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Borovsky D, Rougé P. Cloning and characterization of Aedes aegypti blood downregulated chymotrypsin II. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 113:e22018. [PMID: 37106507 DOI: 10.1002/arch.22018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Aedes aegypti adult and larval blood downregulated chymotrypsin II was cloned, sequenced and its 3D conformation modeled. Cloning of the enzymes from adult and larval guts indicated that both genes sit at the same location on Chromosome 2. Genomic analyses showed that larval and adult genes are the same and both have four exons and three introns that are located on an 8.32 Kb DNA in direction with the Ae. aegypti genome. The adult and larval transcript synthesis is controlled by alternative splicing explaining small difference in the amino acids sequences. Chymotrypsin II that was extracted from guts of sugar-fed and at 48 after blood feeding showed a pH optimum of 4-5 with a broad shoulder of activity from pH 6 to 10. Dot blot analyses show that the enzyme's transcript is downregulated after females take a blood meal and upregulated at 48 h after the blood meal. A Chymotrypsin II transcript was also detected in the larval gut during different times of larval developmental stages, indication that Ae. aegypti chymotrypsin II is synthesized by adults and larval guts. The possibility that JH III and 20HE play an active role in the regulation is discussed.
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Affiliation(s)
- Dov Borovsky
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz School of Medicine, Aurora, Colorado, USA
| | - Pierre Rougé
- UMR 152 Pharma-Dev, Faculté des Sciences Pharmaceutiques, Institut de Recherche et Développement, Université Toulouse 3, Toulouse, France
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2
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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3
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Beckmann AM, Gilberg E, Gattner S, Huang TL, Vanden Eynde JJ, Mayence A, Bajorath J, Stirnberg M, Gütschow M. Evaluation of bisbenzamidines as inhibitors for matriptase-2. Bioorg Med Chem Lett 2016; 26:3741-5. [DOI: 10.1016/j.bmcl.2016.05.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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4
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Kim Y, Kankanamalage ACG, Damalanka VC, Weerawarna PM, Groutas WC, Chang KO. Potent inhibition of enterovirus D68 and human rhinoviruses by dipeptidyl aldehydes and α-ketoamides. Antiviral Res 2015; 125:84-91. [PMID: 26658373 PMCID: PMC4698184 DOI: 10.1016/j.antiviral.2015.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/21/2015] [Accepted: 11/23/2015] [Indexed: 01/17/2023]
Abstract
Enterovirus D68 (EV-D68) is an emerging pathogen responsible for mild to severe respiratory infections that occur mostly in infants, children and teenagers. EV-D68, one of more than 100 non-polio enteroviruses, is acid-labile and biologically similar to human rhinoviruses (HRV) (originally classified as HRV87). However, there is no approved preventive or therapeutic measure against EV-D68, HRV, or other enteroviruses. In this study, we evaluated the antiviral activity of series of dipeptidyl compounds against EV-D68 and HRV strains, and demonstrated that several peptidyl aldehyde and α-ketoamide peptidyl compounds are potent inhibitors of EV-D68 and HRV strains with high in-vitro therapeutic indices (>1000). One of the α-ketoamide compounds is shown to have favorable pharmacokinetics profiles, including a favorable oral bioavailability in rats. Recent successful development of α-ketoamide protease inhibitors against hepatitis C virus suggests these compounds may have a high potential for further optimization and development against emerging EV-D68, as well as HRV. Series of dipeptidyl aldehyde or ketomide compounds were highly effective against enterovirus-D68 and human rhinoviruses. The highly effective ketoamide compound is shown to have favorable pharmacokinetics profiles. These may have a high potential for further antiviral development against emerging enterovirus-D68 and human rhinoviruses.
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Affiliation(s)
- Yunjeong Kim
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | | | | | | | - William C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS, USA.
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine and Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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5
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He LW, Dai WC, Li NG. Development of Orally Active Thrombin Inhibitors for the Treatment of Thrombotic Disorder Diseases. Molecules 2015; 20:11046-62. [PMID: 26083038 PMCID: PMC6272601 DOI: 10.3390/molecules200611046] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022] Open
Abstract
Thrombotic disorders represent the major share of the various cardiovascular diseases, and significant progress has been made in the development of synthetic thrombin inhibitors as new anticoagulants. In addition to the development of highly potent and selective inhibitors with improved safety and suitable half-life, several allosteric inhibitors have been designed and synthesized, that did not fully nullify the procoagulant signal and thus could result in reduced bleeding complications. Furthermore, natural products with thrombin inhibitory activity have been isolated, and some natural products have been modified in order to improve their inhibitory activity and metabolic stability. This review summarizes the development of orally active thrombin inhibitors for the treatment of thrombotic disorder diseases, which could serve as a reference for the interested researchers.
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Affiliation(s)
- Li-Wei He
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Wei-Chen Dai
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Nian-Guang Li
- Department of Medicinal Chemistry, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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6
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Kankanamalage ACG, Kim Y, Weerawarna PM, Uy RAZ, Damalanka VC, Mandadapu SR, Alliston KR, Mehzabeen N, Battaile KP, Lovell S, Chang KO, Groutas WC. Structure-guided design and optimization of dipeptidyl inhibitors of norovirus 3CL protease. Structure-activity relationships and biochemical, X-ray crystallographic, cell-based, and in vivo studies. J Med Chem 2015; 58:3144-55. [PMID: 25761614 PMCID: PMC4484267 DOI: 10.1021/jm5019934] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.
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Affiliation(s)
| | - Yunjeong Kim
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | | | | | | | | | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260
| | - Nurjahan Mehzabeen
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kevin P. Battaile
- IMCA-CAT, Hauptman-Woodward Medical Research Institute, APS Argonne National Laboratory, Argonne, IL 60439
| | - Scott Lovell
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
| | - Kyeong-Ok Chang
- Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas 66506
| | - William C. Groutas
- Protein Structure Laboratory, The University of Kansas, Lawrence, Kansas 66047
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7
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Schomburg KT, Rarey M. Benchmark Data Sets for Structure-Based Computational Target Prediction. J Chem Inf Model 2014; 54:2261-74. [DOI: 10.1021/ci500131x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Karen T. Schomburg
- Center
for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
| | - Matthias Rarey
- Center
for Bioinformatics, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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8
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Yin X, Scalia A, Leroy L, Cuttitta CM, Polizzo GM, Ericson DL, Roessler CG, Campos O, Ma MY, Agarwal R, Jackimowicz R, Allaire M, Orville AM, Sweet RM, Soares AS. Hitting the target: fragment screening with acoustic in situ co-crystallization of proteins plus fragment libraries on pin-mounted data-collection micromeshes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1177-89. [PMID: 24816088 PMCID: PMC4014116 DOI: 10.1107/s1399004713034603] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/24/2013] [Indexed: 11/17/2022]
Abstract
Acoustic droplet ejection (ADE) is a powerful technology that supports crystallographic applications such as growing, improving and manipulating protein crystals. A fragment-screening strategy is described that uses ADE to co-crystallize proteins with fragment libraries directly on MiTeGen MicroMeshes. Co-crystallization trials can be prepared rapidly and economically. The high speed of specimen preparation and the low consumption of fragment and protein allow the use of individual rather than pooled fragments. The Echo 550 liquid-handling instrument (Labcyte Inc., Sunnyvale, California, USA) generates droplets with accurate trajectories, which allows multiple co-crystallization experiments to be discretely positioned on a single data-collection micromesh. This accuracy also allows all components to be transferred through small apertures. Consequently, the crystallization tray is in equilibrium with the reservoir before, during and after the transfer of protein, precipitant and fragment to the micromesh on which crystallization will occur. This strict control of the specimen environment means that the crystallography experiments remain identical as the working volumes are decreased from the few microlitres level to the few nanolitres level. Using this system, lysozyme, thermolysin, trypsin and stachydrine demethylase crystals were co-crystallized with a small 33-compound mini-library to search for fragment hits. This technology pushes towards a much faster, more automated and more flexible strategy for structure-based drug discovery using as little as 2.5 nl of each major component.
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Affiliation(s)
- Xingyu Yin
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, NY 11794-5215, USA
- Nanjing University, Nanjing, Jiangsu, People’s Republic of China
| | - Alexander Scalia
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biological Sciences, Binghamton University, 4400 Vestal Parkway East, NY 13902, USA
| | - Ludmila Leroy
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- CAPES Foundation, Ministry of Education of Brazil, 70040-020 Brasilia-DF, Brazil
- Universidade Federal de Minas Gerais, 6627 Av. Antonio Carlos, 31270-901 Belo Horizonte-MG, Brazil
| | - Christina M. Cuttitta
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Center for Developmental Neuroscience and Department of Biology, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314, USA
| | - Gina M. Polizzo
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- St Joseph’s College, 155 West Roe Boulevard, East Patchogue, NY 11772, USA
| | - Daniel L. Ericson
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biomedical Engineering, University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260, USA
| | - Christian G. Roessler
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Olven Campos
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Department of Biological Science, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33414, USA
| | - Millie Y. Ma
- Office of Educational Programs, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Comsewogue High School, 565 Bicycle Path, Port Jefferson Station, NY 11776, USA
| | - Rakhi Agarwal
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Rick Jackimowicz
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Marc Allaire
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Allen M. Orville
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
- Biosciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Robert M. Sweet
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
| | - Alexei S. Soares
- Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY 11973-5000, USA
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9
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Gardarsson H, Schweizer WB, Trapp N, Diederich F. Structures and Properties of Molecular Torsion Balances to Decipher the Nature of Substituent Effects on the Aromatic Edge-to-Face Interaction. Chemistry 2014; 20:4608-16. [DOI: 10.1002/chem.201304810] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 11/10/2022]
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10
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Potent inhibition of norovirus by dipeptidyl α-hydroxyphosphonate transition state mimics. Bioorg Med Chem Lett 2013; 23:5941-4. [PMID: 24054123 DOI: 10.1016/j.bmcl.2013.08.073] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/12/2013] [Accepted: 08/15/2013] [Indexed: 12/16/2022]
Abstract
The design, synthesis, and evaluation of a series of dipeptidyl α-hydroxyphosphonates is reported. The synthesized compounds displayed high anti-norovirus activity in a cell-based replicon system, as well as high enzyme selectivity.
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11
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Active site mapping of trypsin, thrombin and matriptase-2 by sulfamoyl benzamidines. Bioorg Med Chem 2012; 20:6489-505. [DOI: 10.1016/j.bmc.2012.08.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 08/16/2012] [Indexed: 12/16/2022]
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12
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Cubrilovic D, Biela A, Sielaff F, Steinmetzer T, Klebe G, Zenobi R. Quantifying protein-ligand binding constants using electrospray ionization mass spectrometry: a systematic binding affinity study of a series of hydrophobically modified trypsin inhibitors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1768-77. [PMID: 22869298 DOI: 10.1007/s13361-012-0451-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 07/12/2012] [Accepted: 07/17/2012] [Indexed: 05/22/2023]
Abstract
NanoESI-MS is used for determining binding strengths of trypsin in complex with two different series of five congeneric inhibitors, whose binding affinity in solution depends on the size of the P3 substituent. The ligands of the first series contain a 4-amidinobenzylamide as P1 residue, and form a tight complex with trypsin. The inhibitors of the second series have a 2-aminomethyl-5-chloro-benzylamide as P1 group, and represent a model system for weak binders. The five different inhibitors of each group are based on the same scaffold and differ only in the length of the hydrophobic side chain of their P3 residue, which modulates the interactions in the S3/4 binding pocket of trypsin. The dissociation constants (K(D)) for high affinity ligands investigated by nanoESI-MS ranges from 15 nM to 450 nM and decreases with larger hydrophobic P3 side chains. Collision-induced dissociation (CID) experiments of five trypsin and benzamidine-based complexes show a correlation between trends in K(D) and gas-phase stability. For the second inhibitor series we could show that the effect of imidazole, a small stabilizing additive, can avoid the dissociation of the complex ions and as a result increases the relative abundance of weakly bound complexes. Here the K(D) values ranging from 2.9 to 17.6 μM, some 1-2 orders of magnitude lower than the first series. For both ligand series, the dissociation constants (K(D)) measured via nanoESI-MS were compared with kinetic inhibition constants (K(i)) in solution.
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Affiliation(s)
- Dragana Cubrilovic
- Department of Chemistry and Applied Biosciences, ETH Zurich, Switzerland
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13
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Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores. J Comput Aided Mol Des 2012; 26:647-59. [PMID: 22476578 DOI: 10.1007/s10822-012-9567-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Two families of binding affinity estimation methodologies are described which were utilized in the SAMPL3 trypsin/fragment binding affinity challenge. The first is a free energy decomposition scheme based on a thermodynamic cycle, which included separate contributions from enthalpy and entropy of binding as well as a solvent contribution. Enthalpic contributions were estimated with PM6-DH2 semiempirical quantum mechanical interaction energies, which were modified with a statistical error correction procedure. Entropic contributions were estimated with the rigid-rotor harmonic approximation, and solvent contributions to the free energy were estimated with several different methods. The second general methodology is the empirical score LISA, which contains several physics-based terms trained with the large PDBBind database of protein/ligand complexes. Here we also introduce LISA+, an updated version of LISA which, prior to scoring, classifies systems into one of four classes based on a ligand's hydrophobicity and molecular weight. Each version of the two methodologies (a total of 11 methods) was trained against a compiled set of known trypsin binders available in the Protein Data Bank to yield scaling parameters for linear regression models. Both raw and scaled scores were submitted to SAMPL3. Variants of LISA showed relatively low absolute errors but also low correlation with experiment, while the free energy decomposition methods had modest success when scaling factors were included. Nonetheless, re-scaled LISA yielded the best predictions in the challenge in terms of RMS error, and six of these models placed in the top ten best predictions by RMS error. This work highlights some of the difficulties of predicting binding affinities of small molecular fragments to protein receptors as well as the benefit of using training data.
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14
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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15
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1172] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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16
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Sanders JM. Optimal π-Stacking Interaction Energies in Parallel-Displaced Aryl/Aryl Dimers are Predicted by the Dimer Heavy Atom Count. J Phys Chem A 2010; 114:9205-11. [DOI: 10.1021/jp912094q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John M. Sanders
- Department of Chemistry Modeling and Informatics, Merck Research Laboratories, West Point, Pennsylvania 19486
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17
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Structural binding evidence of the trypanocidal drugs berenil and pentacarinate active principles to a serine protease model. Int J Biol Macromol 2010; 46:502-11. [PMID: 20356563 DOI: 10.1016/j.ijbiomac.2010.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2010] [Revised: 03/12/2010] [Accepted: 03/16/2010] [Indexed: 11/22/2022]
Abstract
Bovine trypsin is a model system for the serine protease class of enzymes, which is an important target for contemporary medicinal chemistry. Some structural and thermodynamic reports are available on its interaction with benzamidine-based compounds but no structural information is available so far on its binding modes to the active principles of the trypanocidal drugs Pentacarinate (pentamidine) and Berenil (diminazene). The crystallographic structures of bovine beta-trypsin in complex with the ligands were determined to a resolution of 1.57 A (diminazene) and 1.70 A (diminazene and pentamidine). The second benzamidine moieties in these inhibitors are bound to the enzyme in different hot spots and only few hydrogen bonds mediate these interactions. Thermodynamic parameters for the association of pentamidine with beta-trypsin reveal that this inhibitor has about 1.3-fold lower affinity than diminazene. Moreover its binding mode resembles other benzamidine-based compounds that assess the aryl binding pocket of the enzyme; however, with almost 2.5-fold higher affinity. This is the first structural evidence of the binding of Berenil and Pentacarinate active principles trypanocidal drugs to serine proteases.
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19
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Page MJ, Carrell CJ, Di Cera E. Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin. J Mol Biol 2008; 378:666-72. [PMID: 18377928 DOI: 10.1016/j.jmb.2008.03.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 02/29/2008] [Accepted: 03/04/2008] [Indexed: 11/28/2022]
Abstract
Some trypsin-like proteases are endowed with Na(+)-dependent allosteric enhancement of catalytic activity, but this important mechanism has been difficult to engineer in other members of the family. Replacement of 19 amino acids in Streptomyces griseus trypsin targeting the active site and the Na(+)-binding site were found necessary to generate efficient Na(+) activation. Remarkably, this property was linked to the acquisition of a new substrate selectivity profile similar to that of factor Xa, a Na(+)-activated protease involved in blood coagulation. The X-ray crystal structure of the mutant trypsin solved to 1.05 A resolution defines the engineered Na(+) site and active site loops in unprecedented detail. The results demonstrate that trypsin can be engineered into an efficient allosteric protease, and that Na(+) activation is interwoven with substrate selectivity in the trypsin scaffold.
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Affiliation(s)
- Michael J Page
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Box 8231, St. Louis, MO 63110, USA
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20
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Lindner HA, Alary A, Wilke M, Sulea T. Probing the Acyl-Binding Pocket of Aminoacylase-1. Biochemistry 2008; 47:4266-75. [DOI: 10.1021/bi702156h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Holger A. Lindner
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
| | - Alain Alary
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
| | - Marsha Wilke
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
| | - Traian Sulea
- Biotechnology Research Institute, National Research Council Canada, 6100 Royalmount Avenue, Montreal, Quebec, Canada H4P 2R2
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Ersmark K, Del Valle J, Hanessian S. Aeruginosine: Chemie und Biologie der Serinprotease-Inhibitoren. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200605219] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Ersmark K, Del Valle J, Hanessian S. Chemistry and Biology of the Aeruginosin Family of Serine Protease Inhibitors. Angew Chem Int Ed Engl 2008; 47:1202-23. [DOI: 10.1002/anie.200605219] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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