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Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity. Biophys Rev 2022; 14:277-301. [PMID: 35340592 PMCID: PMC8921380 DOI: 10.1007/s12551-021-00921-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/18/2021] [Indexed: 01/09/2023] Open
Abstract
The urokinase plasminogen activator (uPA) is a widely studied anticancer drug target with multiple classes of inhibitors reported to date. Many of these inhibitors contain amidine or guanidine groups, while others lacking these groups show improved oral bioavailability. Most of the X-ray co-crystal structures of small molecule uPA inhibitors show a key salt bridge with the side chain carboxylate of Asp189 in the S1 pocket of uPA. This review summarises the different classes of uPA inhibitors, their binding interactions and experimentally measured inhibitory potencies and highlights species selectivity issues with attention to recently described 6-substituted amiloride and 5‑N,N-(hexamethylene)amiloride (HMA) derivatives.
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2
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S El Salamouni N, Buckley BJ, Jiang L, Huang M, Ranson M, Kelso MJ, Yu H. Disruption of Water Networks is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA). J Med Chem 2021; 65:1933-1945. [PMID: 34898192 DOI: 10.1021/acs.jmedchem.1c01423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The urokinase plasminogen activator (uPA) plays a critical role in tumor cell invasion and migration and is a promising antimetastasis target. 6-Substituted analogues of 5-N,N-(hexamethylene)amiloride (HMA) are potent and selective uPA inhibitors that lack the diuretic and antikaliuretic properties of the parent drug amiloride. However, the compounds display pronounced selectivity for human over mouse uPA, thus confounding interpretation of data from human xenograft mouse models of cancer. Here, computational and experimental findings reveal that residue 99 is a key contributor to the observed species selectivity, whereby enthalpically unfavorable expulsion of a water molecule by the 5-N,N-hexamethylene ring occurs when residue 99 is Tyr (as in mouse uPA). Analogue 7 lacking the 5-N,N-hexamethylene ring maintained similar water networks when bound to human and mouse uPA and displayed reduced selectivity, thus supporting this conclusion. The study will guide further optimization of dual-potent human/mouse uPA inhibitors from the amiloride class as antimetastasis drugs.
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Affiliation(s)
- Nehad S El Salamouni
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Benjamin J Buckley
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,CONCERT-Translational Cancer Research Centre, Sydney, NSW 2750, Australia
| | - Longguang Jiang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fujian 350116, China
| | - Mingdong Huang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fujian 350116, China
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,CONCERT-Translational Cancer Research Centre, Sydney, NSW 2750, Australia
| | - Michael J Kelso
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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3
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Sandner A, Ngo K, Schiebel J, Pizarroso AIM, Schmidt L, Wenzel B, Steinmetzer T, Ostermann A, Heine A, Klebe G. How a Fragment Draws Attention to Selectivity Discriminating Features between the Related Proteases Trypsin and Thrombin. J Med Chem 2021; 64:1611-1625. [PMID: 33471524 DOI: 10.1021/acs.jmedchem.0c01809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the S1 pocket, the serine proteases thrombin and trypsin commonly feature Asp189 and a Ala190Ser and Glu192Gln exchange. Nevertheless, thrombin cleaves peptide chains solely after Arg, and trypsin after Lys and Arg. Thrombin exhibits a Na+-binding site next to Asp189, which is missing in trypsin. The fragment benzylamine shows direct H-bonding to Asp189 in trypsin, while in thrombin, it forms an H-bond to Glu192. A series of fragments and expanded ligands were studied against both enzymes and mutated variants by crystallography and ITC. The selectivity-determining features of both S1 pockets are difficult to assign to one dominating factor. The Ala190Ser and Glu192Gln replacements may be regarded as highly conserved as no structural and affinity changes are observed between both proteases. With respect to charge distribution, Glu192, together with the thrombin-specific sodium ion, helps in creating an electrostatic gradient across the S1 pocket. This feature is definitely absent in trypsin but important for selectivity along with solvation-pattern differences in the S1 pocket.
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Affiliation(s)
- Anna Sandner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Khang Ngo
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Johannes Schiebel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | | | - Linda Schmidt
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Benjamin Wenzel
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Ostermann
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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4
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Kolarič A, Germe T, Hrast M, Stevenson CEM, Lawson DM, Burton NP, Vörös J, Maxwell A, Minovski N, Anderluh M. Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds. Nat Commun 2021; 12:150. [PMID: 33420011 PMCID: PMC7794245 DOI: 10.1038/s41467-020-20405-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/25/2020] [Indexed: 12/13/2022] Open
Abstract
Novel bacterial type II topoisomerase inhibitors (NBTIs) stabilize single-strand DNA cleavage breaks by DNA gyrase but their exact mechanism of action has remained hypothetical until now. We have designed a small library of NBTIs with an improved DNA gyrase-binding moiety resulting in low nanomolar inhibition and very potent antibacterial activity. They stabilize single-stranded cleavage complexes and, importantly, we have obtained the crystal structure where an NBTI binds gyrase–DNA in a single conformation lacking apparent static disorder. This directly proves the previously postulated NBTI mechanism of action and shows that they stabilize single-strand cleavage through asymmetric intercalation with a shift of the scissile phosphate. This crystal stucture shows that the chlorine forms a halogen bond with the backbone carbonyls of the two symmetry-related Ala68 residues. To the best of our knowledge, such a so-called symmetrical bifurcated halogen bond has not been identified in a biological system until now. The mechanism of DNA gyrase inhibitor stabilization of single-strand DNA cleavage breaks by DNA gyrase has been hypothetical. Here, the authors show experimental evidence of the mechanism using a library of inhibitors with improved binding and employ crystal analysis to show bifurcated halogen bonding.
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Affiliation(s)
- Anja Kolarič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Thomas Germe
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Martina Hrast
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Clare E M Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nicolas P Burton
- Inspiralis Ltd., Innovation Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7GJ, UK
| | - Judit Vörös
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.
| | - Marko Anderluh
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.
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5
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Huggins DJ. Structural analysis of experimental drugs binding to the SARS-CoV-2 target TMPRSS2. J Mol Graph Model 2020; 100:107710. [PMID: 32829149 PMCID: PMC7417922 DOI: 10.1016/j.jmgm.2020.107710] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 12/17/2022]
Abstract
The emergence of SARS-CoV-2 has prompted a worldwide health emergency. There is an urgent need for therapeutics, both through the repurposing of approved drugs and the development of new treatments. In addition to the viral drug targets, a number of human drug targets have been suggested. In theory, targeting human proteins should provide an advantage over targeting viral proteins in terms of drug resistance, which is commonly a problem in treating RNA viruses. This paper focuses on the human protein TMPRSS2, which supports coronavirus life cycles by cleaving viral spike proteins. The three-dimensional structure of TMPRSS2 is not known and so we have generated models of the TMPRSS2 in the apo state as well as in complex with a peptide substrate and putative inhibitors to aid future work. Importantly, many related human proteases have 80% or higher identity with TMPRSS2 in the S1-S1' subsites, with plasminogen and urokinase-type plasminogen activator (uPA) having 95% identity. We highlight 376 approved, investigational or experimental drugs targeting S1A serine proteases that may also inhibit TMPRSS2. Whilst the presence of a relatively uncommon lysine residue in the S2/S3 subsites means that some serine protease inhibitors will not inhibit TMPRSS2, this residue is likely to provide a handle for selective targeting in a focused drug discovery project. We discuss how experimental drugs targeting related serine proteases might be repurposed as TMPRSS2 inhibitors to treat coronaviruses.
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Affiliation(s)
- David J Huggins
- Tri-Institutional Therapeutics Discovery Institute, New York, NY, USA; Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA.
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6
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Ross GA, Russell E, Deng Y, Lu C, Harder ED, Abel R, Wang L. Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo. J Chem Theory Comput 2020; 16:6061-6076. [PMID: 32955877 DOI: 10.1021/acs.jctc.0c00660] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The prediction of protein-ligand binding affinities using free energy perturbation (FEP) is becoming increasingly routine in structure-based drug discovery. Most FEP packages use molecular dynamics (MD) to sample the configurations of proteins and ligands, as MD is well-suited to capturing coupled motion. However, MD can be prohibitively inefficient at sampling water molecules that are buried within binding sites, which has severely limited the domain of applicability of FEP and its prospective usage in drug discovery. In this paper, we present an advancement of FEP that augments MD with grand canonical Monte Carlo (GCMC), an enhanced sampling method, to overcome the problem of sampling water. We accomplished this without degrading computational performance. On both old and newly assembled data sets of protein-ligand complexes, we show that the use of GCMC in FEP is essential for accurate and robust predictions for ligand perturbations that disrupt buried water.
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Affiliation(s)
- Gregory A Ross
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ellery Russell
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Yuqing Deng
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chao Lu
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Edward D Harder
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Robert Abel
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
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7
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Lorthiois E, Roache J, Barnes-Seeman D, Altmann E, Hassiepen U, Turner G, Duvadie R, Hornak V, Karki RG, Schiering N, Weihofen WA, Perruccio F, Calhoun A, Fazal T, Dedic D, Durand C, Dussauge S, Fettis K, Tritsch F, Dentel C, Druet A, Liu D, Kirman L, Lachal J, Namoto K, Bevan D, Mo R, Monnet G, Muller L, Zessis R, Huang X, Lindsley L, Currie T, Chiu YH, Fridrich C, Delgado P, Wang S, Hollis-Symynkywicz M, Berghausen J, Williams E, Liu H, Liang G, Kim H, Hoffmann P, Hein A, Ramage P, D’Arcy A, Harlfinger S, Renatus M, Ruedisser S, Feldman D, Elliott J, Sedrani R, Maibaum J, Adams CM. Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach. J Med Chem 2020; 63:8088-8113. [DOI: 10.1021/acs.jmedchem.0c00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Edwige Lorthiois
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - James Roache
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - David Barnes-Seeman
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Eva Altmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Gordon Turner
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rohit Duvadie
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rajeshri G. Karki
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Wilhelm A. Weihofen
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Francesca Perruccio
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Amy Calhoun
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Tanzina Fazal
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Darija Dedic
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Corinne Durand
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Solene Dussauge
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Kamal Fettis
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Fabien Tritsch
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Celine Dentel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Adelaide Druet
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Donglei Liu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Louise Kirman
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Julie Lachal
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Kenji Namoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Douglas Bevan
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rose Mo
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Gabriela Monnet
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Lionel Muller
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard Zessis
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Xueming Huang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Loren Lindsley
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Treeve Currie
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yu-Hsin Chiu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Cary Fridrich
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Delgado
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Shuangxi Wang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Joerg Berghausen
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Eric Williams
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Hong Liu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Guiqing Liang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Hyungchul Kim
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Hoffmann
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreas Hein
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Allan D’Arcy
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Stefanie Harlfinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Simon Ruedisser
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - David Feldman
- Novartis Institutes for BioMedical Research, East Hanover, New Jersey 07396, United States
| | - Jason Elliott
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Richard Sedrani
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Juergen Maibaum
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christopher M. Adams
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
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8
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De Vita E, Smits N, van den Hurk H, Beck EM, Hewitt J, Baillie G, Russell E, Pannifer A, Hamon V, Morrison A, McElroy SP, Jones P, Ignatenko NA, Gunkel N, Miller AK. Synthesis and Structure-Activity Relationships of N-(4-Benzamidino)-Oxazolidinones: Potent and Selective Inhibitors of Kallikrein-Related Peptidase 6. ChemMedChem 2020; 15:79-95. [PMID: 31675166 PMCID: PMC7004151 DOI: 10.1002/cmdc.201900536] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Indexed: 12/16/2022]
Abstract
Kallikrein-related peptidase 6 (KLK6) is a secreted serine protease that belongs to the family of tissue kallikreins. Aberrant expression of KLK6 has been found in different cancers and neurodegenerative diseases, and KLK6 is currently studied as a potential target in these pathologies. We report a novel series of KLK6 inhibitors discovered in a high-throughput screen within the European Lead Factory program. Structure-guided design based on docking studies enabled rapid progression of a hit cluster to inhibitors with improved potency, selectivity and pharmacokinetic properties. In particular, inhibitors 32 ((5R)-3-(4-carbamimidoylphenyl)-N-((S)-1-(naphthalen-1-yl)propyl)-2-oxooxazolidine-5-carboxamide) and 34 ((5R)-3-(6-carbamimidoylpyridin-3-yl)-N-((1S)-1-(naphthalen-1-yl)propyl)-2-oxooxazolidine-5-carboxamide) have single-digit nanomolar potency against KLK6, with over 25-fold and 100-fold selectivities against the closely related enzyme trypsin, respectively. The most potent compound, 32, effectively reduces KLK6-dependent invasion of HCT116 cells. The high potency in combination with good solubility and low clearance of 32 make it a good chemical probe for KLK6 target validation in vitro and potentially in vivo.
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Affiliation(s)
- Elena De Vita
- Cancer Drug Development GroupGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- Faculty of BiosciencesUniversity of Heidelberg69120HeidelbergGermany
| | - Niels Smits
- Pivot Park Screening CentreKloosterstraat 95349 ABOss (TheNetherlands
| | | | - Elizabeth M. Beck
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Joanne Hewitt
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Gemma Baillie
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Emily Russell
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Andrew Pannifer
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Véronique Hamon
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Angus Morrison
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Stuart P. McElroy
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Philip Jones
- European Screening Centre Newhouse (ESC) Biocity ScotlandBo'ness RoadML15UHNewhouseScotland
| | - Natalia A. Ignatenko
- University of Arizona Cancer CenterUniversity of ArizonaTucsonAZ 85721USA
- Department of Cellular and Molecular MedicineUniversity of ArizonaTucsonAZ 85721USA
| | - Nikolas Gunkel
- Cancer Drug Development GroupGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- German Cancer Consortium (DKTK)69120HeidelbergGermany
| | - Aubry K. Miller
- Cancer Drug Development GroupGerman Cancer Research Center (DKFZ)Im Neuenheimer Feld 28069120HeidelbergGermany
- German Cancer Consortium (DKTK)69120HeidelbergGermany
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9
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Wyganowska-Świątkowska M, Tarnowski M, Murtagh D, Skrzypczak-Jankun E, Jankun J. Proteolysis is the most fundamental property of malignancy and its inhibition may be used therapeutically (Review). Int J Mol Med 2018; 43:15-25. [PMID: 30431071 PMCID: PMC6257838 DOI: 10.3892/ijmm.2018.3983] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022] Open
Abstract
The mortality rates of cancer patients decreased by ~1.5% per year between 2001 and 2015, although the decrease depends on patient sex, ethnic group and type of malignancy. Cancer remains a significant global health problem, requiring a search for novel treatments. The most common property of malignant tumors is their capacity to invade adjacent tissue and to metastasize, and this cancer aggressiveness is contingent on overexpression of proteolytic enzymes. The components of the plasminogen activation system (PAS) and the metal-loproteinase family [mainly matrix metalloproteinases (MMPs)] are overexpressed in malignant tumors, driving the local invasion, metastasis and angiogenesis. This is the case for numerous types of cancer, such as breast, colon, prostate and oral carcinoma, among others. Present chemotherapeutics agents typically attack all dividing cells; however, for future therapeutic agents to be clinically successful, they need to be highly selective for a specific protein(s) and act on the cancerous tissues without adverse systemic effects. Inhibition of proteolysis in cancerous tissue has the ability to attenuate tumor invasion, angiogenesis and migration. For that purpose, inhibiting both PAS and MMPs may be another approach, since the two groups of enzymes are overexpressed in cancer. In the present review, the roles and new findings on PAS and MMP families in cancer formation, growth and possible treatments are discussed.
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Affiliation(s)
| | | | - Daniel Murtagh
- Urology Research Center, Department of Urology, Health Science Campus, The University of Toledo, Toledo, OH 43614‑2598, USA
| | - Ewa Skrzypczak-Jankun
- Urology Research Center, Department of Urology, Health Science Campus, The University of Toledo, Toledo, OH 43614‑2598, USA
| | - Jerzy Jankun
- Urology Research Center, Department of Urology, Health Science Campus, The University of Toledo, Toledo, OH 43614‑2598, USA
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10
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Can components of the plasminogen activation system predict the outcome of kidney transplants? Cent Eur J Immunol 2018; 43:222-230. [PMID: 30135637 PMCID: PMC6102612 DOI: 10.5114/ceji.2018.77394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/27/2017] [Indexed: 12/03/2022] Open
Abstract
Proteolytic and antiproteolytic enzymes play a critical role in the physiology and pathology of different stages of human life. One of the important members of the proteolytic family is the plasminogen activation system (PAS), which includes several elements crucial for this review: the 50 kDa glycoprotein plasminogen activator inhibitor 1 (PAI-1) that inhibits tissue-type (tPA) and urokinase-type plasminogen activator (uPA). These two convert plasminogen into its active form named plasmin that can lyse a broad spectrum of proteins. Urokinase receptor (uPAR) is the binding site of uPA. This glycoprotein on the cell surface facilitates urokinase activation of plasminogen, creating high proteolytic activity close to the cell surface. PAS activities have been reported to predict the outcome of kidney transplants. However, reports on expression of PAS in kidney transplants seem to be controversial. On the one hand there are reports that impaired proteolytic activity leads to induction of chronic allograft nephropathy, while on the other hand treatment with uPA and tPA can restore function of acute renal transplants. In this comprehensive review we describe the complexity of the PAS as well as biological effects of the PAS on renal allografts, and provide a possible explanation of the reported controversy.
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11
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Sananes A, Cohen I, Shahar A, Hockla A, De Vita E, Miller AK, Radisky ES, Papo N. A potent, proteolysis-resistant inhibitor of kallikrein-related peptidase 6 (KLK6) for cancer therapy, developed by combinatorial engineering. J Biol Chem 2018; 293:12663-12680. [PMID: 29934309 DOI: 10.1074/jbc.ra117.000871] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 06/12/2018] [Indexed: 01/01/2023] Open
Abstract
Human tissue kallikrein (KLK) proteases are hormone-like signaling molecules with important functions in cancer pathophysiology. KLK-related peptidase 6 (KLK6), specifically, is highly up-regulated in several types of cancer, where its increased activity promotes cancer invasion and metastasis. This characteristic suggests KLK6 as an attractive target for therapeutic interventions. However, inhibitors that specifically target KLK6 have not yet been reported, possibly because KLK6 shares a high sequence homology and structural similarity with other serine proteases and resists inhibition by many polypeptide inhibitors. Here, we present an innovative combinatorial approach to engineering KLK6 inhibitors via flow cytometry-based screening of a yeast-displayed mutant library of the human amyloid precursor protein Kunitz protease inhibitor domain (APPI), an inhibitor of other serine proteases, such as anionic and cationic trypsins. On the basis of this screening, we generated APPIM17L,I18F,S19F,F34V (APPI-4M), an APPI variant with a KLK6 inhibition constant (Ki ) of 160 pm and a turnover time of 10 days. To the best of our knowledge, APPI-4M is the most potent KLK6 inhibitor reported to date, displaying 146-fold improved affinity and 13-fold improved proteolytic stability compared with WT APPI (APPIWT). We further demonstrate that APPI-4M acts as a functional inhibitor in a cell-based model of KLK6-dependent breast cancer invasion. Finally, the crystal structures of the APPIWT/KLK6 and APPI-4M/KLK6 complexes revealed the structural and mechanistic bases for the improved KLK6 binding and proteolytic resistance of APPI-4M. We anticipate that APPI-4M will have substantial translational potential as both imaging agent and therapeutic.
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Affiliation(s)
- Amiram Sananes
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105 Israel
| | - Itay Cohen
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105 Israel
| | - Anat Shahar
- The National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva, 84105 Israel
| | - Alexandra Hockla
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Elena De Vita
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Aubry K Miller
- Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Evette S Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Niv Papo
- Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105 Israel.
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12
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Subramanian V, Ain QU, Henno H, Pietilä LO, Fuchs JE, Prusis P, Bender A, Wohlfahrt G. 3D proteochemometrics: using three-dimensional information of proteins and ligands to address aspects of the selectivity of serine proteases. MEDCHEMCOMM 2017; 8:1037-1045. [PMID: 30108817 PMCID: PMC6072133 DOI: 10.1039/c6md00701e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/14/2017] [Indexed: 11/21/2022]
Abstract
The high similarity between certain sub-pockets of serine proteases may lead to low selectivity of protease inhibitors. Therefore the application of proteochemometrics (PCM), which quantifies the relationship between protein/ligand descriptors and affinity for multiple ligands and targets simultaneously, is useful to understand and improve the selectivity profiles of potential inhibitors. In this study, protein field-based PCM that uses knowledge-based and WaterMap derived fields to describe proteins in combination with 2D (RDKit and MOE fingerprints) and 3D (4 point pharmacophoric fingerprints and GRIND) ligand descriptors was used to model the bioactivities of 24 homologous serine proteases and 5863 inhibitors in an integrated fashion. Of the multiple field-based PCM models generated based on different ligand descriptors, RDKit fingerprints showed the best performance in terms of external prediction with Rtest2 of 0.72 and RMSEP of 0.81. Further, visual interpretation of the models highlights sub-pocket specific regions that influence affinity and selectivity of serine protease inhibitors.
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Affiliation(s)
- Vigneshwari Subramanian
- Division of Pharmaceutical Chemistry and Technology , Faculty of Pharmacy , University of Helsinki , 00014 Helsinki , Finland
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Qurrat Ul Ain
- Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , CB2 1EW Cambridge , UK
| | - Helena Henno
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Lars-Olof Pietilä
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Julian E Fuchs
- Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , CB2 1EW Cambridge , UK
- Institute of General , Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 82 , 6020 Innsbruck , Austria
| | - Peteris Prusis
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
| | - Andreas Bender
- Centre for Molecular Informatics , Department of Chemistry , Lensfield Road , CB2 1EW Cambridge , UK
| | - Gerd Wohlfahrt
- Computer-Aided Drug Design , Orion Pharma , Orionintie 1 , 02101 Espoo , Finland .
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13
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Rowe RK, Ho PS. Relationships between hydrogen bonds and halogen bonds in biological systems. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:255-264. [PMID: 28362290 DOI: 10.1107/s2052520617003109] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/24/2017] [Indexed: 06/07/2023]
Abstract
The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.
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Affiliation(s)
- Rhianon K Rowe
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
| | - P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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14
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Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends Pharmacol Sci 2015; 36:724-736. [PMID: 26538314 DOI: 10.1016/j.tips.2015.08.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 01/01/2023]
Abstract
Analysis of binding energy hot spots at protein surfaces can provide crucial insights into the prospects for successful application of fragment-based drug discovery (FBDD), and whether a fragment hit can be advanced into a high-affinity, drug-like ligand. The key factor is the strength of the top ranking hot spot, and how well a given fragment complements it. We show that published data are sufficient to provide a sophisticated and quantitative understanding of how hot spots derive from a protein 3D structure, and how their strength, number, and spatial arrangement govern the potential for a surface site to bind to fragment-sized and larger ligands. This improved understanding provides important guidance for the effective application of FBDD in drug discovery.
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Affiliation(s)
- David R Hall
- Acpharis Inc., 160 North Mill Street, Holliston, MA 01746, USA
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA, 02215, USA.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA; Department of Chemistry, Boston University, Boston, MA, 02215, USA.
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15
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Cheney DL, Bozarth JM, Metzler WJ, Morin PE, Mueller L, Newitt JA, Nirschl AH, Rendina AR, Tamura JK, Wei A, Wen X, Wurtz NR, Seiffert DA, Wexler RR, Priestley ES. Discovery of novel P1 groups for coagulation factor VIIa inhibition using fragment-based screening. J Med Chem 2015; 58:2799-808. [PMID: 25764119 DOI: 10.1021/jm501982k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A multidisciplinary, fragment-based screening approach involving protein ensemble docking and biochemical and NMR assays is described. This approach led to the discovery of several structurally diverse, neutral surrogates for cationic factor VIIa P1 groups, which are generally associated with poor pharmacokinetic (PK) properties. Among the novel factor VIIa inhibitory fragments identified were aryl halides, lactams, and heterocycles. Crystallographic structures for several bound fragments were obtained, leading to the successful design of a potent factor VIIa inhibitor with a neutral lactam P1 and improved permeability.
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Affiliation(s)
- Daniel L Cheney
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Jeffrey M Bozarth
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | | | | | | | | | - Alexandra H Nirschl
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Alan R Rendina
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | | | - Anzhi Wei
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Xiao Wen
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Nicholas R Wurtz
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Dietmar A Seiffert
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - Ruth R Wexler
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
| | - E Scott Priestley
- †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States
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16
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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17
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Application of molecular modeling to urokinase inhibitors development. BIOMED RESEARCH INTERNATIONAL 2014; 2014:625176. [PMID: 24967388 PMCID: PMC4055159 DOI: 10.1155/2014/625176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/22/2014] [Indexed: 01/01/2023]
Abstract
Urokinase-type plasminogen activator (uPA) plays an important role in the regulation of diverse physiologic and pathologic processes. Experimental research has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients, whereas suppression of proteolytic activity of uPA leads to evident decrease of metastasis. Therefore, uPA has been considered as a promising molecular target for development of anticancer drugs. The present study sets out to develop the new selective uPA inhibitors using computer-aided structural based drug design methods. Investigation involves the following stages: computer modeling of the protein active site, development and validation of computer molecular modeling methods: docking (SOL program), postprocessing (DISCORE program), direct generalized docking (FLM program), and the application of the quantum chemical calculations (MOPAC package), search of uPA inhibitors among molecules from databases of ready-made compounds to find new uPA inhibitors, and design of new chemical structures and their optimization and experimental examination. On the basis of known uPA inhibitors and modeling results, 18 new compounds have been designed, calculated using programs mentioned above, synthesized, and tested in vitro. Eight of them display inhibitory activity and two of them display activity about 10 μM.
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18
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Identification of the first synthetic inhibitors of the type II transmembrane serine protease TMPRSS2 suitable for inhibition of influenza virus activation. Biochem J 2013; 452:331-43. [PMID: 23527573 DOI: 10.1042/bj20130101] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TMPRSS2 (transmembrane serine proteinase 2) is a multidomain type II transmembrane serine protease that cleaves the surface glycoprotein HA (haemagglutinin) of influenza viruses with a monobasic cleavage site, which is a prerequisite for virus fusion and propagation. Furthermore, it activates the fusion protein F of the human metapneumovirus and the spike protein S of the SARS-CoV (severe acute respiratory syndrome coronavirus). Increased TMPRSS2 expression was also described in several tumour entities. Therefore TMPRSS2 emerged as a potential target for drug design. The catalytic domain of TMPRSS2 was expressed in Escherichia coli and used for an inhibitor screen with previously synthesized inhibitors of various trypsin-like serine proteases. Two inhibitor types were identified which inhibit TMPRSS2 in the nanomolar range. The first series comprises substrate analogue inhibitors containing a 4-amidinobenzylamide moiety at the P1 position, whereby some of these analogues possess inhibition constants of approximately 20 nM. An improved potency was found for a second type derived from sulfonylated 3-amindinophenylalanylamide derivatives. The most potent derivative of this series inhibits TMPRSS2 with a K(i) value of 0.9 nM and showed an efficient blockage of influenza virus propagation in human airway epithelial cells. On the basis of the inhibitor studies, a series of new fluorogenic substrates containing a D-arginine residue at the P3 position was synthesized, some of them were efficiently cleaved by TMPRSS2.
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19
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Sathler PC, Lourenço AL, Miceli LA, Rodrigues CR, Albuquerque MG, Cabral LM, Castro HC. Structural model of haptoglobin and its complex with the anticoagulant ecotin variants: structure-activity relationship study and analysis of interactions. J Enzyme Inhib Med Chem 2013; 29:256-62. [PMID: 23477410 DOI: 10.3109/14756366.2013.774389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recently the literature described the binding of Haptoglobin (HP) with ecotin, a fold-specific serine-proteases inhibitor with an anticoagulant profile and produced by Escherichia coli. In this work, we used some in silico and in vitro techniques to evaluate HP 3D-fold and its interaction with wild-type ecotin and two variants. Our data showed HP models conserved trypsin fold, in agreement to the in vitro immunological recognition of HP by trypsin antibodies. The analysis of the three ecotin-HP complexes using the mutants RR and TSRR/R besides the wild type revealed several hydrogen bonds between HP and ecotin secondary site. These data are in agreement with the in vitro PAGE assays that showed the HP-RR complex in native gel conditions. Interestingly, the ternary complex interactions varied depending on the inhibitor structure and site-directed mutation. The interaction of HP with TSRR/R involved new residues compared to wild type, which infers a binding energy increase caused by the mutation.
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20
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Wilcken R, Zimmermann MO, Lange A, Joerger AC, Boeckler FM. Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology. J Med Chem 2013; 56:1363-88. [DOI: 10.1021/jm3012068] [Citation(s) in RCA: 839] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rainer Wilcken
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Markus O. Zimmermann
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Andreas Lange
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Andreas C. Joerger
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Frank M. Boeckler
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
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21
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Swedberg JE, Harris JM. Natural and engineered plasmin inhibitors: applications and design strategies. Chembiochem 2012; 13:336-48. [PMID: 22238174 DOI: 10.1002/cbic.201100673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Indexed: 12/17/2022]
Abstract
The serine protease plasmin is ubiquitously expressed throughout the human body in the form of the zymogen plasminogen. Conversion to active plasmin occurs through enzymatic cleavage by plasminogen activators. The plasminogen activator/plasmin system has a well-established function in the removal of intravascular fibrin deposition through fibrinolysis and the inhibition of plasmin activity; this has found widespread clinical use in reducing perioperative bleeding. Increasing evidence also suggests diverse, although currently less defined, roles for plasmin in a number of physiological and pathological processes relating to extracellular matrix degradation, cell migration and tissue remodelling. In particular, dysregulation of plasmin has been linked to cancer invasion/metastasis and various chronic inflammatory conditions; this has prompted efforts to develop inhibitors of this protease. Although a number of plasmin inhibitors exist, they commonly suffer from poor potency and/or specificity of inhibition that either results in reduced efficacy or prevents clinical use. Consequently, there is a need for further development of high-affinity plasmin inhibitors that maintain selectivity over other serine proteases. This review summarises clearly defined and potential applications for plasmin inhibition. The properties of naturally occurring and engineered plasmin inhibitors are discussed in the context of current knowledge regarding plasmin structure, specificity and function. This includes design strategies to obtain the potency and specificity of inhibition in addition to controlled temporal and spatial distribution tailored for the intended use.
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Affiliation(s)
- Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072 (Australia)
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22
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Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. J Chem Inf Model 2011; 52:199-209. [PMID: 22145575 DOI: 10.1021/ci200468p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Fragment-based drug design (FBDD) starts with finding fragment-sized compounds that are highly ligand efficient and can serve as a core moiety for developing high-affinity leads. Although the core-bound structure of a protein facilitates the construction of leads, effective design is far from straightforward. We show that protein mapping, a computational method developed to find binding hot spots and implemented as the FTMap server, provides information that complements the fragment screening results and can drive the evolution of core fragments into larger leads with a minimal loss or, in some cases, even a gain in ligand efficiency. The method places small molecular probes, the size of organic solvents, on a dense grid around the protein and identifies the hot spots as consensus clusters formed by clusters of several probes. The hot spots are ranked based on the number of probe clusters, which predicts the binding propensity of the subsites and hence their importance for drug design. Accordingly, with a single exception the main hot spot identified by FTMap binds the core compound found by fragment screening. The most useful information is provided by the neighboring secondary hot spots, indicating the regions where the core can be extended to increase its affinity. To quantify this information, we calculate the density of probes from mapping, which describes the binding propensity at each point, and show that the change in the correlation between a ligand position and the probe density upon extending or repositioning the core moiety predicts the expected change in ligand efficiency.
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Affiliation(s)
- David R Hall
- Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA
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23
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Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. ChemMedChem 2011; 6:1049-66. [PMID: 21506273 DOI: 10.1002/cmdc.201000533] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/08/2011] [Indexed: 11/12/2022]
Abstract
The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.
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24
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Schaller J, Gerber SS. The plasmin-antiplasmin system: structural and functional aspects. Cell Mol Life Sci 2011; 68:785-801. [PMID: 21136135 PMCID: PMC11115092 DOI: 10.1007/s00018-010-0566-5] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 09/03/2010] [Accepted: 10/12/2010] [Indexed: 10/18/2022]
Abstract
The plasmin-antiplasmin system plays a key role in blood coagulation and fibrinolysis. Plasmin and α(2)-antiplasmin are primarily responsible for a controlled and regulated dissolution of the fibrin polymers into soluble fragments. However, besides plasmin(ogen) and α(2)-antiplasmin the system contains a series of specific activators and inhibitors. The main physiological activators of plasminogen are tissue-type plasminogen activator, which is mainly involved in the dissolution of the fibrin polymers by plasmin, and urokinase-type plasminogen activator, which is primarily responsible for the generation of plasmin activity in the intercellular space. Both activators are multidomain serine proteases. Besides the main physiological inhibitor α(2)-antiplasmin, the plasmin-antiplasmin system is also regulated by the general protease inhibitor α(2)-macroglobulin, a member of the protease inhibitor I39 family. The activity of the plasminogen activators is primarily regulated by the plasminogen activator inhibitors 1 and 2, members of the serine protease inhibitor superfamily.
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Affiliation(s)
- Johann Schaller
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, Switzerland.
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25
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Szabó G, Veres G, Radovits T, Haider H, Krieger N, Bährle S, Niklisch S, Miesel-Gröschel C, van de Locht A, Karck M. The novel synthetic serine protease inhibitor CU-2010 dose-dependently reduces postoperative blood loss and improves postischemic recovery after cardiac surgery in a canine model. J Thorac Cardiovasc Surg 2010; 139:732-40. [DOI: 10.1016/j.jtcvs.2009.10.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 10/04/2009] [Accepted: 10/31/2009] [Indexed: 11/27/2022]
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26
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Szabó G, Veres G, Radovits T, Haider H, Krieger N, Bährle S, Miesel-Gröschel C, Niklisch S, Karck M, van de Locht A. Effects of novel synthetic serine protease inhibitors on postoperative blood loss, coagulation parameters, and vascular relaxation after cardiac surgery. J Thorac Cardiovasc Surg 2010; 139:181-8; discussion 188. [DOI: 10.1016/j.jtcvs.2009.09.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Revised: 08/09/2009] [Accepted: 09/07/2009] [Indexed: 10/20/2022]
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27
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Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Application of a polarizable force field to calculations of relative protein-ligand binding affinities. Proc Natl Acad Sci U S A 2008; 105:10378-83. [PMID: 18653760 DOI: 10.1073/pnas.0803847105] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An explicitly polarizable force field based exclusively on quantum data is applied to calculations of relative binding affinities of ligands to proteins. Five ligands, differing by replacement of an atom or functional group, in complexes with three serine proteases-trypsin, thrombin, and urokinase-type plasminogen activator-with available experimental binding data are used as test systems. A special protocol of thermodynamic integration was developed and used to provide sufficiently low levels of systematic error along with high numerical efficiency and statistical stability. The calculated results are in excellent quantitative (rmsd = 1.0 kcal/mol) and qualitative (R(2) = 0.90) agreement with experimental data. The potential of the methodology to explain the observed differences in the ligand affinities is also demonstrated.
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29
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Zhu M, Gokhale VM, Szabo L, Munoz RM, Baek H, Bashyam S, Hurley LH, Von Hoff DD, Han H. Identification of a novel inhibitor of urokinase-type plasminogen activator. Mol Cancer Ther 2007; 6:1348-56. [PMID: 17431113 DOI: 10.1158/1535-7163.mct-06-0520] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Urokinase-type plasminogen activator (uPA), a highly restricted serine protease, plays an important role in the regulation of diverse physiologic and pathologic processes. Strong clinical and experimental evidence has shown that elevated uPA expression is associated with cancer progression, metastasis, and shortened survival in patients. uPA has been considered as a promising molecular target for development of anticancer drugs. Here, we report the identification of several new uPA inhibitors using a high-throughput screen from a chemical library. From these uPA inhibitors, molecular modeling and docking studies identified 4-oxazolidinone as a novel lead pharmacophore. Optimization of the 4-oxazolidinone pharmacophore resulted in a series of structurally modified compounds with improved potency and selectivity. One of the 4-oxazolidinone analogues, UK122, showed the highest inhibition of uPA activity. The IC(50) of UK122 in a cell-free indirect uPA assay is 0.2 micromol/L. This compound also showed no or little inhibition of other serine proteases such as thrombin, trypsin, plasmin, and the tissue-type plasminogen activator, indicating its high specificity against uPA. Moreover, UK122 showed little cytotoxicity against CFPAC-1 cells (IC(50) >100 micromol/L) but significantly inhibited the migration and invasion of this pancreatic cancer cell line. Our data show that UK122 could potentially be developed as a new anticancer agent that prevents the invasion and metastasis of pancreatic cancer.
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Affiliation(s)
- Ming Zhu
- Division of Clinical Translational Research, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
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30
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Kochanny MJ, Adler M, Ewing J, Griedel BD, Ho E, Karanjawala R, Lee W, Lentz D, Liang AM, Morrissey MM, Phillips GB, Post J, Sacchi KL, Sakata ST, Subramanyam B, Vergona R, Walters J, White KA, Whitlow M, Ye B, Zhao Z, Shaw KJ. Substituted thiophene-anthranilamides as potent inhibitors of human factor Xa. Bioorg Med Chem 2006; 15:2127-46. [PMID: 17227710 DOI: 10.1016/j.bmc.2006.12.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 11/30/2006] [Accepted: 12/11/2006] [Indexed: 11/22/2022]
Abstract
A series of thiophene-containing non-amidine factor Xa inhibitors is described. Simple methyl-substituted thiophene analogs were relatively weak inhibitors. However, introduction of hydrophilic substituents at C-4 or C-5 of the thiophene afforded inhibitors with low nanomolar potency. Optimization of the thiophene substituent at C-4 afforded subnanomolar inhibitors with improved in vitro anticoagulant activity. Incorporating basic amine substituents on the thiophene increased hydrophilicity and improved anticoagulant activity. The pharmacokinetic profile of one inhibitor was evaluated in dogs, and the X-ray crystal structure of this compound bound to factor Xa provides insight into the observed SAR for binding to factor Xa.
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31
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Schweizer E, Hoffmann-Röder A, Schärer K, Olsen JA, Fäh C, Seiler P, Obst-Sander U, Wagner B, Kansy M, Diederich F. A fluorine scan at the catalytic center of thrombin: C--F, C--OH, and C--OMe bioisosterism and fluorine effects on pKa and log D values. ChemMedChem 2006; 1:611-21. [PMID: 16892401 DOI: 10.1002/cmdc.200600015] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A series of 16 tricyclic thrombin inhibitors was prepared by using the 1,3-dipolar cycloaddition of azomethine ylides derived from 3- or 4-hydroxyproline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide as the key step. The terminal pyrrolidine ring of the inhibitors was systematically substituted to explore the potential bioisosteric behavior of C-F, C-OH, and C-OMe residues pointing into the environment of the catalytic center of a serine protease. X-ray crystal structure analyses revealed a distinct puckering preference of this ring. Substitution by F, HO, and MeO has a strong effect on the basicity of the adjacent pyrrolidine nitrogen center which originates from two sigma-inductive pathways between this center and the electronegative O and F atoms. gem-Difluorination decreases the pKa value of this tertiary amine center to <2, making the conjugated ammonium ion a moderately strong acid. Unexpectedly, F substitution next to the nitrogen center reduced the lipophilicity of the ligands, as revealed by measurements of the logarithmic partition coefficient log D. The biological assays showed that all compounds are thrombin inhibitors with activities between Ki=0.08 and 2.17 microM. Bioisosteric behavior of F, HO, and MeO substituents was observed. Their electronegative F and O atoms undergo energetically similar polar interactions with positively polarized centers, such as the N atom of His 57 which is hydrogen bonded to the catalytic Ser 195. However, for energetically similar polar interactions of C-F, C-OH, and C-OMe to occur, sufficient space is necessary for the accommodation of the Me group of the C-OMe residue, and a H-bond acceptor must be present to prevent unfavorable desolvation of the C-OH residue.
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Affiliation(s)
- Eliane Schweizer
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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32
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Hoffmann-Röder A, Schweizer E, Egger J, Seiler P, Obst-Sander U, Wagner B, Kansy M, Banner DW, Diederich F. Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups into the P Pocket. ChemMedChem 2006; 1:1205-15. [PMID: 17001711 DOI: 10.1002/cmdc.200600124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.
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Affiliation(s)
- Anja Hoffmann-Röder
- Institut für Organische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
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33
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Bottoms CA, White TA, Tanner JJ. Exploring structurally conserved solvent sites in protein families. Proteins 2006; 64:404-21. [PMID: 16700049 DOI: 10.1002/prot.21014] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein-bound water molecules are important components of protein structure, and therefore, protein function and energetics. Although structural conservation of solvent has been studied in a few protein families, a lack of suitable computational tools has hindered more comprehensive analyses. Herein we present a semiautomated computational approach for identifying solvent sites that are conserved among proteins sharing a common three-dimensional structure. This method is tested on six protein families: (1) monodomain cytochrome c, (2) fatty-acid binding protein, (3) lactate/malate dehydrogenase, (4) parvalbumin, (5) phospholipase A2, and (6) serine protease. For each family, the method successfully identified previously known conserved solvent sites. Moreover, the method discovered 22 novel conserved solvent sites, some of which have higher degrees of conservation than the previously known sites. All six families studied had solvent sites with more than 90% conservation and these sites were invariably located in regions of the protein with very high sequence conservation. These results suggest that highly conserved solvent sites, by virtue of their proximity to conserved residues, should be considered as one of the defining three-dimensional structural characteristics of protein families and folds.
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Affiliation(s)
- Christopher A Bottoms
- Department of Chemistry, University of Missouri-Columbia, Columbia, Missouri 65211, USA
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34
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Hansen M, Wind T, Blouse GE, Christensen A, Petersen HH, Kjelgaard S, Mathiasen L, Holtet TL, Andreasen PA. A Urokinase-type Plasminogen Activator-inhibiting Cyclic Peptide with an Unusual P2 Residue and an Extended Protease Binding Surface Demonstrates New Modalities for Enzyme Inhibition. J Biol Chem 2005; 280:38424-37. [PMID: 16141208 DOI: 10.1074/jbc.m505933200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To find new principles for inhibiting serine proteases, we screened phage-displayed random peptide repertoires with urokinase-type plasminogen activator (uPA) as the target. The most frequent of the isolated phage clones contained the disulfide bridge-constrained sequence CSWRGLENHRMC, which we designated upain-1. When expressed recombinantly with a protein fusion partner, upain-1 inhibited the enzymatic activity of uPA competitively with a temperature and pH-dependent K(i), which at 25 degrees C and pH 7.4 was approximately 500 nm. At the same conditions, the equilibrium dissociation constant K(D), monitored by displacement of p-aminobenzamidine from the specificity pocket of uPA, was approximately 400 nm. By an inhibitory screen against other serine proteases, including trypsin, upain-1 was found to be highly selective for uPA. The cyclical structure of upain-1 was indispensable for uPA binding. Alanine-scanning mutagenesis identified Arg(4) of upain-1 as the P(1) residue and indicated an extended binding interaction including the specificity pocket and the 37-, 60-, and 97-loops of uPA and the P(1), P(2), P(3)', P(4)', and the P(5)' residues of upain-1. Substitution with alanine of the P(2) residue, Trp(3), converted upain-1 into a distinct, although poor, uPA substrate. Upain-1 represents a new type of uPA inhibitor that achieves selectivity by targeting uPA-specific surface loops. Most likely, the inhibitory activity depends on its cyclical structure and the unusual P(2) residue preventing the scissile bond from assuming a tetrahedral geometry and thus from undergoing hydrolysis. Peptide-derived inhibitors such as upain-1 may provide novel mechanistic information about enzyme-inhibitor interactions and alternative methodologies for designing effective protease inhibitors.
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Affiliation(s)
- Martin Hansen
- Department of Molecular Biology, University of Aarhus, Gustav Wied's Vej 10C, 8000 Aarhus C, Denmark
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35
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Tang J, Yu CL, Williams SR, Springman E, Jeffery D, Sprengeler PA, Estevez A, Sampang J, Shrader W, Spencer J, Young W, McGrath M, Katz BA. Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. J Biol Chem 2005; 280:41077-89. [PMID: 16199530 DOI: 10.1074/jbc.m506766200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.
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Affiliation(s)
- Jie Tang
- Department of Structural Chemistry, Celera Genomics, South San Francisco, California 94080, USA
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36
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Jensen CM, Lindsay KB, Andreasen P, Skrydstrup T. Synthesis of a Hydroxyethylene Isostere of the Tripeptide Arg-Gly-Leu via a Convergent Acyl-like Radical Addition Strategy. J Org Chem 2005; 70:7512-9. [PMID: 16149778 DOI: 10.1021/jo0505775] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A hydroxyethylene isostere of the tripeptide Arg-Gly-Leu, representing an important fragment of a novel cyclic-peptide-based uPA inhibitor, was synthesized in few steps employing as the key step a samarium diiodide promoted coupling of either the 4-thiopyridyl ester of N(alpha)-Fmoc- or N(alpha)-Cbz-protected L-ornithine with the N-acryloyl derivative of L-leucine methyl ester. Epimerization under the coupling conditions at the chiral center in the alpha-position to the ketone was demonstrated not to take place. A stereoselective reduction of the Cbz-protected aminoketone obtained from this radical reaction was promoted by the same single-electron reducing agent in the presence of methanol providing the syn-amino alcohol with a diastereoselectivity of 85:15. With the use of lithium tri-tert-butoxyaluminum hydride in methanol, the corresponding anti-isomer was obtained almost exclusively. Subsequent elaboration of the ornithine moiety in the anti-isomer by introduction of the guanidine group followed by hydrolysis of the C-terminal ester bond and protection of the alcohol as its tert-butyldimethylsilyl ether provided the desired tripeptide mimic. The long reaction times required for the radical addition reactions with N(delta)-Boc-L-ornithine (up to 5 days) led to a short study where a series of 4-thiopyridyl esters of Cbz-protected amino acids were reacted with two acrylates. Whereas N(delta)-Boc-L-ornithine, alanine, phenylalanine, proline, and leucine all provided the aminoketone in 43-79% yield, valine only afforded traces of the coupling product.
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Affiliation(s)
- Christina M Jensen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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37
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Ilies MA, Supuran CT, Scozzafava A. Therapeutic applications of serine protease inhibitors. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.12.8.1181] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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38
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Jin L, Pandey P, Babine RE, Gorga JC, Seidl KJ, Gelfand E, Weaver DT, Abdel-Meguid SS, Strickler JE. Crystal Structures of the FXIa Catalytic Domain in Complex with Ecotin Mutants Reveal Substrate-like Interactions. J Biol Chem 2005; 280:4704-12. [PMID: 15545266 DOI: 10.1074/jbc.m411309200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thrombosis can lead to life-threatening conditions such as acute myocardial infarction, pulmonary embolism, and stroke. Although commonly used anti-coagulant drugs, such as low molecular weight heparin and warfarin, are effective, they carry a significant risk of inducing severe bleeding complications, and there is a need for safer drugs. Activated Factor XI (FXIa) is a key enzyme in the amplification phase of the coagulation cascade. Anti-human FXI antibody significantly reduces thrombus growth in a baboon thrombosis model without bleeding problems (Gruber, A., and Hanson, S. R. (2003) Blood 102, 953-955). Therefore, FXIa is a potential target for anti-thrombosis therapy. To determine the structure of FXIa, we derived a recombinant catalytic domain of FXI, consisting of residues 370-607 (rhFXI370-607). Here we report the first crystal structure of rhFXI370-607 in complex with a substitution mutant of ecotin, a panserine protease protein inhibitor secreted by Escherichia coli, to 2.2 A resolution. The presence of ecotin not only assisted in the crystallization of the enzyme but also revealed unique structural features in the active site of FXIa. Subsequently, the sequence from P5 to P2' in ecotin was mutated to the FXIa substrate sequence, and the structures of the rhFXI370-607-ecotin mutant complexes were determined. These structures provide us with an understanding of substrate binding interactions of FXIa, the structural information essential for the structure-based design of FXIa-selective inhibitors.
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Affiliation(s)
- Lei Jin
- Daiichi Asubio Medical Research Laboratories LLC, Cambridge, Massachusetts 02139, USA.
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39
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Silva FP, De-Simone SG. S1 subsite in snake venom thrombin-like enzymes: can S1 subsite lipophilicity be used to sort binding affinities of trypsin-like enzymes to small-molecule inhibitors? Bioorg Med Chem 2004; 12:2571-87. [PMID: 15110839 DOI: 10.1016/j.bmc.2004.03.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 03/01/2004] [Accepted: 03/14/2004] [Indexed: 11/27/2022]
Abstract
Thrombin-like enzymes isolated from snake venoms comprise a group of serine proteinases responsible for many important coagulation disorders in the envenomed victims. Besides, these proteinases have great biotechnological interest as antithrombotic agents and as diagnostic tools. However, in spite of the recent overflow of snake venom thrombin-like enzymes (SVTLEs) on protein sequence databases, there is a lack of three-dimensional (3D) structural information on this family. Without such 3D structures available many aspects of the biological function and biochemical properties of these enzymes still remain obscure. Therefore, we have gone through a series of computational techniques, which enabled us to identify the set of residues involved in molecular recognition of inhibitors bound to the S1 subsite of snake venom thrombin-like enzymes (SVTLEs) and ultimately conclude that nonpolar (van der Waals) intermolecular interactions and ligand's hydrophobicity are the most important factors affecting binding affinities to the S1 subsite of a SVTLE isolated from the venom of Lachesis muta muta (Lmm-TLE). Consequently, we have proposed that S1 subsite lipophilicity may be used to sort binding affinities of trypsin-like enzymes to small molecules by showing that the inhibitory potency of several S1-directed compounds follows subsite lipophilicity among Lmm-TLE and other three homologous proteases. Noteworthy, in the course of our analyses we determined that thrombin's S1 subsite should, in fact, be considered less lipophilic than that of trypsin if we account for the presence of the sodium-controlled water channel communicating with the S1 subsite in the coagulant enzyme.
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Affiliation(s)
- Floriano P Silva
- Laboratório de Bioquímica de Proteínas e Peptídeos, Departamento de Bioquímica e Biologia Molecular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
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40
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Katz BA, Luong C, Ho JD, Somoza JR, Gjerstad E, Tang J, Williams SR, Verner E, Mackman RL, Young WB, Sprengeler PA, Chan H, Mortara K, Janc JW, McGrath ME. Dissecting and Designing Inhibitor Selectivity Determinants at the S1 Site Using an Artificial Ala190 Protease (Ala190 uPA). J Mol Biol 2004; 344:527-47. [PMID: 15522303 DOI: 10.1016/j.jmb.2004.09.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 09/14/2004] [Accepted: 09/15/2004] [Indexed: 11/21/2022]
Abstract
A site-directed mutant of the serine protease urokinase-type plasminogen activator (uPA), was produced to assess the contribution of the Ser190 side-chain to the affinity and selectivity of lead uPA inhibitors in the absence of other differences present in comparisons of natural proteases. Crystallography and enzymology involving WT and Ala190 uPA were used to calculate free energy binding contributions of hydrogen bonds involving the Ser190 hydroxyl group (O(gamma)(Ser190)) responsible for the remarkable selectivity of 6-halo-5-amidinoindole and 6-halo-5-amidinobenzimidazole inhibitors toward uPA and against natural Ala190 protease anti-targets. Crystal structures of uPA complexes of novel, active site-directed arylguanidine and 2-aminobenzimidazole inhibitors of WT uPA, together with associated K(i) values for WT and Ala190 uPA, also indicate a significant role of Ser190 in the binding of these classes of uPA inhibitors. Structures and associated K(i) values for a lead inhibitor (CA-11) bound to uPA and to five other proteases, as well as for other leads bound to multiple proteases, help reveal the features responsible for the potency (K(i)=11nM) and selectivity of the remarkably small inhibitor, CA-11. The 6-fluoro-5-amidinobenzimidzole, CA-11, is more than 1000-fold selective against natural Ala190 protease anti-targets, and more than 100-fold selective against other Ser190 anti-targets.
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Affiliation(s)
- Bradley A Katz
- Celera, 180 Kimball Way, South San Francisco, CA 94080, USA.
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41
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Vishweshwar P, Jagadeesh Babu N, Nangia A, Mason SA, Puschmann H, Mondal R, Howard JAK. Variable Temperature Neutron Diffraction Analysis of a Very Short O−H···O Hydrogen Bond in 2,3,5,6-Pyrazinetetracarboxylic Acid Dihydrate: Synthon-Assisted Short Oacid−H···Owater Hydrogen Bonds in a Multicenter Array. J Phys Chem A 2004. [DOI: 10.1021/jp0476848] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Peddy Vishweshwar
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
| | - N. Jagadeesh Babu
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
| | - Ashwini Nangia
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
| | - Sax A. Mason
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
| | - Horst Puschmann
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
| | - Raju Mondal
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
| | - Judith A. K. Howard
- School of Chemistry, University of Hyderabad, Hyderabad 500 046, India, Institut Laue-Langevin (6 rue Jules Horowitz) BP 156, 38042 Grenoble Cedex 9, France, and Department of Chemistry, University of Durham, Durham DH1 3LE, U.K
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42
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Olsen J, Seiler P, Wagner B, Fischer H, Tschopp T, Obst-Sander U, Banner DW, Kansy M, Müller K, Diederich F. A fluorine scan of the phenylamidinium needle of tricyclic thrombin inhibitors: effects of fluorine substitution on pKa and binding affinity and evidence for intermolecular C-F...CN interactions. Org Biomol Chem 2004; 2:1339-52. [PMID: 15105924 DOI: 10.1039/b402515f] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The H-atoms of the phenylamidinium needle of tricyclic thrombin inhibitors, which interacts with Asp189 at the bottom of the selectivity pocket S1 of the enzyme, were systematically exchanged with F-atoms in an attempt to improve the pharmacokinetic properties by lowering the pK(a) value. Both the pK(a) values and the inhibitory constants K(i) against thrombin and trypsin were decreased upon F-substitution. Interestingly, linear free energy relationships (LFERs) revealed that binding affinity against thrombin is much more affected by a decrease in pK(a) than the affinity against trypsin. Surprising effects of F-substitutions in the phenylamidinium needle on the pK(a) value of the tertiary amine centre in the tricyclic scaffold of the inhibitors were observed and subsequently rationalised by X-ray crystallographic analysis and ab initio calculations. Evidence for highly directional intermolecular C-F...CN interactions was obtained by analysis of small-molecule X-ray crystal structures and investigations in the Cambridge Structural Database (CSD).
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Affiliation(s)
- Jacob Olsen
- Laboratorium fur Organische Chemie, ETH-Honggerberg, HCI, CH-8093 Zurich, Switzerland
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Sendzik M, Hui HC. Environmentally friendly and efficient: iron-mediated reduction of 3-methyl-5-aryl-1,2,4-oxadiazoles to benzamidines. Tetrahedron Lett 2003. [DOI: 10.1016/j.tetlet.2003.09.139] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Katz BA, Elrod K, Verner E, Mackman RL, Luong C, Shrader WD, Sendzik M, Spencer JR, Sprengeler PA, Kolesnikov A, Tai VWF, Hui HC, Breitenbucher JG, Allen D, Janc JW. Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors. J Mol Biol 2003; 329:93-120. [PMID: 12742021 DOI: 10.1016/s0022-2836(03)00399-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog. Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (>11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.
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Affiliation(s)
- Bradley A Katz
- Celera, 180 Kimball Way, South San Francisco, CA 94080, USA.
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Sanderson PEJ, Stanton MG, Dorsey BD, Lyle TA, McDonough C, Sanders WM, Savage KL, Naylor-Olsen AM, Krueger JA, Lewis SD, Lucas BJ, Lynch JJ, Yan Y. Azaindoles: moderately basic P1 groups for enhancing the selectivity of thrombin inhibitors. Bioorg Med Chem Lett 2003; 13:795-8. [PMID: 12617893 DOI: 10.1016/s0960-894x(03)00017-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Starting from a 2-amino-6-methylpyridine P1 group and following a strategy of enlarging it whilst reducing its polarity, we have developed a series of potent, moderately basic azaindoles which are intrinsically much more selective for thrombin versus trypsin. Certain pyrazinone acetamide azaindole derivatives have pharmacokinetic parameters after oral administration to dogs, or efficacy in vitro, comparable to an optimized pyrazinone acetamide 2-amino-6-methylpyridine derivative.
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Affiliation(s)
- Philip E J Sanderson
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA.
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Reyda S, Sohn C, Klebe G, Rall K, Ullmann D, Jakubke HD, Stubbs MT. Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity. J Mol Biol 2003; 325:963-77. [PMID: 12527302 DOI: 10.1016/s0022-2836(02)01337-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In order to investigate issues of selectivity and specificity in protein-ligand interactions, we have undertaken the reconstruction of the binding pocket of human factor Xa in the structurally related rat trypsin by site-directed mutagenesis. Three sequential regions (the "99"-, the "175"- and the "190"- loops) were selected as representing the major structural differences between the ligand binding sites of the two enzymes. Wild-type rat trypsin and variants X99rT and X(99/175/190)rT were expressed in yeast, and analysed for their interaction with factor Xa and trypsin inhibitors. For most of the inhibitors studied, progressive loop replacement at the trypsin surface resulted in inhibitory profiles akin to factor Xa. Crystals of the variants were obtained in the presence of benzamidine (3), and could be soaked with the highly specific factor Xa inhibitor (1). Binding of the latter to X99rT results in a series of structural adaptations to the ligand, including the establishment of an "aromatic box" characteristic of factor Xa. In X(99/175/190)rT, introduction of the 175-loop results in a surprising re-orientation of the "intermediate helix", otherwise common to trypsin and factor Xa. The re-orientation is accompanied by an isomerisation of the Cys168-Cys182 disulphide bond, and burial of the critical Phe174 side-chain. In the presence of (1), a major re-organisation of the binding site takes place to yield a geometry identical to that of factor Xa. In all, binding of (1) to trypsin and its variants results in significant structural rearrangements, inducing a binding surface strongly reminiscent of factor Xa, against which the inhibitor was optimised. The structural data reveal a plasticity of the intermediate helix, which has been implicated in the functional cofactor dependency of many trypsin-like serine proteinases. This approach of grafting loops onto scaffolds of known related structures may serve to bridge the gap between structural genomics and drug design.
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Affiliation(s)
- Sabine Reyda
- Institut für Pharmazeutische Chemie der Philipps-Universität Marburg, Marbacher Weg 6, D35032, Marburg, Germany
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Betz SF, Baxter SM, Fetrow JS. Function first: a powerful approach to post-genomic drug discovery. Drug Discov Today 2002; 7:865-71. [PMID: 12546953 DOI: 10.1016/s1359-6446(02)02398-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In the post-genomic era, pharmaceutical researchers must evaluate vast numbers of protein sequences and formulate novel, intelligent strategies for identifying valid targets and discovering leads against them. The identification of small molecules that selectively target proteins or protein families will be aided by knowing the function and/or the structure of the target(s). By identifying protein function first, efficiencies are gained that allow subsequent focus of resources on particular protein families of interest. This article reviews current proteomic-scale approaches to identifying function as a way of accelerating lead discovery.
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Affiliation(s)
- Stephen F Betz
- GeneFormatics, 5830 Oberlin Drive, Suite 200, San Diego, CA 92121, USA
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Mackman RL, Hui HC, Breitenbucher JG, Katz BA, Luong C, Martelli A, McGee D, Radika K, Sendzik M, Spencer JR, Sprengeler PA, Tario J, Verner E, Wang J. 2-(2-Hydroxy-3-alkoxyphenyl)-1H-benzimidazole-5-carboxamidine derivatives as potent and selective urokinase-type plasminogen activator inhibitors. Bioorg Med Chem Lett 2002; 12:2019-22. [PMID: 12113832 DOI: 10.1016/s0960-894x(02)00311-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The development of potent and selective urokinase-type plasminogen activator (uPA) inhibitors based on the lead molecule 2-(2-hydroxy-3-ethoxyphenyl)-1H-benzimidazole-5-carboxamidine (3a) is described.
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Spencer JR, McGee D, Allen D, Katz BA, Luong C, Sendzik M, Squires N, Mackman RL. 4-Aminoarylguanidine and 4-aminobenzamidine derivatives as potent and selective urokinase-type plasminogen activator inhibitors. Bioorg Med Chem Lett 2002; 12:2023-6. [PMID: 12113833 DOI: 10.1016/s0960-894x(02)00312-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The structure-based design of potent and selective urokinase-type plasminogen activator (uPA) inhibitors with 4-aminoarylamidine or 4-aminoarylguanidine S1 binding groups, is described.
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