1
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de Sousa Cutrim TA, Barcelos FF, Meireles LM, Rodrigues Gazolla PA, Almeida Lima ÂM, Teixeira RR, Moreira LC, de Queiroz VT, Almeida Barbosa LC, Bezerra Morais PA, do Nascimento CJ, Junker J, Costa AV, Fronza M, Scherer R. Design, synthesis, docking studies and bioactivity evaluation of 1,2,3-triazole eugenol derivatives. Future Med Chem 2024; 16:1883-1897. [PMID: 39157870 PMCID: PMC11486170 DOI: 10.1080/17568919.2024.2385292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/17/2024] [Indexed: 08/20/2024] Open
Abstract
Aim: The design, synthesis, docking studies and evaluation of the in vitro antifungal and cytotoxic properties of eugenol (EUG) containing 1,2,3-triazole derivatives are reported. Most of the derivatives have not been reported.Materials & methods: The EUG derivatives were synthesized, molecular docked and tested for their antifungal activity.Results: The compounds showed potent antifungal activity against Trichophyton rubrum, associated with dermatophytosis. Compounds 2a and 2i exhibited promising results, with 2a being four-times more potent than EUG. The binding mode prediction was similar to itraconazole in the lanosterol-14-α-demethylase wild-type and G73E mutant binding sites. Additionally, the pharmacokinetic profile prediction suggests good gastrointestinal absorption and potential oral administration.Conclusion: Compound 2a is a promising antifungal agent against dermatophytosis caused by T. rubrum.
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Affiliation(s)
- Thiago Antonio de Sousa Cutrim
- Universidade de Vila Velha, Departamento de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
| | - Fernando Fontes Barcelos
- Universidade de Vila Velha, Programa de Pós-Graduação em Biotecnologia Vegetal, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
| | - Leandra Martins Meireles
- Universidade de Vila Velha, Departamento de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
| | - Poliana Aparecida Rodrigues Gazolla
- Departamento de Química e Física, Grupo de Pesquisa de Estudos Aplicados em Produtos Naturais e Síntese Orgânica (GEAPS), Universidade Federal do Espírito Santo, Alto Universitário, s/n, Alegre, Espírito Santo State, 29500-000, Brazil
| | - Ângela Maria Almeida Lima
- Departamento de Química e Física, Grupo de Pesquisa de Estudos Aplicados em Produtos Naturais e Síntese Orgânica (GEAPS), Universidade Federal do Espírito Santo, Alto Universitário, s/n, Alegre, Espírito Santo State, 29500-000, Brazil
| | - Róbson Ricardo Teixeira
- Departamento de Química, Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/nViçosa, Minas Gerais State, 36570-900, Brazil
| | - Luiza Carvalheira Moreira
- Departamento de Química, Grupo de Síntese e Pesquisa de Compostos Bioativos (GSPCB), Universidade Federal de Viçosa, Av. P.H. Rolfs, s/nViçosa, Minas Gerais State, 36570-900, Brazil
| | - Vagner Tebaldi de Queiroz
- Departamento de Química e Física, Grupo de Pesquisa de Estudos Aplicados em Produtos Naturais e Síntese Orgânica (GEAPS), Universidade Federal do Espírito Santo, Alto Universitário, s/n, Alegre, Espírito Santo State, 29500-000, Brazil
| | - Luiz Cláudio Almeida Barbosa
- Departamento de Química, Universidade Federal de Minas Gerais, Av. Antonio Carlos, 6627, Belo Horizonte, Minas Gerais State, 31270-901, Brazil
| | - Pedro Alves Bezerra Morais
- Departamento de Química e Física, Grupo de Pesquisa de Estudos Aplicados em Produtos Naturais e Síntese Orgânica (GEAPS), Universidade Federal do Espírito Santo, Alto Universitário, s/n, Alegre, Espírito Santo State, 29500-000, Brazil
| | - Cláudia Jorge do Nascimento
- Departamento de Ciências Naturais, Instituto de Biociências, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Av. Pauster, Rio de Janeiro, Rio de Janeiro State, 22290-240, Brazil
| | - Jochen Junker
- Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Av. Brasil, 4365, Rio de Janeiro, Rio de Janeiro State, 21040-900, Brazil
| | - Adilson Vidal Costa
- Departamento de Química e Física, Grupo de Pesquisa de Estudos Aplicados em Produtos Naturais e Síntese Orgânica (GEAPS), Universidade Federal do Espírito Santo, Alto Universitário, s/n, Alegre, Espírito Santo State, 29500-000, Brazil
| | - Marcio Fronza
- Universidade de Vila Velha, Departamento de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
- Universidade de Vila Velha, Programa de Pós-Graduação em Biotecnologia Vegetal, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
| | - Rodrigo Scherer
- Universidade de Vila Velha, Departamento de Farmácia, Programa de Pós-Graduação em Ciências Farmacêuticas, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
- Universidade de Vila Velha, Programa de Pós-Graduação em Biotecnologia Vegetal, Av. Comissário José Dantas de Melo, 21, Vila Velha, Espírito Santo State, 29102-770, Brazil
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2
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Wang Y, Liu Z, Mazumder A, Gianopoulos CG, Kirschbaum K, Peteanu LA, Jin R. Tailoring Carbon Tails of Ligands on Au 52(SR) 32 Nanoclusters Enhances the Near-Infrared Photoluminescence Quantum Yield from 3.8 to 18.3. J Am Chem Soc 2023; 145:26328-26338. [PMID: 37982713 DOI: 10.1021/jacs.3c09846] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
One of the important factors that determine the photoluminescence (PL) properties of gold nanoclusters pertain to the surface. In this study, four Au52(SR)32 nanoclusters that feature a series of aromatic thiolate ligands (-SR) with different bulkiness at the para-position are synthesized and investigated. The near-infrared (NIR) photoluminescence (peaks at 900-940 nm) quantum yield (QY) is largely enhanced with a decrease in the ligand's para-bulkiness. Specifically, the Au52(SR)32 capped with the least bulky p-methylbenzenethiolate (p-MBT) exhibits the highest PLQY (18.3% at room temperature in non-degassed dichloromethane), while Au52 with the bulkiest tert-butylbenzenethiolate (TBBT) only gives 3.8%. The large enhancement of QY with fewer methyl groups on the ligands implies a nonradiative decay via the multiphonon process mediated by C-H bonds. Furthermore, single-crystal X-ray diffraction (SCXRD) comparison of Au52(p-MBT)32 and Au52(TBBT)32 reveals that fewer methyl groups at the para-position lead to a stronger interligand π···π stacking on the Au52 core, thus restricting ligand vibrations and rotations. The emission nature is identified to be phosphorescence and thermally activated delayed fluorescence (TADF) based on the PL lifetime, 3O2 quenching, and temperature-dependent PL and absorption studies. The 1O2 generation efficiencies for the four Au52(SR)32 NCs follow the same trend as the observed PL performance. Overall, the highly NIR-luminescent Au52(p-MBT)32 nanocluster and the revealed mechanisms are expected to find future applications.
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Affiliation(s)
- Yitong Wang
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Zhongyu Liu
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Abhrojyoti Mazumder
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | | | - Kristin Kirschbaum
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606, United States
| | - Linda A Peteanu
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Rongchao Jin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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3
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Parker JL, Kato T, Kuteyi G, Sitsel O, Newstead S. Molecular basis for selective uptake and elimination of organic anions in the kidney by OAT1. Nat Struct Mol Biol 2023; 30:1786-1793. [PMID: 37482561 PMCID: PMC10643130 DOI: 10.1038/s41594-023-01039-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023]
Abstract
In mammals, the kidney plays an essential role in maintaining blood homeostasis through the selective uptake, retention or elimination of toxins, drugs and metabolites. Organic anion transporters (OATs) are responsible for the recognition of metabolites and toxins in the nephron and their eventual urinary excretion. Inhibition of OATs is used therapeutically to improve drug efficacy and reduce nephrotoxicity. The founding member of the renal organic anion transporter family, OAT1 (also known as SLC22A6), uses the export of α-ketoglutarate (α-KG), a key intermediate in the Krebs cycle, to drive selective transport and is allosterically regulated by intracellular chloride. However, the mechanisms linking metabolite cycling, drug transport and intracellular chloride remain obscure. Here, we present cryogenic-electron microscopy structures of OAT1 bound to α-KG, the antiviral tenofovir and clinical inhibitor probenecid, used in the treatment of Gout. Complementary in vivo cellular assays explain the molecular basis for α-KG driven drug elimination and the allosteric regulation of organic anion transport in the kidney by chloride.
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Affiliation(s)
- Joanne L Parker
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Takafumi Kato
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Gabriel Kuteyi
- Department of Biochemistry, University of Oxford, Oxford, UK
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Oleg Sitsel
- Department of Biochemistry, University of Oxford, Oxford, UK
- Max Planck Institute of Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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4
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Darbyshire AL, Wolthers KR. Expanding the β-substitution reactions of serine synthase through mutagenesis of aromatic active site residues. Arch Biochem Biophys 2023; 746:109727. [PMID: 37625767 DOI: 10.1016/j.abb.2023.109727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023]
Abstract
The Gram-negative bacterium, Fusobacterium nucleatum, possesses a fold II type pyridoxal 5'-phosphate-dependent enzyme that catalyzes the reversible β-replacement of l-cysteine and l-serine, generating H2S and H2O, respectively. This enzyme, termed serine synthase (FN1055), contains an active site Asp232 that serves as a general base in the activation of a water molecule for nucleophilic attack of the ⍺-aminoacrylate intermediate. A network of hydrophobic residues surrounding Asp232 are key to catalysis as they increase the basicity of the side chain. However, these residues severely restrict the range of nucleophilic substrates that can react with the ⍺-aminoacrylate, making the enzyme an ineffective biocatalyst for noncanonical amino acid biosynthesis. Herein, we systematically substituted four aromatic active residues (Trp99, Phe125, Phe148 and Phe234) to an alanine to determine their catalytic importance in serine/cysteine synthase reactions and if their substitution could broaden the scope of nucleophiles that could react with the ⍺-aminoacrylate intermediate. All four single site mutants W99A, F125A, F148A, and F234A could form the ⍺-aminoacrylate intermediate upon reaction with either l-cysteine or l-serine; however, the rate constant associated with the elimination of the β-hydroxyl group from l-serine was 150 to 200-fold lower in the F125A and F148A variants. Substitution of Phe125 and Phe148, situated ∼3-4 Å from the general base, also abolished the serine synthase reaction due to their inability to activate a water molecule for nucleophilic attack of the ⍺-aminoacrylate. Overall, the mutational studies indicate that the clustering of aromatic residues disproportionately benefits the serine synthase reaction as they increase the binding affinity for l-cysteine, decrease the binding of the product, l-serine, and promote the activation of a water molecule. Notably, the aminoacrylate species present in F125A and F148A was able to react with thiophenol, signifying that serine synthase has biocatalytic potential in the synthesis of noncanonical amino acids.
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Affiliation(s)
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, Canada.
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5
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Godinez J, Lee CY, Schwans JP. Synthesis and evaluation of Fmoc-amino esters and amides bearing a substrate like quaternary ammonium group as selective butyrylcholinesterase inhibitors. Bioorg Med Chem Lett 2023; 92:129392. [PMID: 37364726 DOI: 10.1016/j.bmcl.2023.129392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
The depletion of the neurotransmitter acetylcholine has been suggested to contribute to the reduced cognitive function observed in individuals suffering from neurodegenerative diseases such as Alzheimer's Disease (AD). For the two major cholinesterases, butyrylcholinesterase (BChE) and acetylcholinesterase (AChE), increased BChE activity observed in individuals with AD has been suggested to deplete acetylcholine levels. To reduce acetylcholine degradation and help restore the pool of the neurotransmitter, specific and potent BChE inhibitors are sought. Our previous findings have identified 9-fluorenylmethoxycarbonyl (Fmoc) amino acid-based inhibitors as effective BChE inhibitors. The amino acid-based compounds offered the opportunity to survey a range of structural features to enhance interactions with the enzyme active site. As enzymes interact with features of their substrates, incorporation of substrate-like features was predicted to lead to better inhibitors. Specifically, incorporation of a trimethylammonium moiety to mimic the cationic group of acetylcholine may lead to increased potency and selectivity. To test this model, a series of inhibitors bearing a cationic trimethylammonium group were synthesized, purified, and characterized. While the Fmoc-ester derivatives inhibited the enzyme, additional experiments showed the compounds acted as substrates and were enzymatically hydrolyzed. Inhibition studies with the Fmoc-amide derivatives showed that the compounds do not act as substrates and selectively inhibit BChE with IC50 values in the 0.06-10.0 µM range. Computational docking studies suggest that the inhibitors can interact with cholinyl binding site and peripheral site. Overall, the results suggest that introducing substrate-like characteristics within the Fmoc-amino acid-based background increases their potency. The versatile and ready access to amino acid-based compounds offers an attractive system to further our understanding of the relative importance of protein-small molecule interactions while guiding the development of better inhibitors.
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Affiliation(s)
- Jonathan Godinez
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9507, United States
| | - Catherine Y Lee
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9507, United States
| | - Jason P Schwans
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840-9507, United States.
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6
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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Affiliation(s)
- Vishal
Annasaheb Adhav
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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7
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Dong Y, Pi X, Bartels-Burgahn F, Saltukoglu D, Liang Z, Yang J, Alt FW, Reth M, Wu H. Structural principles of B cell antigen receptor assembly. Nature 2022; 612:156-161. [PMID: 36228656 PMCID: PMC10499536 DOI: 10.1038/s41586-022-05412-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/05/2022] [Indexed: 12/15/2022]
Abstract
The B cell antigen receptor (BCR) is composed of a membrane-bound class M, D, G, E or A immunoglobulin for antigen recognition1-3 and a disulfide-linked Igα (also known as CD79A) and Igβ (also known as CD79B) heterodimer (Igα/β) that functions as the signalling entity through intracellular immunoreceptor tyrosine-based activation motifs (ITAMs)4,5. The organizing principle of the BCR remains unknown. Here we report cryo-electron microscopy structures of mouse full-length IgM BCR and its Fab-deleted form. At the ectodomain (ECD), the Igα/β heterodimer mainly uses Igα to associate with Cµ3 and Cµ4 domains of one heavy chain (µHC) while leaving the other heavy chain (µHC') unbound. The transmembrane domain (TMD) helices of µHC and µHC' interact with those of the Igα/β heterodimer to form a tight four-helix bundle. The asymmetry at the TMD prevents the recruitment of two Igα/β heterodimers. Notably, the connecting peptide between the ECD and TMD of µHC intervenes in between those of Igα and Igβ to guide TMD assembly through charge complementarity. Weaker but distinct density for the Igβ ITAM nestles next to the TMD, suggesting potential autoinhibition of ITAM phosphorylation. Interfacial analyses suggest that all BCR classes utilize a general organizational architecture. Our studies provide a structural platform for understanding B cell signalling and designing rational therapies against BCR-mediated diseases.
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Affiliation(s)
- Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Xiong Pi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Frauke Bartels-Burgahn
- Signaling Research Centers BIOSS and CIBSS, Freiburg, Germany
- Department of Molecular Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Deniz Saltukoglu
- Signaling Research Centers BIOSS and CIBSS, Freiburg, Germany
- Department of Molecular Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Zhuoyi Liang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- HHMI, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jianying Yang
- Signaling Research Centers BIOSS and CIBSS, Freiburg, Germany
- Department of Molecular Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- HHMI, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael Reth
- Signaling Research Centers BIOSS and CIBSS, Freiburg, Germany.
- Department of Molecular Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany.
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
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8
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Maynard JRJ, Galmés B, Stergiou AD, Symes MD, Frontera A, Goldup SM. Anion-π Catalysis Enabled by the Mechanical Bond. Angew Chem Int Ed Engl 2022; 61:e202115961. [PMID: 35040543 PMCID: PMC9303940 DOI: 10.1002/anie.202115961] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/13/2022]
Abstract
We report a series of rotaxane-based anion-π catalysts in which the mechanical bond between a bipyridine macrocycle and an axle containing an NDI unit is intrinsic to the activity observed, including a [3]rotaxane that catalyses an otherwise disfavoured Michael addition in >60 fold selectivity over a competing decarboxylation pathway that dominates under Brønsted base conditions. The results are rationalized by detailed experimental investigations, electrochemical and computational analysis.
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Affiliation(s)
| | - Bartomeu Galmés
- Department of ChemistryUniversitat de les Illes BalearsCrta de Valldemossa km 7.507122Palma de MallorcaBalearesSpain
| | - Athanasios D. Stergiou
- WestCHEM School of ChemistryUniversity of Glasgow, Joseph Black BuildingUniversity AvenueGlasgowG12 8QQUK
| | - Mark D. Symes
- WestCHEM School of ChemistryUniversity of Glasgow, Joseph Black BuildingUniversity AvenueGlasgowG12 8QQUK
| | - Antonio Frontera
- Department of ChemistryUniversitat de les Illes BalearsCrta de Valldemossa km 7.507122Palma de MallorcaBalearesSpain
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9
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Maynard JRJ, Galmés B, Stergiou A, Symes M, Frontera A, Goldup SM. Anion‐π Catalysis Enabled by the Mechanical Bond. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | | | - Mark Symes
- University of Glasgow Chemistry UNITED KINGDOM
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10
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Kuzniak-Glanowska E, Glanowski M, Kurczab R, Bojarski AJ, Podgajny R. Mining anion-aromatic interactions in the Protein Data Bank. Chem Sci 2022; 13:3984-3998. [PMID: 35440982 PMCID: PMC8985504 DOI: 10.1039/d2sc00763k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/28/2022] [Indexed: 12/01/2022] Open
Abstract
Mutual positioning and non-covalent interactions in anion–aromatic motifs are crucial for functional performance of biological systems. In this context, regular, comprehensive Protein Data Bank (PDB) screening that involves various scientific points of view and individual critical analysis is of utmost importance. Analysis of anions in spheres with radii of 5 Å around all 5- and 6-membered aromatic rings allowed us to distinguish 555 259 unique anion–aromatic motifs, including 92 660 structures out of the 171 588 structural files in the PDB. The use of a scarcely exploited (x, h) coordinate system led to (i) identification of three separate areas of motif accumulation: A – over the ring, B – over the ring-substituent bonds, and C – roughly in the plane of the aromatic ring, and (ii) unprecedented simultaneous comparative description of various anion–aromatic motifs located in these areas. Of the various residues considered, i.e. aminoacids, nucleotides, and ligands, the latter two exhibited a considerable tendency to locate in region Avia archetypal anion–π contacts. The applied model not only enabled statistical quantitative analysis of space around the ring, but also enabled discussion of local intermolecular arrangements, as well as detailed sequence and secondary structure analysis, e.g. anion–π interactions in the GNRA tetraloop in RNA and protein helical structures. As a purely practical issue of this work, the new code source for the PDB research was produced, tested and made freely available at https://github.com/chemiczny/PDB_supramolecular_search. The comprehensive analysis of non-redundant PDB macromolecular structures investigating anion distributions around all aromatic molecules in available biosystems is presented.![]()
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Affiliation(s)
| | - Michał Glanowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences Niezapominajek 8 30-239 Kraków Poland
| | - Rafał Kurczab
- Maj Institute of Pharmacology, Polish Academy of Sciences Smętna 12 31-343 Kraków Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences Smętna 12 31-343 Kraków Poland
| | - Robert Podgajny
- Faculty of Chemistry, Jagiellonian University Gronostajowa 2 30-387 Kraków Poland
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11
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Peters CH, Watkins AR, Poirier OL, Ruben PC. E1784K, the most common Brugada syndrome and long-QT syndrome type 3 mutant, disrupts sodium channel inactivation through two separate mechanisms. J Gen Physiol 2021; 152:151877. [PMID: 32569350 PMCID: PMC7478868 DOI: 10.1085/jgp.202012595] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022] Open
Abstract
Inheritable and de novo variants in the cardiac voltage-gated sodium channel, Nav1.5, are responsible for both long-QT syndrome type 3 (LQT3) and Brugada syndrome type 1 (BrS1). Interestingly, a subset of Nav1.5 variants can cause both LQT3 and BrS1. Many of these variants are found in channel structures that form the channel fast inactivation machinery, altering the rate, voltage dependence, and completeness of the fast inactivation process. We used a series of mutants at position 1784 to show that the most common inheritable Nav1.5 variant, E1784K, alters fast inactivation through two separable mechanisms: (1) a charge-dependent interaction that increases the noninactivating current characteristic of E1784K; and (2) a hyperpolarized voltage dependence and accelerated rate of fast inactivation that decreases the peak sodium current. Using a homology model built on the NavPaS structure, we find that the charge-dependent interaction is between E1784 and K1493 in the DIII-DIV linker of the channel, five residues downstream of the putative inactivation gate. This interaction can be disrupted by a positive charge at position 1784 and rescued with the K1493E/E1784K double mutant that abolishes the noninactivating current. However, the double mutant does not restore either the voltage dependence or rates of fast inactivation. Conversely, a mutant at the bottom of DIVS4, K1641D, causes a hyperpolarizing shift in the voltage dependence of fast inactivation and accelerates the rate of fast inactivation without causing an increase in noninactivating current. These findings provide novel mechanistic insights into how the most common inheritable arrhythmogenic mixed syndrome variant, E1784K, simultaneously decreases transient sodium currents and increases noninactivating currents, leading to both BrS1 and LQT3.
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Affiliation(s)
- Colin H Peters
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Abeline R Watkins
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Olivia L Poirier
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Peter C Ruben
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
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12
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Zeng Y, Havenridge S, Gharib M, Baksi A, Weerawardene KLDM, Ziefuß AR, Strelow C, Rehbock C, Mews A, Barcikowski S, Kappes MM, Parak WJ, Aikens CM, Chakraborty I. Impact of Ligands on Structural and Optical Properties of Ag 29 Nanoclusters. J Am Chem Soc 2021; 143:9405-9414. [PMID: 34138547 DOI: 10.1021/jacs.1c01799] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A ligand exchange strategy has been employed to understand the role of ligands on the structural and optical properties of atomically precise 29 atom silver nanoclusters (NCs). By ligand optimization, ∼44-fold quantum yield (QY) enhancement of Ag29(BDT)12-x(DHLA)x NCs (x = 1-6) was achieved, where BDT and DHLA refer to 1,3-benzene-dithiol and dihydrolipoic acid, respectively. High-resolution mass spectrometry was used to monitor ligand exchange, and structures of the different NCs were obtained through density functional theory (DFT). The DFT results from Ag29(BDT)11(DHLA) NCs were further experimentally verified through collisional cross-section (CCS) analysis using ion mobility mass spectrometry (IM MS). An excellent match in predicted CCS values and optical properties with the respective experimental data led to a likely structure of Ag29(DHLA)12 NCs consisting of an icosahedral core with an Ag16S24 shell. Combining the experimental observation with DFT structural analysis of a series of atomically precise NCs, Ag29-yAuy(BDT)12-x(DHLA)x (where y, x = 0,0; 0,1; 0,12 and 1,12; respectively), it was found that while the metal core is responsible for the origin of photoluminescence (PL), ligands play vital roles in determining their resultant PLQY.
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Affiliation(s)
- Yuan Zeng
- Department of Physics and Center for Hybrid Nanostructure (CHyN), University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Hamburg, Germany
| | - Shana Havenridge
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mustafa Gharib
- Department of Physics and Center for Hybrid Nanostructure (CHyN), University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Hamburg, Germany.,Radiation Biology Department, Egyptian Atomic Energy Authority (EAEA), Cairo 11787, Egypt
| | - Ananya Baksi
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - K L Dimuthu M Weerawardene
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States.,Department of Chemistry, Baylor University, Waco, Texas 76798, United States
| | - Anna Rosa Ziefuß
- Department of Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Essen 45141, Germany
| | - Christian Strelow
- Department of Chemistry, University of Hamburg, Grindelallee 117, Hamburg 20146, Germany
| | - Christoph Rehbock
- Department of Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Essen 45141, Germany
| | - Alf Mews
- Department of Chemistry, University of Hamburg, Grindelallee 117, Hamburg 20146, Germany
| | - Stephan Barcikowski
- Department of Technical Chemistry I, University of Duisburg-Essen and Center for Nanointegration Duisburg-Essen (CENIDE), Essen 45141, Germany
| | - Manfred M Kappes
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Wolfgang J Parak
- Department of Physics and Center for Hybrid Nanostructure (CHyN), University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Grindelallee 117, Hamburg 20146, Germany.,CIC Biomagune, San Sebastian 20014, Spain
| | - Christine M Aikens
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Indranath Chakraborty
- Department of Physics and Center for Hybrid Nanostructure (CHyN), University of Hamburg, Luruper Chaussee 149, Hamburg 22761, Hamburg, Germany
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13
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Pitarch-Jarque J, Zaragozá RJ, Ballesteros R, Abarca B, Garcia-España E, Verdejo B, Ballesteros-Garrido R. About the relevance of anion-π interactions in water. Dalton Trans 2021; 50:6834-6839. [PMID: 33912885 DOI: 10.1039/d1dt00771h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Anion-π interactions are emerging as exotic features with potential applications in chemistry. In the last years, their relevance in living systems has been outlined, and so far there is no concluding significant evidence recognized about the participation of anion-π interactions in water because anion-π sensors contain large aromatic hydrophobic surfaces with limited solubility. By transforming a neutral heterocycle (for example quinoline) into its corresponding salt (quinolinium), we have been able to overcome these solubility issues, and new cationic water-soluble fluorophores have been prepared. Herein, we used N-alkylated heterocycles as π-acidic surfaces to shed light on the nature of anion-π in water by the direct measurement of the fluorescence and UV/Vis spectra in combination with DFT and X-ray analyses.
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Affiliation(s)
- Javier Pitarch-Jarque
- Instituto de Ciencia Molecular (ICMOL), University of Valencia, C/Catedrático José Beltrán, 2, 46980, Paterna, Valencia, Spain
| | - Ramón J Zaragozá
- Department of Organic Chemistry University of Valencia, Av. Vicent Andrés Estellés, s/n., 46100 Burjassot, Valencia, Spain.
| | - Rafael Ballesteros
- Department of Organic Chemistry University of Valencia, Av. Vicent Andrés Estellés, s/n., 46100 Burjassot, Valencia, Spain.
| | - Belen Abarca
- Department of Organic Chemistry University of Valencia, Av. Vicent Andrés Estellés, s/n., 46100 Burjassot, Valencia, Spain.
| | - Enrique Garcia-España
- Instituto de Ciencia Molecular (ICMOL), University of Valencia, C/Catedrático José Beltrán, 2, 46980, Paterna, Valencia, Spain
| | - Begoña Verdejo
- Instituto de Ciencia Molecular (ICMOL), University of Valencia, C/Catedrático José Beltrán, 2, 46980, Paterna, Valencia, Spain
| | - Rafael Ballesteros-Garrido
- Department of Organic Chemistry University of Valencia, Av. Vicent Andrés Estellés, s/n., 46100 Burjassot, Valencia, Spain.
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14
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Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Proc Natl Acad Sci U S A 2020; 117:33204-33215. [PMID: 33376217 DOI: 10.1073/pnas.2011350117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
How enzymes achieve their enormous rate enhancements remains a central question in biology, and our understanding to date has impacted drug development, influenced enzyme design, and deepened our appreciation of evolutionary processes. While enzymes position catalytic and reactant groups in active sites, physics requires that atoms undergo constant motion. Numerous proposals have invoked positioning or motions as central for enzyme function, but a scarcity of experimental data has limited our understanding of positioning and motion, their relative importance, and their changes through the enzyme's reaction cycle. To examine positioning and motions and test catalytic proposals, we collected "room temperature" X-ray crystallography data for Pseudomonas putida ketosteroid isomerase (KSI), and we obtained conformational ensembles for this and a homologous KSI from multiple PDB crystal structures. Ensemble analyses indicated limited change through KSI's reaction cycle. Active site positioning was on the 1- to 1.5-Å scale, and was not exceptional compared to noncatalytic groups. The KSI ensembles provided evidence against catalytic proposals invoking oxyanion hole geometric discrimination between the ground state and transition state or highly precise general base positioning. Instead, increasing or decreasing positioning of KSI's general base reduced catalysis, suggesting optimized Ångstrom-scale conformational heterogeneity that allows KSI to efficiently catalyze multiple reaction steps. Ensemble analyses of surrounding groups for WT and mutant KSIs provided insights into the forces and interactions that allow and limit active-site motions. Most generally, this ensemble perspective extends traditional structure-function relationships, providing the basis for a new era of "ensemble-function" interrogation of enzymes.
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15
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Rather IA, Wagay SA, Ali R. Emergence of anion-π interactions: The land of opportunity in supramolecular chemistry and beyond. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213327] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Acosta-Silva C, Bertran J, Branchadell V, Oliva A. Kemp Elimination Reaction Catalyzed by Electric Fields. Chemphyschem 2020; 21:295-306. [PMID: 31840917 DOI: 10.1002/cphc.201901155] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/12/2019] [Indexed: 12/20/2022]
Abstract
The Kemp elimination reaction is the most widely used in the de novo design of new enzymes. The effect of two different kinds of electric fields in the reactions of acetate as a base with benzisoxazole and 5-nitrobenzisoxazole as substrates have been theoretically studied. The effect of the solvent reaction field has been calculated using the SMD continuum model for several solvents; we have shown that solvents inhibit both reactions, the decrease of the reaction rate being larger as far as the dielectric constant is increased. The diminution of the reaction rate is especially remarkable between aprotic organic solvents and protic solvents as water, the electrostatic term of the hydrogen bonds being the main factor for the large inhibitory effect of water. The presence of an external electric field oriented in the direction of the charge transfer (z axis) increases it and, so, the reaction rate. In the reaction of the nitro compound, if the electric field is oriented in an orthogonal direction (x axis) the charge transfer to the NO2 group is favored and there is a subsequent increase of the reaction rate. However, this increase is smaller than the one produced by the field in the z axis. It is worthwhile mentioning that one of the main effects of external electric fields of intermediate intensity is the reorientation of the reactants. Finally, the implications of our results in the de novo design of enzymes are discussed.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joan Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vicenç Branchadell
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Antoni Oliva
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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17
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Peng F, Cheng X, Wang H, Song S, Chen T, Li X, He Y, Huang Y, Liu S, Yang F, Su Z. Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ 5-3-ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:821-830. [PMID: 31226491 DOI: 10.1016/j.bbapap.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/25/2022]
Abstract
Protein engineering based on structure homology holds the potential to engineer steroid-transforming enzymes on demand. Based on the genome sequencing analysis of industrial Mycobacterium strain HGMS2 to produce 4-androstene-3,17-dione (4-AD), three hypothetical proteins were predicted as putative Δ5-3-ketosteroid isomerases (KSIs) to catalyze an intramolecular proton transfer involving the transformation of 5-androstene-3,17-dione (5-AD) into 4-AD, which were defined as mKSI228, mKSI291 and mKSI753. Activity assays indicated that mKSI228 and mKSI291 exhibited weak activity, as low as 0.7% and 1.5%, respectively, of a well-studied and highly active KSI from Pseudomonas putida KSI (pKSI), while mKSI753 had no activity similar to Mycobacterium tuberculosis KSI (mtKSI). Although the 3D structures of the putative mKSIs were homologous to pKSI, their amino acid sequences were significantly different from those of pKSI and tKSI. Thus, by use of these two KSIs as homology models, we were able to convert the low-active mKSI291 into a high-active active KSI by site-directed mutagenesis. On the other hand, an X-ray crystallographic structure of mKSI291 identified a water molecule in its active site. This unique water molecule might function as a bridge to connect Ser-OH, Tyr57-OH and C3O of the intermediate form a hydrogen-bonding network that was responsible for its weak activity, compared with that of mtKSI. Our results not only demonstrated the use of a protein engineering approach to understanding KSI catalytic mechanism, but also provided an example for engineering the catalytic active sites and gaining a functional enzyme based on homologous structures.
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Affiliation(s)
- Fei Peng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China; Wuhan Amersino Biodevelop Inc, B1-Building, Biolake Park, Wuhan 430075, China
| | - Hongwei Wang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Shikui Song
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Tian Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Xin Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Yijun He
- Hubei Goto Biotech Inc, No. 1 Baiguoshu Road, Shuidu Industrial Park, Danjiangkou, Hubei 442700, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Fei Yang
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China; Wuhan Amersino Biodevelop Inc, B1-Building, Biolake Park, Wuhan 430075, China.
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18
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James N, Shanthi V, Ramanathan K. Discovery of novel anaplastic lymphoma kinase inhibitors: Structure and energy-based pharmacophore strategy. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The clinical outcomes in patients with non-small cell lung cancer have improved, as a result of anaplastic lymphoma kinase (ALK) inhibition. Therefore in the current study, substantial effort has been made to identify ALK inhibitors through systematic virtual screening experiment consisting of e-pharmacophore and pharmacophore perception techniques. Initially, a pharmacophore model (AAAHP.193) and an e-pharmacophore model (DDRRR) encompassing the whole dataset of 12 known ALK inhibitors were developed. The hypotheses could retrieve effective compounds from DrugBank database (8621 molecules), which were then subjected to molecular docking and ADME prediction. These approaches resulted in the identification of five hits, namely, nebivolol, HDY, D42, 796, and LZE having higher Glide docking scores and promising ADME properties with augmented CNS involvement. Moreover, molecular dynamics simulations were performed to validate the inhibitory activity of the hit compounds, and density functional theory calculations were carried out to scrutinize the chemical reactivity of the hits. Subsequent interaction and scaffold analysis identified prominent interactions of the hits with ALK kinase domain and scaffolds with anti-tumor activity against lung cancer cell lines. We strongly believe that the study provides an outlook for the sighting of novel and potent ALK inhibitors in the near future.
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Affiliation(s)
- Nivya James
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - V. Shanthi
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
| | - K. Ramanathan
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore 632014, Tamil Nadu, India
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19
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Zhao Y, Cotelle Y, Liu L, López-Andarias J, Bornhof AB, Akamatsu M, Sakai N, Matile S. The Emergence of Anion-π Catalysis. Acc Chem Res 2018; 51:2255-2263. [PMID: 30188692 DOI: 10.1021/acs.accounts.8b00223] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The objective of this Account is to summarize the first five years of anion-π catalysis. The general idea of anion-π catalysis is to stabilize anionic transition states on aromatic surfaces. This is complementary to the stabilization of cationic transition states on aromatic surfaces, a mode of action that occurs in nature and is increasingly used in chemistry. Anion-π catalysis, however, rarely occurs in nature and has been unexplored in chemistry. Probably because the attraction of anions to π surfaces as such is counterintuitive, anion-π interactions in general are much younger than cation-π interactions and remain under-recognized until today. Anion-π catalysis has emerged from early findings that anion-π interactions can mediate the transport of anions across lipid bilayer membranes. With this evidence for stabilization in the ground state secured, there was no reason to believe that anion-π interactions could not also stabilize anionic transition states. As an attractive reaction to develop anion-π catalysis, the addition of malonic acid half thioesters to enolate acceptors was selected. This choice was also made because without enzymes decarboxylation is preferred and anion-π interactions promised to catalyze selectively the disfavored but relevant enolate addition. Concerning anion-π catalysts, we started with naphthalene diimides (NDIs) because their intrinsic quadrupole moment is highly positive. The NDI scaffold was used to address questions such as the positioning of substrates on the catalytic π surface or the dependence of activity on the π acidity of this π surface. With the basics in place, the next milestone was the creation of anion-π enzymes, that is, enzymes that operate with an interaction rarely used in biology, at least on intrinsically π-acidic or highly polarizable aromatic amino-acid side chains. Electric-field-assisted anion-π catalysis addresses topics such as heterogeneous catalysis on electrodes and remote control of activity by voltage. On π-stacked foldamers, anion-(π) n-π catalysis was discovered. Fullerenes emerged as the scaffold of choice to explore contributions from polarizability. On fullerenes, anionic transition states are stabilized by large macrodipoles that appear only in response to their presence. With this growing collection of anion-π catalysts, several reactions beyond enolate addition have been explored so far. Initial efforts focused on asymmetric anion-π catalysis. Increasing enantioselectivity with increasing π acidity of the active π surface has been exemplified for enamine and iminium chemistry and for anion-π transaminase mimics. However, the delocalized nature of anion-π interactions calls for the stabilization of charge displacements over longer distances. The first step in this direction was the formation of cyclohexane rings with five stereogenic centers from achiral acyclic substrates on π-acidic surfaces. Moreover, the intrinsically disfavored exo transition state of anionic Diels-Alder reactions is stabilized selectively on π-acidic surfaces; endo products and otherwise preferred Michael addition products are completely suppressed. Taken together, we hope that these results on catalyst design and reaction scope will establish anion-π catalysis as a general principle in catalysis in the broadest sense.
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Affiliation(s)
- Yingjie Zhao
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Yoann Cotelle
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Le Liu
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | | | - Anna-Bea Bornhof
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Masaaki Akamatsu
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, CH-1211 Geneva, Switzerland
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20
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Abstract
The ability to rapidly assess the preferred conformation of key fragments in a structure “by visual inspection” is a very useful starting point in the process of drug design. With the ability to do so, one could address questions like: “How could we avoid planarity in a molecule?”, “Will a molecule change its conformational preference if we make it more or less basic?” or “How does this electronic repulsion affect the conformational preference in the system?” in timely fashion. In this paper, we describe how the conformational energy profile (CEP, plot of energy as a function of dihedral bond angle) of a fragment can be interpreted through the understanding the interplay between resonance stabilization, steric effects and electrostatic interactions. Fifty-nine biaryl and aryl carbonyl fragments present in oral drugs or which are close derivatives thereof were selected. Calculation of their CEPs using ab initio methodology allowed us to conclude the relative importance of these factors in the conformational preference of these fragments as follows: “steric repulsion > lone pair—lone pair repulsion > lone pair—fluorine repulsion > resonance stabilization” and to formulate “rules of thumb” that the practicing medicinal/organic chemist can apply when analysing molecules that contain these fragments.
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Affiliation(s)
| | - John M. Schaus
- Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana, United States of America
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21
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Impact of Homologous Resistance Mutations from Pathogenic Yeast on Saccharomyces cerevisiae Lanosterol 14α-Demethylase. Antimicrob Agents Chemother 2018; 62:AAC.02242-17. [PMID: 29263059 DOI: 10.1128/aac.02242-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 12/08/2017] [Indexed: 11/20/2022] Open
Abstract
Fungal infections frequently affect immunodeficient individuals and are estimated to kill 1.35 million people per annum. Azole antifungals target the membrane-bound cytochrome P450 monooxygenase lanosterol 14α-demethylase (CYP51; Erg11p). Mutations in CYP51 can render the widely used triazole drugs less effective. The Candida albicans CYP51 mutation G464S and the double mutation Y132F G464S (Y140F and G464S by Saccharomyces cerevisiae numbering) as well as the CYP51A G54E/R/W mutations of Aspergillus fumigatus (G73E/R/W by S. cerevisiae numbering) have been reproduced in a recombinant C-terminal hexahistidine-tagged version of S. cerevisiae CYP51 (ScErg11p6×His). Phenotypes and X-ray crystal structures were determined for the mutant enzymes. Liquid microdilution assays showed that the G464S mutation in ScErg11p6×His conferred no difference in the susceptibility of yeast to triazole drugs but in combination with the Y140F mutation gave a 4-fold reduction in susceptibility to the short-tailed triazole fluconazole. The ScErg11p6×His Y140F G464S mutant was unstable during purification and was not crystallized. The ScErg11p6×His G73E/R/W mutations conferred increased susceptibly to all triazoles tested in liquid microdilution assays. High-resolution X-ray crystal structures reveal two different conformations of the ligand itraconazole, including a previously unseen conformation, as well as interactions between the tail of this triazole and the E/W73 residue. This study shows that S. cerevisiae CYP51 adequately represents some but not all mutations in CYP51s of pathogenic fungi. Insight into the molecular mechanisms of resistance mutations in CYP51 will assist the development of inhibitors that will overcome antifungal resistance.
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22
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Ieritano C, Featherstone J, Carr PJJ, Marta RA, Loire E, McMahon TB, Hopkins WS. The structures and properties of anionic tryptophan complexes. Phys Chem Chem Phys 2018; 20:26532-26541. [DOI: 10.1039/c8cp04533j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
IRMPD spectroscopy and electronic structure calculations are employed to identify π–π interactions in ionic tryptophan clusters.
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Affiliation(s)
| | | | | | - Rick A. Marta
- Department of Chemistry, University of Waterloo
- Waterloo
- Canada
| | - Estelle Loire
- Laboratoire Chimie Physique – CLIO, Bâtiment 201, Porte 2, Campus Universitaire d’Orsay
- France
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Borrel A, Camproux AC, Xhaard H. Characterization of Ionizable Groups' Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank. ACS OMEGA 2017; 2:7359-7374. [PMID: 31457307 PMCID: PMC6645025 DOI: 10.1021/acsomega.7b00739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/11/2017] [Indexed: 06/10/2023]
Abstract
We conduct a statistical analysis of the molecular environment of common ionizable functional groups in both protein-ligand complexes and inside proteins from the Protein Data Bank (PDB). In particular, we characterize the frequency, type, and density of the interacting atoms as well as the presence of a potential counterion. We found that for ligands, most guanidinium groups, half of primary and secondary amines, and one-fourth of imidazole neighbor a carboxylate group. Tertiary amines bind more rarely near carboxylate groups, which may be explained by a crowded neighborhood and hydrophobic character. In comparison to the environment seen by the ligands, inside proteins, an environment enriched in main-chain atoms is found, and the prevalence of direct charge neutralization by carboxylate groups is different. When the ionizable character of water molecules and phenolic or hydroxyl groups is accounted, considering a high-resolution dataset (less than 1.5 Å), charge neutralization could occur for well above 80% of the ligand functional groups considered, but for tertiary amines.
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Affiliation(s)
- Alexandre Borrel
- Molécules
Thérapeutiques in silico (MTi), INSERM UMRS-973, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France
- Faculty
of Pharmacy, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, P.O. Box 56, FI-00014 Helsinki, Finland
| | - Anne-Claude Camproux
- Molécules
Thérapeutiques in silico (MTi), INSERM UMRS-973, University Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France
| | - Henri Xhaard
- Faculty
of Pharmacy, Division of Pharmaceutical Chemistry and Technology, University of Helsinki, Viikinkaari 5E, P.O. Box 56, FI-00014 Helsinki, Finland
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24
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Measuring inter-protein pairwise interaction energies from a single native mass spectrum by double-mutant cycle analysis. Nat Commun 2017; 8:212. [PMID: 28794496 PMCID: PMC5550451 DOI: 10.1038/s41467-017-00285-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/18/2017] [Indexed: 11/27/2022] Open
Abstract
The strength and specificity of protein complex formation is crucial for most life processes and is determined by interactions between residues in the binding partners. Double-mutant cycle analysis provides a strategy for studying the energetic coupling between amino acids at the interfaces of such complexes. Here we show that these pairwise interaction energies can be determined from a single high-resolution native mass spectrum by measuring the intensities of the complexes formed by the two wild-type proteins, the complex of each wild-type protein with a mutant protein, and the complex of the two mutant proteins. This native mass spectrometry approach, which obviates the need for error-prone measurements of binding constants, can provide information regarding multiple interactions in a single spectrum much like nuclear Overhauser effects (NOEs) in nuclear magnetic resonance. Importantly, our results show that specific inter-protein contacts in solution are maintained in the gas phase. Double mutant cycle (DMC) analyses can provide the interaction energies between amino acids at the interface of protein complexes. Here, the authors determine pairwise interaction energies using high-resolution native mass spectroscopy, offering a straightforward route for the DMC methodology.
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25
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Lamba V, Yabukarski F, Herschlag D. An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant. J Am Chem Soc 2017; 139:11089-11095. [PMID: 28719738 DOI: 10.1021/jacs.7b03547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Control of enzyme activity is fundamental to biology and represents a long-term goal in bioengineering and precision therapeutics. While several powerful molecular strategies have been developed, limitations remain in their generalizability and dynamic range. We demonstrate a control mechanism via separate small molecules that turn on the enzyme (activator) and turn off the activation (blocker). We show that a pocket created near the active site base of the enzyme ketosteriod isomerase (KSI) allows efficient and saturable base rescue when the enzyme's natural general base is removed. Binding a small molecule with similar properties but lacking general-base capability in this pocket shuts off rescue. The ability of small molecules to directly participate in and directly block catalysis may afford a broad controllable dynamic range. This approach may be amenable to numerous enzymes and to engineering and screening approaches to identify activators and blockers with strong, specific binding for engineering and therapeutic applications.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, §Department of Chemical Engineering, and ∥Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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26
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Desjardins M, Mak WS, O’Brien TE, Carlin DA, Tantillo DJ, Siegel JB. Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium. ACS OMEGA 2017; 2:3308-3314. [PMID: 31457655 PMCID: PMC6641618 DOI: 10.1021/acsomega.7b00519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/20/2017] [Indexed: 06/10/2023]
Abstract
Enzymes have been through millions of years of evolution during which their active-site microenvironments are fine-tuned. Active-site residues are commonly conserved within protein families, indicating their importance for substrate recognition and catalysis. In this work, we systematically mutated active-site residues of l-threonine dehydrogenase from Thermoplasma volcanium and characterized the mutants against a panel of substrate analogs. Our results demonstrate that only a subset of these residues plays an essential role in substrate recognition and catalysis and that the native enzyme activity can be further enhanced roughly 4.6-fold by a single point mutation. Kinetic characterization of mutants on substrate analogs shows that l-threonine dehydrogenase possesses promiscuous activities toward other chemically similar compounds not previously observed. Quantum chemical calculations on the hydride-donating ability of these substrates also reveal that this enzyme did not evolve to harness the intrinsic substrate reactivity for enzyme catalysis. Our analysis provides insights into connections between the details of enzyme active-site structure and specific function. These results are directly applicable to rational enzyme design and engineering.
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Affiliation(s)
- Morgan Desjardins
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wai Shun Mak
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Terrence E. O’Brien
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dylan Alexander Carlin
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
| | - Justin B. Siegel
- Department
of Chemistry, University of California,
Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Biochemistry and Molecular Medicine, University of California,
Davis, 2700 Stockton
Boulevard, Suite 2102, Sacramento, California 95817, United States
- Genome
Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
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27
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Papp D, Rovó P, Jákli I, Császár AG, Perczel A. Four faces of the interaction between ions and aromatic rings. J Comput Chem 2017; 38:1762-1773. [DOI: 10.1002/jcc.24816] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Dóra Papp
- MTA-ELTE Complex Chemical Systems Research Group; H-1518 Budapest 112, P.O. Box 32 Hungary
- Laboratory of Molecular Structure and Dynamics; Institute of Chemistry, Eötvös Loránd University; Pázmány Péter sétány 1/A Budapest H-1117 Hungary
| | - Petra Rovó
- Department Chemie und Pharmazie; Ludwig-Maximilians-Universität München; Butenandstraße 5-11 Munich D-81377 Germany
| | - Imre Jákli
- MTA-ELTE Protein Modeling Research Group, Institute of Chemistry, Eötvös Loránd University; H-1518 Budapest 112, P.O. Box 32 Hungary
| | - Attila G. Császár
- MTA-ELTE Complex Chemical Systems Research Group; H-1518 Budapest 112, P.O. Box 32 Hungary
- Laboratory of Molecular Structure and Dynamics; Institute of Chemistry, Eötvös Loránd University; Pázmány Péter sétány 1/A Budapest H-1117 Hungary
| | - András Perczel
- MTA-ELTE Protein Modeling Research Group, Institute of Chemistry, Eötvös Loránd University; H-1518 Budapest 112, P.O. Box 32 Hungary
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry, Eötvös Loránd University; Pázmány Péter sétány 1/A Budapest H-1117 Hungary
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28
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Discovery of Potent ALK Inhibitors Using Pharmacophore-Informatics Strategy. Cell Biochem Biophys 2017; 76:111-124. [DOI: 10.1007/s12013-017-0800-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/27/2017] [Indexed: 02/07/2023]
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29
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Wilson KA, Wetmore SD. Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature. Struct Chem 2017. [DOI: 10.1007/s11224-017-0954-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Kapoor K, Duff MR, Upadhyay A, Bucci JC, Saxton AM, Hinde RJ, Howell EE, Baudry J. Highly Dynamic Anion-Quadrupole Networks in Proteins. Biochemistry 2016; 55:6056-6069. [PMID: 27753291 DOI: 10.1021/acs.biochem.6b00624] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.
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Affiliation(s)
- Karan Kapoor
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
| | - Michael R Duff
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Amit Upadhyay
- UT/ORNL Graduate School of Genome Science and Technology, University of Tennessee , F337 Walters Life Science, Knoxville, Tennessee 37996, United States
| | - Joel C Bucci
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Arnold M Saxton
- Department of Animal Science, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Robert J Hinde
- Department of Chemistry, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Elizabeth E Howell
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States
| | - Jerome Baudry
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , M407 Walters Life Sciences, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics , Building 2040, Oak Ridge, Tennessee 37830, United States
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31
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Lamba V, Yabukarski F, Pinney M, Herschlag D. Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase. J Am Chem Soc 2016; 138:9902-9. [PMID: 27410422 DOI: 10.1021/jacs.6b04796] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Proton transfer reactions are ubiquitous in enzymes and utilize active site residues as general acids and bases. Crystal structures and site-directed mutagenesis are routinely used to identify these residues, but assessment of their catalytic contribution remains a major challenge. In principle, effective molarity measurements, in which exogenous acids/bases rescue the reaction in mutants lacking these residues, can estimate these catalytic contributions. However, these exogenous moieties can be restricted in reactivity by steric hindrance or enhanced by binding interactions with nearby residues, thereby resulting in over- or underestimation of the catalytic contribution, respectively. With these challenges in mind, we investigated the catalytic contribution of an aspartate general base in ketosteroid isomerase (KSI) by exogenous rescue. In addition to removing the general base, we systematically mutated nearby residues and probed each mutant with a series of carboxylate bases of similar pKa but varying size. Our results underscore the need for extensive and multifaceted variation to assess and minimize steric and positioning effects and determine effective molarities that estimate catalytic contributions. We obtained consensus effective molarities of ∼5 × 10(4) M for KSI from Comamonas testosteroni (tKSI) and ∼10(3) M for KSI from Pseudomonas putida (pKSI). An X-ray crystal structure of a tKSI general base mutant showed no additional structural rearrangements, and double mutant cycles revealed similar contributions from an oxyanion hole mutation in the wild-type and base-rescued reactions, providing no indication of mutational effects extending beyond the general base site. Thus, the high effective molarities suggest a large catalytic contribution associated with the general base. A significant portion of this effect presumably arises from positioning of the base, but its large magnitude suggests the involvement of additional catalytic mechanisms as well.
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Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Filip Yabukarski
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Margaux Pinney
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Daniel Herschlag
- Department of Biochemistry, ‡Department of Chemistry, #Department of Chemical Engineering, §Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
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32
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Last NB, Kolmakova-Partensky L, Shane T, Miller C. Mechanistic signs of double-barreled structure in a fluoride ion channel. eLife 2016; 5. [PMID: 27449280 PMCID: PMC4969038 DOI: 10.7554/elife.18767] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 07/22/2016] [Indexed: 12/04/2022] Open
Abstract
The Fluc family of F− ion channels protects prokaryotes and lower eukaryotes from the toxicity of environmental F−. In bacteria, these channels are built as dual-topology dimers whereby the two subunits assemble in antiparallel transmembrane orientation. Recent crystal structures suggested that Fluc channels contain two separate ion-conduction pathways, each with two F− binding sites, but no functional correlates of this unusual architecture have been reported. Experiments here fill this gap by examining the consequences of mutating two conserved F−-coordinating phenylalanine residues. Substitution of each phenylalanine specifically extinguishes its associated F− binding site in crystal structures and concomitantly inhibits F− permeation. Functional analysis of concatemeric channels, which permit mutagenic manipulation of individual pores, show that each pore can be separately inactivated without blocking F− conduction through its symmetry-related twin. The results strongly support dual-pathway architecture of Fluc channels. DOI:http://dx.doi.org/10.7554/eLife.18767.001
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Affiliation(s)
- Nicholas B Last
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | | | - Tania Shane
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Christopher Miller
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
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33
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Cha HJ, Jang DS, Jeong JH, Hong BH, Yun YS, Shin EJ, Choi KY. Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1322-7. [PMID: 27375051 DOI: 10.1016/j.bbapap.2016.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core.
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Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Bee Hak Hong
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Young Sung Yun
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Eun Ju Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kwan Yong Choi
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea.
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34
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Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Correction to "Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase". J Am Chem Soc 2016; 138:7801-2. [PMID: 27299372 DOI: 10.1021/jacs.6b04665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Bijelic A, Theiner S, Keppler BK, Rompel A. X-ray Structure Analysis of Indazolium trans-[Tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019) Bound to Human Serum Albumin Reveals Two Ruthenium Binding Sites and Provides Insights into the Drug Binding Mechanism. J Med Chem 2016; 59:5894-903. [PMID: 27196130 PMCID: PMC4921950 DOI: 10.1021/acs.jmedchem.6b00600] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Ruthenium(III) complexes are promising
candidates for anticancer
drugs, especially the clinically studied indazolium trans-[tetrachlorobis(1H-indazole)ruthenate(III)] (KP1019)
and its analogue sodium trans-[tetrachlorobis(1H-indazole)ruthenate(III)] (NKP-1339). Several studies have
emphasized the likely role of human serum proteins in the transportation
and accumulation of ruthenium(III) complexes in tumors. Therefore,
the interaction between KP1019 and human serum albumin was investigated
by means of X-ray crystallography and inductively coupled plasma mass
spectrometry (ICP-MS). The structural data unambiguously reveal the
binding of two ruthenium atoms to histidine residues 146 and 242,
which are both located within well-known hydrophobic binding pockets
of albumin. The ruthenium centers are octahedrally coordinated by
solvent molecules revealing the dissociation of both indazole ligands
from the ruthenium-based drug. However, a binding mechanism is proposed
indicating the importance of the indazole ligands for binding site
recognition and thus their indispensable role for the binding of KP1019.
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Affiliation(s)
- Aleksandar Bijelic
- Fakultät für Chemie, Institut für Biophysikalische Chemie, Universität Wien , Althanstraße 14, 1090 Wien, Austria
| | | | | | - Annette Rompel
- Fakultät für Chemie, Institut für Biophysikalische Chemie, Universität Wien , Althanstraße 14, 1090 Wien, Austria
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36
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Das AA, Krishna R. PICI: A web server with a multi-parametric algorithm for identifying interaction sites within protein complexes. Bioinformation 2016; 12:78-81. [PMID: 28104965 PMCID: PMC5237652 DOI: 10.6026/97320630012078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 11/23/2022] Open
Abstract
Identifying interactions between proteins in a complex is essential to analyze their role in various cellular activities and structural stability. Therefore, effective algorithms and computer programs are required for the better understanding of various interactions exist at the protein-protein interface. The protein inter-chain interaction (PICI) server was developed to identify these interaction sites and various interactions that contribute to the specificity and strength of the protein complex by using Protein Interaction Identification Algorithm (PIIA). The multi-parametric approach of this algorithm involves the interface area between the subunits, the atomic coordinate distance, the linearity of bonds, the orientation of aromatic side-chains, and physicochemical properties of the residues. Particular advantages of PICI include its ability to identify various strong and weak interactions, including those which have not been considered before by any other server. Representation of interface data in text tables, 3D interaction visualizer, colored sequence viewer, and a dynamic colored graphical matrix display makes it distinct from similar web servers. Users can analyze interactions within multi-chain proteins by their PDBids or by uploading a structure atomic coordinate file and can download the result in plain text or XML format.
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Affiliation(s)
- Arindam Atanu Das
- Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
| | - Ramadas Krishna
- Centre for Bioinformatics, Pondicherry University, Puducherry 605014, India
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37
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Manjunath GP, Soni N, Vaddavalli PL, Shewale DJ, Madhusudhan MS, Muniyappa K. Molecular Mechanism Underlying ATP-Induced Conformational Changes in the Nucleoprotein Filament of Mycobacterium smegmatis RecA. Biochemistry 2016; 55:1850-62. [PMID: 26915388 DOI: 10.1021/acs.biochem.5b01383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
RecA plays a central role in bacterial DNA repair, homologous recombination, and restoration of stalled replication forks by virtue of its active extended nucleoprotein filament. Binding of ATP and its subsequent recognition by the carboxamide group of a highly conserved glutamine (Gln196 in MsRecA) have been implicated in the formation of active RecA nucleoprotein filaments. Although the mechanism of ATP-dependent structural transitions in RecA has been proposed on the basis of low-resolution electron microscopic reconstructions, the precise sequence of events that constitute these transitions is poorly understood. On the basis of biochemical and crystallographic analyses of MsRecA variants carrying mutations in highly conserved Gln196 and Arg198 residues, we propose that the disposition of the interprotomer interface is the structural basis of allosteric activation of RecA. Furthermore, this study accounts for the contributions of several conserved amino acids to ATP hydrolysis and to the transition from collapsed to extended filament forms in Mycobacterium smegmatis RecA (MsRecA). In addition to their role in the inactive compressed state, the study reveals a role for Gln196 and Arg198 along with Phe219 in ATP hydrolysis in the active extended nucleoprotein filament. Finally, our data suggest that the primary, but not secondary, nucleotide binding site in MsRecA isomerizes into the ATP binding site present in the extended nucleoprotein filament.
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Affiliation(s)
- G P Manjunath
- Department of Biochemistry, Indian Institute of Science (IISc) , Bangalore 560012, India.,Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER) , Pune 411008, India
| | - Neelesh Soni
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) , Pune 411008, India
| | - Pavana L Vaddavalli
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER) , Pune 411008, India
| | - Dipeshwari J Shewale
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research (IISER) , Pune 411008, India
| | - M S Madhusudhan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) , Pune 411008, India
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science (IISc) , Bangalore 560012, India
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38
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Abstract
The σ-hole and π-hole are the regions with positive surface electrostatic potential on the molecule entity; the former specifically refers to the positive region of a molecular entity along extension of the Y-Ge/P/Se/X covalent σ-bond (Y = electron-rich group; Ge/P/Se/X = Groups IV-VII), while the latter refers to the positive region in the direction perpendicular to the σ-framework of the molecular entity. The directional noncovalent interactions between the σ-hole or π-hole and the negative or electron-rich sites are named σ-hole bond or π-hole bond, respectively. The contributions from electrostatic, charge transfer, and other terms or Coulombic interaction to the σ-hole bond and π-hole bond were reviewed first followed by a brief discussion on the interplay between the σ-hole bond and the π-hole bond as well as application of the two types of noncovalent interactions in the field of anion recognition. It is expected that this review could stimulate further development of the σ-hole bond and π-hole bond in theoretical exploration and practical application in the future.
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Affiliation(s)
- Hui Wang
- College of Chemistry, Beijing Normal University , Beijing 100875, People's Republic of China
| | - Weizhou Wang
- College of Chemistry and Chemical Engineering, Luoyang Normal University , Luoyang 471022, People's Republic of China
| | - Wei Jun Jin
- College of Chemistry, Beijing Normal University , Beijing 100875, People's Republic of China
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39
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Gu J, Tong H, Ye L, Yu H. The role of aromatic residue W20 in the activity and enantioselectivity control of esterase BioH toward aryl substrate. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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Fried SD, Boxer SG. BIOPHYSICS. Response to Comments on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase". Science 2015; 349:936. [PMID: 26315428 DOI: 10.1126/science.aab1627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Natarajan et al. and Chen and Savidge comment that comparing the electric field in ketosteroid isomerase's (KSI's) active site to zero overestimates the catalytic effect of KSI's electric field because the reference reaction occurs in water, which itself exerts a sizable electrostatic field. To compensate, Natarajan et al. argue that additional catalytic weight arises from positioning of the general base, whereas Chen and Savidge propose a separate contribution from desolvation of the general base. We note that the former claim is not well supported by published results, and the latter claim is intriguing but lacks experimental basis. We also take the opportunity to clarify some of the more conceptually subtle aspects of electrostatic catalysis.
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Affiliation(s)
- Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.
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41
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Singh V, Snigdha K, Singh C, Sinha N, Thakur AK. Understanding the self-assembly of Fmoc-phenylalanine to hydrogel formation. SOFT MATTER 2015; 11:5353-5364. [PMID: 26059479 DOI: 10.1039/c5sm00843c] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hydrogels of low molecular weight molecules are important in biomedical applications. Multiple factors are responsible for hydrogel formation, but their role in governing self-assembly to hydrogel formation is poorly understood. Herein, we report the hydrogel formation of fluorenylmethyloxycarbonyl phenylalanine (FmocF) molecule. We used physical and thermal stimuli for solubilizing FmocF above the critical concentration to induce gel formation. The key role of Fmoc, Fmoc and phenylalanine covalent linkage, flexibility of phe side chain, pH, and buffer ions in self-assembly of FmocF to gel formation is described. We found that the collective action of different non-covalent interactions play a role in making FmocF hydrogel. Using powder diffraction and infrared spectroscopy, we also report a new polymorphic form of FmocF after transitioning to hydrogel. In addition, we are proposing a model for drug release from FmocF hydrogel.
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Affiliation(s)
- Virender Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India.
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42
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Wilson KA, Wells RA, Abendong MN, Anderson CB, Kung RW, Wetmore SD. Landscape of π-π and sugar-π contacts in DNA-protein interactions. J Biomol Struct Dyn 2015; 34:184-200. [PMID: 25723403 DOI: 10.1080/07391102.2015.1013157] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There were 1765 contacts identified between DNA nucleobases or deoxyribose and cyclic (W, H, F, Y) or acyclic (R, E, D) amino acids in 672 X-ray structures of DNA-protein complexes. In this first study to compare π-interactions between the cyclic and acyclic amino acids, visual inspection was used to categorize amino acid interactions as nucleobase π-π (according to biological edge) or deoxyribose sugar-π (according to sugar edge). Overall, 54% of contacts are nucleobase π-π interactions, which involve all amino acids, but are more common for Y, F, and R, and involve all DNA nucleobases with similar frequencies. Among binding arrangements, cyclic amino acids prefer more planar (stacked) π-systems than the acyclic counterparts. Although sugar-π interactions were only previously identified with the cyclic amino acids and were found to be less common (38%) than nucleobase-cyclic amino acid contacts, sugar-π interactions are more common than nucleobase π-π contacts for the acyclic series (61% of contacts). Similar to DNA-protein π-π interactions, sugar-π contacts most frequently involve Y and R, although all amino acids adopt many binding orientations relative to deoxyribose. These DNA-protein π-interactions stabilize biological systems, by up to approximately -40 kJ mol(-1) for neutral nucleobase or sugar-amino acid interactions, but up to approximately -95 kJ mol(-1) for positively or negatively charged contacts. The high frequency and strength, despite variation in structure and composition, of these π-interactions point to an important function in biological systems.
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Affiliation(s)
- Katie A Wilson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Rachael A Wells
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Minette N Abendong
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Colin B Anderson
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Ryan W Kung
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
| | - Stacey D Wetmore
- a Department of Chemistry and Biochemistry , University of Lethbridge , 4401 University Drive West, Lethbridge , AB T1K 3M4 , Canada
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43
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Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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44
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Affiliation(s)
- François N. Miros
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Guangxi Huang
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Yingjie Zhao
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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45
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Zhao Y, Sakai N, Matile S. Enolate chemistry with anion–π interactions. Nat Commun 2014; 5:3911. [DOI: 10.1038/ncomms4911] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/17/2014] [Indexed: 12/12/2022] Open
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46
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Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry 2014; 53:2541-55. [PMID: 24597914 PMCID: PMC4004248 DOI: 10.1021/bi401671t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
positioning of catalytic groups within proteins plays an important
role in enzyme catalysis, and here we investigate the positioning
of the general base in the enzyme ketosteroid isomerase (KSI). The
oxygen atoms of Asp38, the general base in KSI, were previously shown
to be involved in anion–aromatic interactions with two neighboring
Phe residues. Here we ask whether those interactions are sufficient,
within the overall protein architecture, to position Asp38 for catalysis
or whether the side chains that pack against Asp38 and/or the residues
of the structured loop that is capped by Asp38 are necessary to achieve
optimal positioning for catalysis. To test positioning, we mutated
each of the aforementioned residues, alone and in combinations, in
a background with the native Asp general base and in a D38E mutant
background, as Glu at position 38 was previously shown to be mispositioned
for general base catalysis. These double-mutant cycles reveal positioning
effects as large as 103-fold, indicating that structural
features in addition to the overall protein architecture and the Phe
residues neighboring the carboxylate oxygen atoms play roles in positioning.
X-ray crystallography and molecular dynamics simulations suggest that
the functional effects arise from both restricting dynamic fluctuations
and disfavoring potential mispositioned states. Whereas it may have
been anticipated that multiple interactions would be necessary for
optimal general base positioning, the energetic contributions from
positioning and the nonadditive nature of these interactions are not
revealed by structural inspection and require functional dissection.
Recognizing the extent, type, and energetic interconnectivity of interactions
that contribute to positioning catalytic groups has implications for
enzyme evolution and may help reveal the nature and extent of interactions
required to design enzymes that rival those found in biology.
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Affiliation(s)
- Jason P Schwans
- Department of Biochemistry, Stanford University , B400 Beckman Center, 279 Campus Drive, Stanford, California 94305, United States
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47
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Richard JP, Amyes TL, Goryanova B, Zhai X. Enzyme architecture: on the importance of being in a protein cage. Curr Opin Chem Biol 2014; 21:1-10. [PMID: 24699188 DOI: 10.1016/j.cbpa.2014.03.001] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/01/2014] [Indexed: 11/30/2022]
Abstract
Substrate binding occludes water from the active sites of many enzymes. There is a correlation between the burden to enzymatic catalysis of deprotonation of carbon acids and the substrate immobilization at solvent-occluded active sites for ketosteroid isomerase (KSI--small burden, substrate pKa=13), triosephosphate isomerase (TIM, substrate pKa≈18) and diaminopimelate epimerase (DAP epimerase, large burden, substrate pKa≈29) catalyzed reaction. KSI binds substrates at a surface cleft, TIM binds substrate at an exposed 'cage' formed by closure of flexible loops; and, DAP epimerase binds substrate in a tight cage formed by an 'oyster-like' clamping motion of protein domains. Directed evolution of a solvent-occluded active site at a designed protein catalyst of the Kemp elimination reaction is discussed.
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Affiliation(s)
- John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA.
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Bogdana Goryanova
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
| | - Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260-3000, USA
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48
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Mechanistic insight into the reaction catalysed by bacterial type II dehydroquinases1. Biochem J 2014; 458:547-57. [DOI: 10.1042/bj20131103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present study identified the residue that deprotonates the essential tyrosine that triggers the catalytic process and provides details of the required motions for the catalytic turnover. A previously unknown key role for the essential arginine and two conserved arginines is also reported.
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49
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Gamez P. The anion–π interaction: naissance and establishment of a peculiar supramolecular bond. Inorg Chem Front 2014. [DOI: 10.1039/c3qi00055a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase. Biochemistry 2013; 52:7840-55. [PMID: 24151972 PMCID: PMC3890242 DOI: 10.1021/bi401083b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active-site energetics. The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects.
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Affiliation(s)
- Jason P. Schwans
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Yingssu Tsai
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305
- Department of Chemistry, Stanford University, Stanford, California 94305
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