is homologous to trypsin and chymotrypsin that are involved in various pathologies like inflammatory disease, Chronic Obstructive Pulmonary Disease (COPD), acute respiratory distress syndrome, cystic fibrosis, and atherosclerosis. PPE if remained uninhibited would lead to digestion of important connective tissue. We developed new structurally diverse series of adamantyl-iminothiazolidinone hybrids to divulge elastase inhibition assay. To identify potent derivatives, in silico screening was conducted and in vitro studies disclosed that the compounds 5a, 5f, 5g, and 5h showed excellent binding energies and low IC50 values. In silico studies including molecular docking, DFT studies (using the B3LYP/SVP basis set in the gas phase) drug likeness scores and molecular dynamic simulation studies were conducted to evaluate protein–ligand interactions and to determine the stability of top ranked conformation. In silico studies further supported the results of in vitro experiments and suggest these derivatives as novel inhibitors of elastase enzyme. Structurally diverse adamantyl-iminothiazolidinone conjugates were synthesized, evaluated for elastase inhibition, and subjected to in silico ADMET prediction. The inhibition studies revealed compounds 5a, 5f, 5g, and 5h to show significant activity.![]()
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Affiliation(s)
- Atteeque Ahmed
- Department of Chemistry, Quaid-I-Azam University Islamabad 45320 Pakistan +92-51-9064-2241 +92-51-9064-2128
| | - Aamer Saeed
- Department of Chemistry, Quaid-I-Azam University Islamabad 45320 Pakistan +92-51-9064-2241 +92-51-9064-2128
| | - Syeda Abida Ejaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
| | - Mubashir Aziz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, The Islamia University of Bahawalpur Bahawalpur 63100 Pakistan
| | | | - Pervaiz Ali Channar
- Department of Chemistry, Quaid-I-Azam University Islamabad 45320 Pakistan +92-51-9064-2241 +92-51-9064-2128.,Department of Basic Sciences, Mathematics and Humanities, Dawood University of Engineering and Technology Karachi 74800 Pakistan
| | - Qamar Abbas
- Department of Biology, College of Science, University of Bahrain Sakhir Kingdom of Bahrain
| | - Hussain Raza
- Department of Biological Sciences, College of Natural Sciences, Kongju National University 56 Gongjudehak-Ro Gongju Chungnam 314-701 Republic of Korea
| | - Zahid Shafiq
- Department of Chemistry, Bahauddin Zakariya University Bosan Road Multan Pakistan
| | - Hesham R El-Seedi
- School of Food and Biological Engineering, Jiangsu University Zhenjiang 212013 China.,International Joint Research Laboratory of Intelligent Agriculture and Agri-Products Processing, Jiangsu Education Department, Jiangsu University Zhenjiang China.,Department of Chemistry, Faculty of Science, Menoufia University Shebin El-Kom 32512 Egypt
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Griese JJ, Högbom M. Location-specific quantification of protein-bound metal ions by X-ray anomalous dispersion: Q-XAD. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:764-771. [PMID: 31373575 DOI: 10.1107/s2059798319009926] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/10/2019] [Indexed: 12/18/2022]
Abstract
Here, a method is described which exploits X-ray anomalous dispersion (XAD) to quantify mixtures of metal ions in the binding sites of proteins and can be applied to metalloprotein crystals of average quality. This method has successfully been used to study site-specific metal binding in a protein from the R2-like ligand-binding oxidase family which assembles a heterodinuclear Mn/Fe cofactor. While previously only the relative contents of Fe and Mn in each metal-binding site have been assessed, here it is shown that the method can be extended to quantify the relative occupancies of at least three different transition metals, enabling complex competition experiments. The number of different metal ions that can be quantified is only limited by the number of high-quality anomalous data sets that can be obtained from one crystal, as one data set has to be collected for each transition-metal ion that is present (or is suspected to be present) in the protein, ideally at the absorption edge of each metal. A detailed description of the method, Q-XAD, is provided.
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Affiliation(s)
- Julia J Griese
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 106 91 Stockholm, Sweden
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Hofbauer S, Brito JA, Mulchande J, Nogly P, Pessanha M, Moreira R, Archer M. Stabilization of porcine pancreatic elastase crystals by glutaraldehyde cross-linking. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:1346-51. [PMID: 26457529 DOI: 10.1107/s2053230x15017045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022]
Abstract
Elastase is a serine protease from the chymotrypsin family of enzymes with the ability to degrade elastin, an important component of connective tissues. Excessive elastin proteolysis leads to a number of pathological diseases. Porcine pancreatic elastase (PPE) is often used for drug development as a model for human leukocyte elastase (HLE), with which it shares high sequence identity. Crystals of PPE were grown overnight using sodium sulfate and sodium acetate at acidic pH. Cross-linking the crystals with glutaraldehyde was needed to resist the soaking procedure with a diethyl N-(methyl)pyridinyl-substituted oxo-β-lactam inhibitor. Crystals of PPE bound to the inhibitor belonged to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a = 51.0, b = 58.3, c = 74.9 Å, and diffracted to 1.8 Å resolution using an in-house X-ray source.
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Affiliation(s)
- Stefan Hofbauer
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - José A Brito
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - Jalmira Mulchande
- Research Institute for Medicines (i-Med.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Przemyslaw Nogly
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Pessanha
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
| | - Rui Moreira
- Research Institute for Medicines (i-Med.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica - António Xavier, Universidade Nova de Lisboa, Avenida da República, EAN, 2780-157 Oeiras, Portugal
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Bénas P, Auzeil N, Legrand L, Brachet F, Regazzetti A, Riès-Kautt M. Weak protein-cationic co-ion interactions addressed by X-ray crystallography and mass spectrometry. ACTA ACUST UNITED AC 2014; 70:2217-31. [PMID: 25084340 DOI: 10.1107/s1399004714011304] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/15/2014] [Indexed: 11/10/2022]
Abstract
The adsorption of Rb(+), Cs(+), Mn(2+), Co(2+) and Yb(3+) onto the positively charged hen egg-white lysozyme (HEWL) has been investigated by solving 13 X-ray structures of HEWL crystallized with their chlorides and by applying electrospray ionization mass spectrometry (ESI-MS) first to dissolved protein crystals and then to the protein in buffered salt solutions. The number of bound cations follows the order Cs(+) < Mn(2+) ≃ Co(2+) < Yb(3+) at 293 K. HEWL binds less Rb(+) (qtot = 0.7) than Cs(+) (qtot = 3.9) at 100 K. Crystal flash-cooling drastically increases the binding of Cs(+), but poorly affects that of Yb(3+), suggesting different interactions. The addition of glycerol increases the number of bound Yb(3+) cations, but only slightly increases that of Rb(+). HEWL titrations with the same chlorides, followed by ESI-MS analysis, show that only about 10% of HEWL binds Cs(+) and about 40% binds 1-2 Yb(3+) cations, while the highest binding reaches 60-70% for protein binding 1-3 Mn(2+) or Co(2+) cations. The binding sites identified by X-ray crystallography show that the monovalent Rb(+) and Cs(+) preferentially bind to carbonyl groups, whereas the multivalent Mn(2+), Co(2+) and Yb(3+) interact with carboxylic groups. This work elucidates the basis of the effect of the Hofmeister cation series on protein solubility.
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Affiliation(s)
- Philippe Bénas
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Nicolas Auzeil
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire EA 4463, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Laurent Legrand
- Institut des NanoSciences de Paris (INSP), UMR 7588 CNRS/UPMC (Université Paris 6), 4 Place Jussieu, 75252 Paris CEDEX 05, France
| | - Franck Brachet
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Anne Regazzetti
- Laboratoire de Chimie-Toxicologie Analytique et Cellulaire EA 4463, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
| | - Madeleine Riès-Kautt
- Laboratoire de Cristallographie et RMN Biologiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Avenue de l'Observatoire, 75270 Paris CEDEX 06, France
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Unge J, Mueller-Dieckmann C, Panjikar S, Tucker PA, Lamzin VS, Weiss MS. On the routine use of soft X-rays in macromolecular crystallography. Part V. Molecular replacement and anomalous scattering. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:729-38. [DOI: 10.1107/s0907444911024887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 06/24/2011] [Indexed: 11/10/2022]
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Harding MM, Nowicki MW, Walkinshaw MD. Metals in protein structures: a review of their principal features. CRYSTALLOGR REV 2010. [DOI: 10.1080/0889311x.2010.485616] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Marjorie M. Harding
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Matthew W. Nowicki
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
| | - Malcolm D. Walkinshaw
- a Centre for Translational and Chemical Biology, University of Edinburgh, Michael Swann Building , Mayfield Road, Edinburgh , EH9 3JR , UK
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Kauffmann B, Weiss MS, Lamzin VS, Schmidt A. How to avoid premature decay of your macromolecular crystal: a quick soak for long life. Structure 2006; 14:1099-105. [PMID: 16843891 DOI: 10.1016/j.str.2006.05.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Revised: 05/03/2006] [Accepted: 05/03/2006] [Indexed: 11/22/2022]
Abstract
Radiation damage to biological samples is currently one of the major limiting factors in macromolecular X-ray crystallography, since it severely and irreversibly affects the quality of the data that can be obtained from a diffraction experiment. However, radiation damage can effectively be reduced by utilizing the electron and radical scavenging potential of certain small-molecule compounds. We propose an approach to protect macromolecular crystals prior to data collection by quick soaking with scavengers. This, in favorable cases, can more than double crystal lifetime in the X-ray beam. The approach has the potential to yield diffraction data of superior quality and hence to increase the amount of high-quality diffraction data and of structural information attainable from a single crystal.
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Affiliation(s)
- Brice Kauffmann
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
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Kinoshita T, Yamaguchi A, Tada T. Tris(hydroxymethyl)aminomethane induces conformational change and crystal-packing contraction of porcine pancreatic elastase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:623-6. [PMID: 16820677 PMCID: PMC2242949 DOI: 10.1107/s1744309106023001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2006] [Accepted: 06/15/2006] [Indexed: 11/11/2022]
Abstract
Porcine pancreatic elastase (PPE) was crystallized under new sulfate-free conditions containing 0.3 M NaCl and 50 mM tris(hydroxymethyl)aminomethane-HCl at pH 7.0. The crystal structure determined at 1.5 angstroms resolution had a unique conformation in four regions which contained loop portions. A chloride ion was bound near the catalytic triad instead of the sulfate ion in PDB entry 1qnj, a typical PPE crystal structure. However, the chloride ion did not affect the configuration of the catalytic triad. A tris(hydroxymethyl)aminomethane (Tris) molecule was bound to the S4 and S5 subsites in place of the adjacent molecule in the 1qnj crystal and played a significant role in the structural change of the region. The distortion in this region may subsequently have induced conformational changes in the other three regions. The fact that Tris and these four regions make a diagonal line in the ac plane may have affected the crystal-packing contraction along the a and c axes in the crystal compared with the typical crystal.
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Affiliation(s)
- Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, Osaka 599-8531, Japan.
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Horio T, Murai M, Inoue T, Hamasaki T, Tanaka T, Ohgi T. Crystal structure of human ISG20, an interferon-induced antiviral ribonuclease. FEBS Lett 2005; 577:111-6. [PMID: 15527770 DOI: 10.1016/j.febslet.2004.09.074] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Revised: 09/10/2004] [Accepted: 09/27/2004] [Indexed: 11/29/2022]
Abstract
ISG20 is an interferon-induced antiviral exoribonuclease that acts on single-stranded RNA and also has minor activity towards single-stranded DNA. It belongs to the DEDDh group of RNases of the DEDD exonuclease superfamily. We have solved the crystal structure of human ISG20 complexed with two Mn2+ ions and uridine 5'-monophosphate (UMP) at 1.9 A resolution. Its structure, including that of the active site, is very similar to those of the corresponding domains of two DEDDh-group DNases, the epsilon subunit of Escherichia coli DNA polymerase III and E. coli exonuclease I, strongly suggesting that its catalytic mechanism is identical to that of the two DNases. However, ISG20 also has distinctive residues, Met14 and Arg53, to accommodate hydrogen bonds with the 2'-OH group of the UMP ribose, and these residues may be responsible for the preference of ISG20 for RNA substrates.
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Affiliation(s)
- Tatsuya Horio
- Research Laboratories, Nippon Shinyaku Co. Ltd, 3-14-1 Sakura, Tsukuba, Ibaraki 305-0003, Japan.
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