PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and... more PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and are targets of interest for therapeutic intervention. We have identified a low-nanomolar pan-PIM inhibitor (PIM1/2/3 potency 5:14:2nM) using structure based modeling. The crystal structure of this compound with PIM1 confirmed the predicted binding mode and protein-ligand interactions except those in the acidic ribose pocket. We show the SAR suggesting the importance of having a hydrogen bond donor in this pocket for inhibiting PIM2; however, this interaction is not important for inhibiting PIM1 or PIM3. In addition, we report the discovery of a new class of PIM inhibitors by using computational de novo design tool implemented in MOE software (Chemical Computing Group). These inhibitors have a different interaction profile.
Analytic formulae are used to estimate the error for two virtual screening metrics, enrichment fa... more Analytic formulae are used to estimate the error for two virtual screening metrics, enrichment factor and area under the ROC curve. These analytic error estimates are then compared to bootstrapping error estimates, and shown to have excellent agreement with respect to area under the ROC curve and good agreement with respect to enrichment factor. The major advantage of the analytic formulae is that they are trivial to calculate and depend only on the number of actives and inactives and the measured value of the metric, information commonly reported in papers. In contrast to this, the bootstrapping method requires the individual compound scores. Methods for converting the error, which is calculated as a variance, into more familiar error bars are also discussed.
Over the past two decades, solvent mapping has emerged as a useful tool for identifying hot spots... more Over the past two decades, solvent mapping has emerged as a useful tool for identifying hot spots within binding sites on proteins for drug-like molecules and suggesting properties of potential binders. While the experimental technique requires solving multiple crystal structures of a protein in different solvents, computational solvent mapping allows for fast analysis of a protein for potential binding sites and their druggability. Recent advances in genomics, systems biology and interactomics provide a multitude of potential targets for drug development and solvent mapping can provide useful information to help prioritize targets for drug discovery projects. Here, we review various approaches to computational solvent mapping, highlight some key advances and provide our opinion on future directions in the field.
Protein kinases, which play an important role in the regulation of the majority of cellular proce... more Protein kinases, which play an important role in the regulation of the majority of cellular processes, especially those involved in cellular signal transduction, by catalyzing the phosphorylation of specific proteins, are the attractive targets of drug design in pharmaceuticals industry. Interestingly, up to 10% of proteins in the human kinome termed pseudokinases are predicted to be enzymatically inactive, but are still pivotal in regulating diverse cellular processes and thus may be a potential therapeutic target to a certain extent. To study the underlying molecular mechanisms, molecular dynamics simulations were performed to investigate the role of bivalent cations Mg²⁺ and Mn²⁺ in the structural stabilities and dynamical behaviors of vaccinia related kinase 3 (VRK3), which was the first solved crystal structure of the pseudokinase, and that of its closest active relatives VRK1 and VRK2. Toward this end, a series of molecular dynamics simulations have been performed with different divalent cations binding modes in the active site. The simulations suggested that the binding of Mg²⁺ in the active site played a key structural role in the stabilization of VRK1 and VRK2, and Mn²⁺ was slightly required for VRK2. By contrast, the pseudokinase VRK3 was well ordered with lower RMSD values indicating it was rigid and very stable regardless of whether the bivalent cations were bound or not during the simulations. The present study provided evidence for the role of bivalent cations in structural stabilities of VRKs and the proposed simulation model reconciled the interpretation of available experimental structural and thermal denaturation assay data. These results gave us further information on the dynamical behaviors of the active site of VRKs and suggested a mechanism of regulation of their structural stabilities, and might provide a starting point for the more detailed follow- up investigation of drug design.
The nuclear receptor RORγ plays a central role in controlling a pro-inflammatory gene expression ... more The nuclear receptor RORγ plays a central role in controlling a pro-inflammatory gene expression program in several lymphocyte lineages including TH17 cells. RORγ-dependent inflammation has been implicated in the pathogenesis of several major autoimmune diseases and thus RORγ is an attractive target for therapeutic intervention in these diseases. Starting from a lead biaryl compound 4a, replacement of the head phenyl moiety with a substituted aminopyrazole group resulted in a series with improved physical properties. Further SAR exploration led to analogues (e.g., 4j and 5m) as potent RORγ inverse agonists.
RORγt is a pivotal regulator of a pro-inflammatory gene expression program implicated in the path... more RORγt is a pivotal regulator of a pro-inflammatory gene expression program implicated in the pathology of several major human immune-mediated diseases. Evidence from mouse models demonstrates that genetic or pharmacological inhibition of RORγ activity can block the production of pathogenic cytokines, including IL-17, and convey therapeutic benefit. We have identified and developed a biaryl-carboxylamide series of RORγ inverse agonists via a structure based design approach. Co-crystal structures of compounds 16 and 48 supported the design approach and confirmed the key interactions with RORγ protein; the hydrogen bonding with His479 was key to the significant improvement in inverse agonist effect. The results have shown this is a class of potent and selective RORγ inverse agonists, with demonstrated oral bioavailability in rodents.
Burger's Medicinal Chemistry and Drug Discovery, 2003
Page 1. VIRTUAL SCREENING INGO MUEGGE SCOTT OLOFF Boehringer Ingelheim Pharmaceuticals, Inc., Rid... more Page 1. VIRTUAL SCREENING INGO MUEGGE SCOTT OLOFF Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 1. INTRODUCTION Since the 6th edition of Burger's Medicinal Chemistry and Drug Discovery went ...
Several advances in the fields of crystallography, molecular modeling, biophysical assays and che... more Several advances in the fields of crystallography, molecular modeling, biophysical assays and chemistry are converging to making protein-protein interaction targets more amenable to drug design. These include steps towards improving crystallization of protein-protein complexes, identifying the clusters of residues that constitute putative small molecule binding 'hot spots', generating new methods for detecting the binding of small molecules to target proteins, and generating custom libraries via diversity oriented synthesis to enable the identification of natural-product-like hits.
Phosphorus, Sulfur, and Silicon and the Related Elements, 1996
ABSTRACT The stabilizing interactions in pentavalent and tetravalent phosphonate esters of the ac... more ABSTRACT The stabilizing interactions in pentavalent and tetravalent phosphonate esters of the active-site Ser in selected serine hydrolase enzymes can be used to explain how these man-made molecules recruit enzyme catalytic power up to 70% of that of the natural substrate. The removal of the leaving group of a substrate or inhibitor is very efficient by acetylcholinesterase (AChE) because it is aided by hydrophobic forces and the repulsive interaction with the negatively charged Glu199 at the active site of AChE. The interactions between protein and small molecular fragments were evaluated with molecular mechanics and dynamics. The conclusions should be informative to the design of haptens for antibodies and efforts to drug design and detoxification after enzyme inhibition.
... Probing the Active Site of Acetylcholinesterase by Molecular Dynamics of Its Phosphonate Este... more ... Probing the Active Site of Acetylcholinesterase by Molecular Dynamics of Its Phosphonate Ester Adducts . ... 7,22 The calculations complemented experimental findings and addressed issues inaccessible to experimental observation at this time. ...
... The fasciculin-inhibited Mo AChE has an active site somewhat distorted and displaced toward t... more ... The fasciculin-inhibited Mo AChE has an active site somewhat distorted and displaced toward the Ω loop which seems to have a key role in enzyme function. Fascination with substrate entry and product release, a key issue ...
Kinases have become a major area of drug discovery and structure-based design. Hundreds of 3D str... more Kinases have become a major area of drug discovery and structure-based design. Hundreds of 3D structures for more than thirty different kinases are available to the public. High structural and sequence homology within the kinase gene family makes the remaining kinases ideal targets for homology modeling and virtual screening. Somewhat surprisingly, however, the number of publications about virtual screening of kinases is very low. Therefore, rather than reviewing the field of virtual screening for kinases, we attempt here a hybrid approach of presenting what is known and common practice together with new studies on CDK2 and SRC kinase. To illustrate the challenges and pitfalls of virtual screening for kinase targets we focus on the question of how ranking is influenced by the database screened, the docking scheme, the scoring function, the activity of the compounds used for testing, and small changes in the binding pocket. In addition, a case study of finding irreversible inhibitors of ErbB2 through in silico screening is presented.
PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and... more PIM kinases are implicated in variety of cancers by promoting cell survival and proliferation and are targets of interest for therapeutic intervention. We have identified a low-nanomolar pan-PIM inhibitor (PIM1/2/3 potency 5:14:2nM) using structure based modeling. The crystal structure of this compound with PIM1 confirmed the predicted binding mode and protein-ligand interactions except those in the acidic ribose pocket. We show the SAR suggesting the importance of having a hydrogen bond donor in this pocket for inhibiting PIM2; however, this interaction is not important for inhibiting PIM1 or PIM3. In addition, we report the discovery of a new class of PIM inhibitors by using computational de novo design tool implemented in MOE software (Chemical Computing Group). These inhibitors have a different interaction profile.
Analytic formulae are used to estimate the error for two virtual screening metrics, enrichment fa... more Analytic formulae are used to estimate the error for two virtual screening metrics, enrichment factor and area under the ROC curve. These analytic error estimates are then compared to bootstrapping error estimates, and shown to have excellent agreement with respect to area under the ROC curve and good agreement with respect to enrichment factor. The major advantage of the analytic formulae is that they are trivial to calculate and depend only on the number of actives and inactives and the measured value of the metric, information commonly reported in papers. In contrast to this, the bootstrapping method requires the individual compound scores. Methods for converting the error, which is calculated as a variance, into more familiar error bars are also discussed.
Over the past two decades, solvent mapping has emerged as a useful tool for identifying hot spots... more Over the past two decades, solvent mapping has emerged as a useful tool for identifying hot spots within binding sites on proteins for drug-like molecules and suggesting properties of potential binders. While the experimental technique requires solving multiple crystal structures of a protein in different solvents, computational solvent mapping allows for fast analysis of a protein for potential binding sites and their druggability. Recent advances in genomics, systems biology and interactomics provide a multitude of potential targets for drug development and solvent mapping can provide useful information to help prioritize targets for drug discovery projects. Here, we review various approaches to computational solvent mapping, highlight some key advances and provide our opinion on future directions in the field.
Protein kinases, which play an important role in the regulation of the majority of cellular proce... more Protein kinases, which play an important role in the regulation of the majority of cellular processes, especially those involved in cellular signal transduction, by catalyzing the phosphorylation of specific proteins, are the attractive targets of drug design in pharmaceuticals industry. Interestingly, up to 10% of proteins in the human kinome termed pseudokinases are predicted to be enzymatically inactive, but are still pivotal in regulating diverse cellular processes and thus may be a potential therapeutic target to a certain extent. To study the underlying molecular mechanisms, molecular dynamics simulations were performed to investigate the role of bivalent cations Mg²⁺ and Mn²⁺ in the structural stabilities and dynamical behaviors of vaccinia related kinase 3 (VRK3), which was the first solved crystal structure of the pseudokinase, and that of its closest active relatives VRK1 and VRK2. Toward this end, a series of molecular dynamics simulations have been performed with different divalent cations binding modes in the active site. The simulations suggested that the binding of Mg²⁺ in the active site played a key structural role in the stabilization of VRK1 and VRK2, and Mn²⁺ was slightly required for VRK2. By contrast, the pseudokinase VRK3 was well ordered with lower RMSD values indicating it was rigid and very stable regardless of whether the bivalent cations were bound or not during the simulations. The present study provided evidence for the role of bivalent cations in structural stabilities of VRKs and the proposed simulation model reconciled the interpretation of available experimental structural and thermal denaturation assay data. These results gave us further information on the dynamical behaviors of the active site of VRKs and suggested a mechanism of regulation of their structural stabilities, and might provide a starting point for the more detailed follow- up investigation of drug design.
The nuclear receptor RORγ plays a central role in controlling a pro-inflammatory gene expression ... more The nuclear receptor RORγ plays a central role in controlling a pro-inflammatory gene expression program in several lymphocyte lineages including TH17 cells. RORγ-dependent inflammation has been implicated in the pathogenesis of several major autoimmune diseases and thus RORγ is an attractive target for therapeutic intervention in these diseases. Starting from a lead biaryl compound 4a, replacement of the head phenyl moiety with a substituted aminopyrazole group resulted in a series with improved physical properties. Further SAR exploration led to analogues (e.g., 4j and 5m) as potent RORγ inverse agonists.
RORγt is a pivotal regulator of a pro-inflammatory gene expression program implicated in the path... more RORγt is a pivotal regulator of a pro-inflammatory gene expression program implicated in the pathology of several major human immune-mediated diseases. Evidence from mouse models demonstrates that genetic or pharmacological inhibition of RORγ activity can block the production of pathogenic cytokines, including IL-17, and convey therapeutic benefit. We have identified and developed a biaryl-carboxylamide series of RORγ inverse agonists via a structure based design approach. Co-crystal structures of compounds 16 and 48 supported the design approach and confirmed the key interactions with RORγ protein; the hydrogen bonding with His479 was key to the significant improvement in inverse agonist effect. The results have shown this is a class of potent and selective RORγ inverse agonists, with demonstrated oral bioavailability in rodents.
Burger's Medicinal Chemistry and Drug Discovery, 2003
Page 1. VIRTUAL SCREENING INGO MUEGGE SCOTT OLOFF Boehringer Ingelheim Pharmaceuticals, Inc., Rid... more Page 1. VIRTUAL SCREENING INGO MUEGGE SCOTT OLOFF Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT 1. INTRODUCTION Since the 6th edition of Burger's Medicinal Chemistry and Drug Discovery went ...
Several advances in the fields of crystallography, molecular modeling, biophysical assays and che... more Several advances in the fields of crystallography, molecular modeling, biophysical assays and chemistry are converging to making protein-protein interaction targets more amenable to drug design. These include steps towards improving crystallization of protein-protein complexes, identifying the clusters of residues that constitute putative small molecule binding 'hot spots', generating new methods for detecting the binding of small molecules to target proteins, and generating custom libraries via diversity oriented synthesis to enable the identification of natural-product-like hits.
Phosphorus, Sulfur, and Silicon and the Related Elements, 1996
ABSTRACT The stabilizing interactions in pentavalent and tetravalent phosphonate esters of the ac... more ABSTRACT The stabilizing interactions in pentavalent and tetravalent phosphonate esters of the active-site Ser in selected serine hydrolase enzymes can be used to explain how these man-made molecules recruit enzyme catalytic power up to 70% of that of the natural substrate. The removal of the leaving group of a substrate or inhibitor is very efficient by acetylcholinesterase (AChE) because it is aided by hydrophobic forces and the repulsive interaction with the negatively charged Glu199 at the active site of AChE. The interactions between protein and small molecular fragments were evaluated with molecular mechanics and dynamics. The conclusions should be informative to the design of haptens for antibodies and efforts to drug design and detoxification after enzyme inhibition.
... Probing the Active Site of Acetylcholinesterase by Molecular Dynamics of Its Phosphonate Este... more ... Probing the Active Site of Acetylcholinesterase by Molecular Dynamics of Its Phosphonate Ester Adducts . ... 7,22 The calculations complemented experimental findings and addressed issues inaccessible to experimental observation at this time. ...
... The fasciculin-inhibited Mo AChE has an active site somewhat distorted and displaced toward t... more ... The fasciculin-inhibited Mo AChE has an active site somewhat distorted and displaced toward the Ω loop which seems to have a key role in enzyme function. Fascination with substrate entry and product release, a key issue ...
Kinases have become a major area of drug discovery and structure-based design. Hundreds of 3D str... more Kinases have become a major area of drug discovery and structure-based design. Hundreds of 3D structures for more than thirty different kinases are available to the public. High structural and sequence homology within the kinase gene family makes the remaining kinases ideal targets for homology modeling and virtual screening. Somewhat surprisingly, however, the number of publications about virtual screening of kinases is very low. Therefore, rather than reviewing the field of virtual screening for kinases, we attempt here a hybrid approach of presenting what is known and common practice together with new studies on CDK2 and SRC kinase. To illustrate the challenges and pitfalls of virtual screening for kinase targets we focus on the question of how ranking is influenced by the database screened, the docking scheme, the scoring function, the activity of the compounds used for testing, and small changes in the binding pocket. In addition, a case study of finding irreversible inhibitors of ErbB2 through in silico screening is presented.
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