Morten Grøtli - Academia.edu (original) (raw)
Papers by Morten Grøtli
Physical Chemistry Chemical Physics, 2018
Ultrasensitive detection of DNA is achieved via two-photon excitation of a fluorescent base analo... more Ultrasensitive detection of DNA is achieved via two-photon excitation of a fluorescent base analogue.
Drug discovery today, Oct 20, 2017
Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease (NAFLD).... more Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease (NAFLD). We surveyed NASH therapies currently in development, and found a significant variety of targets and approaches. Evaluation and clinical testing of these targets is an expensive and time-consuming process. Systems biology approaches could enable the quantitative evaluation of the likely efficacy and safety of different targets. This motivated our review of recent systems biology studies that focus on the identification of targets and development of effective treatments for NASH. We discuss the potential broader use of genome-scale metabolic models and integrated networks in the validation of drug targets, which could facilitate more productive and efficient drug development decisions for the treatment of NASH.
Physical chemistry chemical physics : PCCP, Jan 16, 2016
Mutations in the rearranged during transfection (RET) tyrosine kinase gene leading to gain or los... more Mutations in the rearranged during transfection (RET) tyrosine kinase gene leading to gain or loss of function have been associated with the development of several human cancers and Hirschsprung's disease (HSCR). However, to what extent these mutations affect individual bio-molecular functions remains unclear. In this article, the functionally significant mutations in the RET CLD1-4 calcium-binding site which lead to HSCR, and depletion of calcium ions in the RET CLD1-4 calcium binding site, were investigated by molecular dynamics simulations - to understand the mechanistic action of the mutations or loss of calcium ions in altering the protein kinase structure, dynamics, and stability. The mutations or loss of calcium ions change the local conformation and change the free energy landscape. Specifically, the mutations and loss of calcium ions decrease the radius of gyration of the whole structure, leading to improper protein folding and GFL-GFRα contact site reduction. Furthermo...
Journal of the Chemical Society, Perkin Transactions 1, 2000
Journal of the Chemical Society, Perkin Transactions 1, 2000
A chemically inert poly(ethylene glycol) (PEG)-based resin was synthesised by reductive amination... more A chemically inert poly(ethylene glycol) (PEG)-based resin was synthesised by reductive amination of a mixture of mono-and dialdehyde PEG 1500 and the branched cross-linker tris(2-aminoethyl)amine. This unique concept of resin polymerisation yields a polar resin ...
Journal of the Chemical Society, Perkin Transactions 1, 2000
A complete NMR structure analysis of an eight-residue peptide, covalently bound to a single-bead ... more A complete NMR structure analysis of an eight-residue peptide, covalently bound to a single-bead of a poly (ethylene glycol) based (POEPOP 1500) resin, is described. Well resolved 1D and 2D 1 H NMR spectra were obtained using magic angle spinning (MAS) Nanoprobe ...
European Journal of Medicinal Chemistry, 2014
Inhibition or allosteric modulation of mitogen-activated protein kinase kinases MEK1 and MEK2 (ME... more Inhibition or allosteric modulation of mitogen-activated protein kinase kinases MEK1 and MEK2 (MEK1/2) represent a promising strategy for the discovery of new specific anticancer agents. In this paper, structure-based design, beginning from the lead compound PD98059, was used to study potential structural modifications on the chromone structure in order to obtain highly potent derivatives that target the allosteric pocket in MEK1. Subsequently, a small series of PD98059 analogs were synthesized to provide a first generation of chromone-based derivatives that inhibit the activation of MEK1 with IC50 values as low as 30 nM in vitro. Complementary cellular studies also showed that two of the compounds in the series inhibit the activity of MEK1/2 with IC50 values in the nanomolar range (73-97 nM). In addition, compounds in this series were found to inhibit the proliferation of a small panel of human cancer cell lines.
Understanding Biology Using Peptides
Introduction Chromones and flavones (R2=phenyl) are widely distributed in nature and have an inte... more Introduction Chromones and flavones (R2=phenyl) are widely distributed in nature and have an interesting range of biological activities, including anti-cancer [1], anti-HIV [2], and anti-oxidant [3] properties. They have also been considered as privileged structures in drug discovery [4]. We have been interested in using the chromone ring system as a scaffold for peptidomimetics. The substituents on the chromone scaffold have a possibility to mimic important side chains in target peptides.
Current Trends in Organic Synthesis, 1999
Tetrahedron, 1999
ABSTRACT Fully modified oligonucleotides containing 2′-O-cyanomethylribonucleotides were synthesi... more ABSTRACT Fully modified oligonucleotides containing 2′-O-cyanomethylribonucleotides were synthesised on automated DNA synthesisers using protected 2′-O-cyanomethylribonucleoside-3′-O-phosphoramidite building blocks. The 2′-O-cyanomethyloligoribonucleotides were post-synthetically converted into 2′-O-carbamoylmethyloligoribonucleotides during standard deprotection conditions with aqueous ammonia. The complete conversion was proven using ion- exchange HPLC and MALDI mass spectrometry of the final oligomer. The 2′-O-carbamoylmethylribonucleotides showed an substantial increase the melting temperature (Tm) of duplexes with complementary RNA relative to the corresponding RNA homoduplex. Consequently these analogues should prove useful for a variety of antisense applications.
Tetrahedron, 2007
A practical and efficient synthesis of 2′-aminoacylamino-2′-deoxyadenosine derivatives is reporte... more A practical and efficient synthesis of 2′-aminoacylamino-2′-deoxyadenosine derivatives is reported. EDCI/HOBt-mediated coupling of a 3′,5′-diprotected 2′-amino-2′-deoxyadenosine derivative to various N-Cbz-l-amino acid derivatives followed by global deprotection ...
PROTEOMICS, 2012
Global phosphoproteomic studies based on MS have generated qualitative and quantitative data desc... more Global phosphoproteomic studies based on MS have generated qualitative and quantitative data describing protein phosphorylation events in various biological systems. Since high‐throughput data for protein modifications are inherently incomplete, we developed a strategy to extend and validate such primary datasets. We selected interesting protein candidates from a global screen in yeast and employed a modified histidine biotin tag that allows tandem affinity purifications of our targets under denaturing conditions. Products in question can be digested directly from affinity resins and phosphopeptides can be further enriched via TiO2 before MS analysis. Our robust protocol can be amended for SILAC as well as iTRAQ quantifications or label‐free approaches based on selective reaction monitoring, allowing completion of the phosphorylation pattern in a first step, followed by a detailed analysis of the phosphorylation kinetics. We exemplify the value of such a strategy by an in‐depth anal...
Organic Letters, 2009
An approach using water as a solvent (coupling and deprotection) was developed for the solid-phas... more An approach using water as a solvent (coupling and deprotection) was developed for the solid-phase synthesis of peptides using the most common Boc-amino acid derivatives. Key aspects of this methodology are the use of a PEG-based resin, EDC-HONB as a coupling method, and microwave irradiation as an energy source.
Molecular Cell, 2003
The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fid... more The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fidelity relies on hydrolytic editing that destroys incorrectly activated amino acids or mischarged tRNAs. We present structures of leucyl-tRNA synthetase complexed with analogs of the distinct pre- and posttransfer editing substrates. The editing active site binds the two different substrates using a single amino acid discriminatory pocket while preserving the same mode of adenine recognition. This suggests a similar mechanism of hydrolysis for both editing substrates that depends on a key, completely conserved aspartic acid, which interacts with the alpha-amino group of the noncognate amino acid and positions both substrates for hydrolysis. Our results demonstrate the economy by which a single active site accommodates two distinct substrates in a proofreading process critical to the fidelity of protein synthesis.
Journal of the American Chemical Society, 1999
SPOCC resin 1, a novel, highly permeable, polar support for chemical and enzymatic solid-phase me... more SPOCC resin 1, a novel, highly permeable, polar support for chemical and enzymatic solid-phase methods, is presented. The synthesis of SPOCC resin is based on the cross-linking of long-chain poly(ethylene glycol) (PEG) terminally substituted with oxetane by cationic ring-opening polymerization, affording a polymer containing only primary ether and alcohol CO bonds. The polymer was prepared using Et 2 O‚BF 3 as initiator either via bulk polymerization in solution or via suspension polymerization in silicon oil, the latter yielding a beaded resin. The polymerization reaction was investigated with respect to the effects of PEG chain length, the fraction of bisoxetanylated PEG, initiator amount, and temperature in order to vary the swelling, loading, and mechanical stability of the resin. Furthermore, the resin was derivatized with various functional groups and subsequently applied to peptide synthesis and organic reactions in both organic solvents and water. An N-terminal peptide aldehyde was generated on the solid phase and employed to synthesize peptide isosteres by nucleophilic addition of various ylides. Solid-phase glycosylation of peptides and enzymatic reactions were successfully performed with SPOCC resin. Enzymatic proteolytic cleavage of a resin-bound decapeptide on treatment with the 27 kDa protease subtilisin BNP′ demonstrated the accessibility of the interior of the SPOCC resin for enzymes. * To whom correspondence should be addressed. † SPOCC resin) superpermeable organic combinatorial chemistry resin.
The Journal of Organic Chemistry, 2012
This note describes a rapid and mild strategy for the loading of alcohols and anilines onto a pol... more This note describes a rapid and mild strategy for the loading of alcohols and anilines onto a polystyrene triphenylmethyl (trityl) resin. High loadings were obtained in a matter of minutes by treating resin bound trityl chloride with triethyloxonium tetrafluoroborate followed by alcohols or anilines. Yields were comparable or better than known literature methods. Recycling of the recovered resin was also possible using the developed method.
Journal of Molecular Biology, 2011
Escherichia coli peptidyl-tRNA hydrolase activity is inhibited by 3′-(L-[N,Ndiacetyl-lysinyl)amin... more Escherichia coli peptidyl-tRNA hydrolase activity is inhibited by 3′-(L-[N,Ndiacetyl-lysinyl)amino-3′-deoxyadenosine, a stable mimic of the minimalist substrate 2′(3′)-O-(L-[N,N-diacetyl-lysinyl)adenosine. The complex of this mimic with the enzyme has been analyzed by NMR spectroscopy, enabling experimental mapping of the catalytic center for the first time. Chemical shift variations point out the sensitivity of residues Asn10,
Journal of Molecular Biology, 2004
The Escherichia coli biotin repressor functions in biotin retention and regulation of biotin bios... more The Escherichia coli biotin repressor functions in biotin retention and regulation of biotin biosynthesis. Biotin retention is accomplished via the two-step biotinylation of the biotin-dependent enzyme, acetyl-CoA carboxylase. In the first step of this reaction the substrates biotin and ATP are utilized in synthesis of the activated biotin, biotinyl-5'-AMP, while in the second step this activated biotin is transferred to a unique lysine residue of the biotin carboxyl carrier protein subunit of the carboxylase. Regulation of biotin biosynthesis is accomplished through binding of the repressor to the transcription control region of the biotin biosynthetic operon. The adenylated or activated biotin functions as the corepressor in this DNA binding process. The activated biotin is a mixed anhydride and thus labile. In efforts to develop tools for structural and thermodynamic studies of the biotin regulatory interactions, two analogs of the adenylate, a sulfamoyl derivative and an ester derivative, have been synthesized and functionally characterized. Results of fluorescence measurements indicate that both analogs bind with high affinity to the repressor and that both are inactive in biotin transfer to the acceptor protein. Functional studies of their corepressor properties indicate that while the sulfamoyl is a weak allosteric activator, the ester closely mimics the physiological corepressor in activation of assembly of the transcription repression complex. Results of these studies also provide further insight into the allosteric mechanism of the biotin repressor.
Chemistry - A European Journal, 2009
We present the synthesis and photophysical characterisation of a series of structurally diverse, ... more We present the synthesis and photophysical characterisation of a series of structurally diverse, fluorescent 2,6,8-trisubstituted 3-hydroxychromone derivatives with high fluorescence quantum yields and molar extinction coefficients. Two of these derivatives (9 and 10 a) have been studied as fluorophores for cellular imaging in HeLa cells and show excellent permeability and promising fluorescence properties in a cellular environment. In addition, we have demonstrated by photophysical characterisation of 3-isobutyroxychromone derivatives that esterification of the 3-hydroxyl group results in acceptable and useful fluorescence properties.
Physical Chemistry Chemical Physics, 2018
Ultrasensitive detection of DNA is achieved via two-photon excitation of a fluorescent base analo... more Ultrasensitive detection of DNA is achieved via two-photon excitation of a fluorescent base analogue.
Drug discovery today, Oct 20, 2017
Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease (NAFLD).... more Nonalcoholic steatohepatitis (NASH) is a severe form of nonalcoholic fatty liver disease (NAFLD). We surveyed NASH therapies currently in development, and found a significant variety of targets and approaches. Evaluation and clinical testing of these targets is an expensive and time-consuming process. Systems biology approaches could enable the quantitative evaluation of the likely efficacy and safety of different targets. This motivated our review of recent systems biology studies that focus on the identification of targets and development of effective treatments for NASH. We discuss the potential broader use of genome-scale metabolic models and integrated networks in the validation of drug targets, which could facilitate more productive and efficient drug development decisions for the treatment of NASH.
Physical chemistry chemical physics : PCCP, Jan 16, 2016
Mutations in the rearranged during transfection (RET) tyrosine kinase gene leading to gain or los... more Mutations in the rearranged during transfection (RET) tyrosine kinase gene leading to gain or loss of function have been associated with the development of several human cancers and Hirschsprung's disease (HSCR). However, to what extent these mutations affect individual bio-molecular functions remains unclear. In this article, the functionally significant mutations in the RET CLD1-4 calcium-binding site which lead to HSCR, and depletion of calcium ions in the RET CLD1-4 calcium binding site, were investigated by molecular dynamics simulations - to understand the mechanistic action of the mutations or loss of calcium ions in altering the protein kinase structure, dynamics, and stability. The mutations or loss of calcium ions change the local conformation and change the free energy landscape. Specifically, the mutations and loss of calcium ions decrease the radius of gyration of the whole structure, leading to improper protein folding and GFL-GFRα contact site reduction. Furthermo...
Journal of the Chemical Society, Perkin Transactions 1, 2000
Journal of the Chemical Society, Perkin Transactions 1, 2000
A chemically inert poly(ethylene glycol) (PEG)-based resin was synthesised by reductive amination... more A chemically inert poly(ethylene glycol) (PEG)-based resin was synthesised by reductive amination of a mixture of mono-and dialdehyde PEG 1500 and the branched cross-linker tris(2-aminoethyl)amine. This unique concept of resin polymerisation yields a polar resin ...
Journal of the Chemical Society, Perkin Transactions 1, 2000
A complete NMR structure analysis of an eight-residue peptide, covalently bound to a single-bead ... more A complete NMR structure analysis of an eight-residue peptide, covalently bound to a single-bead of a poly (ethylene glycol) based (POEPOP 1500) resin, is described. Well resolved 1D and 2D 1 H NMR spectra were obtained using magic angle spinning (MAS) Nanoprobe ...
European Journal of Medicinal Chemistry, 2014
Inhibition or allosteric modulation of mitogen-activated protein kinase kinases MEK1 and MEK2 (ME... more Inhibition or allosteric modulation of mitogen-activated protein kinase kinases MEK1 and MEK2 (MEK1/2) represent a promising strategy for the discovery of new specific anticancer agents. In this paper, structure-based design, beginning from the lead compound PD98059, was used to study potential structural modifications on the chromone structure in order to obtain highly potent derivatives that target the allosteric pocket in MEK1. Subsequently, a small series of PD98059 analogs were synthesized to provide a first generation of chromone-based derivatives that inhibit the activation of MEK1 with IC50 values as low as 30 nM in vitro. Complementary cellular studies also showed that two of the compounds in the series inhibit the activity of MEK1/2 with IC50 values in the nanomolar range (73-97 nM). In addition, compounds in this series were found to inhibit the proliferation of a small panel of human cancer cell lines.
Understanding Biology Using Peptides
Introduction Chromones and flavones (R2=phenyl) are widely distributed in nature and have an inte... more Introduction Chromones and flavones (R2=phenyl) are widely distributed in nature and have an interesting range of biological activities, including anti-cancer [1], anti-HIV [2], and anti-oxidant [3] properties. They have also been considered as privileged structures in drug discovery [4]. We have been interested in using the chromone ring system as a scaffold for peptidomimetics. The substituents on the chromone scaffold have a possibility to mimic important side chains in target peptides.
Current Trends in Organic Synthesis, 1999
Tetrahedron, 1999
ABSTRACT Fully modified oligonucleotides containing 2′-O-cyanomethylribonucleotides were synthesi... more ABSTRACT Fully modified oligonucleotides containing 2′-O-cyanomethylribonucleotides were synthesised on automated DNA synthesisers using protected 2′-O-cyanomethylribonucleoside-3′-O-phosphoramidite building blocks. The 2′-O-cyanomethyloligoribonucleotides were post-synthetically converted into 2′-O-carbamoylmethyloligoribonucleotides during standard deprotection conditions with aqueous ammonia. The complete conversion was proven using ion- exchange HPLC and MALDI mass spectrometry of the final oligomer. The 2′-O-carbamoylmethylribonucleotides showed an substantial increase the melting temperature (Tm) of duplexes with complementary RNA relative to the corresponding RNA homoduplex. Consequently these analogues should prove useful for a variety of antisense applications.
Tetrahedron, 2007
A practical and efficient synthesis of 2′-aminoacylamino-2′-deoxyadenosine derivatives is reporte... more A practical and efficient synthesis of 2′-aminoacylamino-2′-deoxyadenosine derivatives is reported. EDCI/HOBt-mediated coupling of a 3′,5′-diprotected 2′-amino-2′-deoxyadenosine derivative to various N-Cbz-l-amino acid derivatives followed by global deprotection ...
PROTEOMICS, 2012
Global phosphoproteomic studies based on MS have generated qualitative and quantitative data desc... more Global phosphoproteomic studies based on MS have generated qualitative and quantitative data describing protein phosphorylation events in various biological systems. Since high‐throughput data for protein modifications are inherently incomplete, we developed a strategy to extend and validate such primary datasets. We selected interesting protein candidates from a global screen in yeast and employed a modified histidine biotin tag that allows tandem affinity purifications of our targets under denaturing conditions. Products in question can be digested directly from affinity resins and phosphopeptides can be further enriched via TiO2 before MS analysis. Our robust protocol can be amended for SILAC as well as iTRAQ quantifications or label‐free approaches based on selective reaction monitoring, allowing completion of the phosphorylation pattern in a first step, followed by a detailed analysis of the phosphorylation kinetics. We exemplify the value of such a strategy by an in‐depth anal...
Organic Letters, 2009
An approach using water as a solvent (coupling and deprotection) was developed for the solid-phas... more An approach using water as a solvent (coupling and deprotection) was developed for the solid-phase synthesis of peptides using the most common Boc-amino acid derivatives. Key aspects of this methodology are the use of a PEG-based resin, EDC-HONB as a coupling method, and microwave irradiation as an energy source.
Molecular Cell, 2003
The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fid... more The aminoacyl-tRNA synthetases link tRNAs with their cognate amino acid. In some cases, their fidelity relies on hydrolytic editing that destroys incorrectly activated amino acids or mischarged tRNAs. We present structures of leucyl-tRNA synthetase complexed with analogs of the distinct pre- and posttransfer editing substrates. The editing active site binds the two different substrates using a single amino acid discriminatory pocket while preserving the same mode of adenine recognition. This suggests a similar mechanism of hydrolysis for both editing substrates that depends on a key, completely conserved aspartic acid, which interacts with the alpha-amino group of the noncognate amino acid and positions both substrates for hydrolysis. Our results demonstrate the economy by which a single active site accommodates two distinct substrates in a proofreading process critical to the fidelity of protein synthesis.
Journal of the American Chemical Society, 1999
SPOCC resin 1, a novel, highly permeable, polar support for chemical and enzymatic solid-phase me... more SPOCC resin 1, a novel, highly permeable, polar support for chemical and enzymatic solid-phase methods, is presented. The synthesis of SPOCC resin is based on the cross-linking of long-chain poly(ethylene glycol) (PEG) terminally substituted with oxetane by cationic ring-opening polymerization, affording a polymer containing only primary ether and alcohol CO bonds. The polymer was prepared using Et 2 O‚BF 3 as initiator either via bulk polymerization in solution or via suspension polymerization in silicon oil, the latter yielding a beaded resin. The polymerization reaction was investigated with respect to the effects of PEG chain length, the fraction of bisoxetanylated PEG, initiator amount, and temperature in order to vary the swelling, loading, and mechanical stability of the resin. Furthermore, the resin was derivatized with various functional groups and subsequently applied to peptide synthesis and organic reactions in both organic solvents and water. An N-terminal peptide aldehyde was generated on the solid phase and employed to synthesize peptide isosteres by nucleophilic addition of various ylides. Solid-phase glycosylation of peptides and enzymatic reactions were successfully performed with SPOCC resin. Enzymatic proteolytic cleavage of a resin-bound decapeptide on treatment with the 27 kDa protease subtilisin BNP′ demonstrated the accessibility of the interior of the SPOCC resin for enzymes. * To whom correspondence should be addressed. † SPOCC resin) superpermeable organic combinatorial chemistry resin.
The Journal of Organic Chemistry, 2012
This note describes a rapid and mild strategy for the loading of alcohols and anilines onto a pol... more This note describes a rapid and mild strategy for the loading of alcohols and anilines onto a polystyrene triphenylmethyl (trityl) resin. High loadings were obtained in a matter of minutes by treating resin bound trityl chloride with triethyloxonium tetrafluoroborate followed by alcohols or anilines. Yields were comparable or better than known literature methods. Recycling of the recovered resin was also possible using the developed method.
Journal of Molecular Biology, 2011
Escherichia coli peptidyl-tRNA hydrolase activity is inhibited by 3′-(L-[N,Ndiacetyl-lysinyl)amin... more Escherichia coli peptidyl-tRNA hydrolase activity is inhibited by 3′-(L-[N,Ndiacetyl-lysinyl)amino-3′-deoxyadenosine, a stable mimic of the minimalist substrate 2′(3′)-O-(L-[N,N-diacetyl-lysinyl)adenosine. The complex of this mimic with the enzyme has been analyzed by NMR spectroscopy, enabling experimental mapping of the catalytic center for the first time. Chemical shift variations point out the sensitivity of residues Asn10,
Journal of Molecular Biology, 2004
The Escherichia coli biotin repressor functions in biotin retention and regulation of biotin bios... more The Escherichia coli biotin repressor functions in biotin retention and regulation of biotin biosynthesis. Biotin retention is accomplished via the two-step biotinylation of the biotin-dependent enzyme, acetyl-CoA carboxylase. In the first step of this reaction the substrates biotin and ATP are utilized in synthesis of the activated biotin, biotinyl-5'-AMP, while in the second step this activated biotin is transferred to a unique lysine residue of the biotin carboxyl carrier protein subunit of the carboxylase. Regulation of biotin biosynthesis is accomplished through binding of the repressor to the transcription control region of the biotin biosynthetic operon. The adenylated or activated biotin functions as the corepressor in this DNA binding process. The activated biotin is a mixed anhydride and thus labile. In efforts to develop tools for structural and thermodynamic studies of the biotin regulatory interactions, two analogs of the adenylate, a sulfamoyl derivative and an ester derivative, have been synthesized and functionally characterized. Results of fluorescence measurements indicate that both analogs bind with high affinity to the repressor and that both are inactive in biotin transfer to the acceptor protein. Functional studies of their corepressor properties indicate that while the sulfamoyl is a weak allosteric activator, the ester closely mimics the physiological corepressor in activation of assembly of the transcription repression complex. Results of these studies also provide further insight into the allosteric mechanism of the biotin repressor.
Chemistry - A European Journal, 2009
We present the synthesis and photophysical characterisation of a series of structurally diverse, ... more We present the synthesis and photophysical characterisation of a series of structurally diverse, fluorescent 2,6,8-trisubstituted 3-hydroxychromone derivatives with high fluorescence quantum yields and molar extinction coefficients. Two of these derivatives (9 and 10 a) have been studied as fluorophores for cellular imaging in HeLa cells and show excellent permeability and promising fluorescence properties in a cellular environment. In addition, we have demonstrated by photophysical characterisation of 3-isobutyroxychromone derivatives that esterification of the 3-hydroxyl group results in acceptable and useful fluorescence properties.