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Pearlstein RA, MacCannell KA, Erdemli G, Yeola S, Helmlinger G, Hu QY, Farid R, Egan W, Whitebread S, Springer C, Beck J, Wang HR, Maciejewski M, Urban L, Duca JS. Implications of Dynamic Occupancy, Binding Kinetics, and Channel Gating Kinetics for hERG Blocker Safety Assessment and Mitigation. Curr Top Med Chem 2017; 16:1792-818. [PMID: 26975508 DOI: 10.2174/1568026616666160315142156] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 11/22/2022]
Abstract
Blockade of the hERG potassium channel prolongs the ventricular action potential (AP) and QT interval, and triggers early after depolarizations (EADs) and torsade de pointes (TdP) arrhythmia. Opinions differ as to the causal relationship between hERG blockade and TdP, the relative weighting of other contributing factors, definitive metrics of preclinical proarrhythmicity, and the true safety margin in humans. Here, we have used in silico techniques to characterize the effects of channel gating and binding kinetics on hERG occupancy, and of blockade on the human ventricular AP. Gating effects differ for compounds that are sterically compatible with closed channels (becoming trapped in deactivated channels) versus those that are incompatible with the closed/closing state, and expelled during deactivation. Occupancies of trappable blockers build to equilibrium levels, whereas those of non-trappable blockers build and decay during each AP cycle. Occupancies of ~83% (non-trappable) versus ~63% (trappable) of open/inactive channels caused EADs in our AP simulations. Overall, we conclude that hERG occupancy at therapeutic exposure levels may be tolerated for nontrappable, but not trappable blockers capable of building to the proarrhythmic occupancy level. Furthermore, the widely used Redfern safety index may be biased toward trappable blockers, overestimating the exposure-IC50 separation in nontrappable cases.
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Affiliation(s)
- Robert A Pearlstein
- Novartis Institutes for Bio- Medical Research, Inc., 100 Technology Square, Cambridge, MA 02139, USA.
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Bidkhori H, Bahrami A, Farshchian M, Naderi-Meshkin H, Heirani A, Mirahmadi M, Dastpak M, Hasanzade H, Farid R, Ahmadiankia N, Bakhtiari H, Matin M. Genetically Modified Human Adipose-Derived Mesenchymal Stem Cells Overexpressing CXCR4R334X, a Hyper Functional Mutant Receptor, Display Enhanced Migration. Cytotherapy 2016. [DOI: 10.1016/j.jcyt.2016.03.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Murphy RB, Repasky MP, Greenwood JR, Tubert-Brohman I, Jerome S, Annabhimoju R, Boyles NA, Schmitz CD, Abel R, Farid R, Friesner RA. WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand–Receptor Docking. J Med Chem 2016; 59:4364-84. [DOI: 10.1021/acs.jmedchem.6b00131] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Robert B. Murphy
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | - Matthew P. Repasky
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | - Jeremy R. Greenwood
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ivan Tubert-Brohman
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Steven Jerome
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | - Nicholas A. Boyles
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | | | - Robert Abel
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ramy Farid
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A. Friesner
- Department of
Chemistry, Columbia University, New York, 3000 Broadway,
MC 3110, New York 10036, United States
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4
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Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc 2015; 137:2695-703. [PMID: 25625324 DOI: 10.1021/ja512751q] [Citation(s) in RCA: 770] [Impact Index Per Article: 85.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well as the advent of low-cost parallel computing. However, it has proven to be challenging to reliably achieve the level of accuracy that would be needed to guide lead optimization (∼5× in binding affinity) for a wide range of ligands and protein targets. Not surprisingly, widespread commercial application of free-energy simulations has been limited due to the lack of large-scale validation coupled with the technical challenges traditionally associated with running these types of calculations. Here, we report an approach that achieves an unprecedented level of accuracy across a broad range of target classes and ligands, with retrospective results encompassing 200 ligands and a wide variety of chemical perturbations, many of which involve significant changes in ligand chemical structures. In addition, we have applied the method in prospective drug discovery projects and found a significant improvement in the quality of the compounds synthesized that have been predicted to be potent. Compounds predicted to be potent by this approach have a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches. Furthermore, the results are consistent with those obtained from our retrospective studies, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.
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Affiliation(s)
- Lingle Wang
- Schrödinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
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5
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Abbas F, Farid R, Nada I, El-Sharnouby M. Evaluation of ethanolamine oleate sclerotherapy on the submandibular glands of canines as a potential therapy for sialorrhea. Int J Pediatr Otorhinolaryngol 2013; 77:351-5. [PMID: 23246419 DOI: 10.1016/j.ijporl.2012.11.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/15/2012] [Accepted: 11/18/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Sialorrhea can have major negative effects on the physical and social well-being. Sclerotherapy may be useful in patients with sialorrhea by decreasing the amount of saliva production. The aim of this study was to test the effect of ethanolamine oleate (EO) in an experimental model as a preliminary step for its application in humans. METHODS Histopathological and morphometric analysis of submandibular glands from thirteen dogs was preformed. A total of 25 glands were injected with 1ml of 2.5% EO (n=5), 1ml of 5% EO (n=5), 5ml of 2.5% EO (n=5) and 5ml of 5% EO (n=5). Five glands were used as control. RESULTS EO significantly induced a dose dependent scaring of the gland ending in lobular transformation (salivary gland cirrhosis). Morphometric measurements showed that 1ml of 2.5% or 5% EO significantly induced fibrosis compared to normal glands (p=0.014 and 0.021, respectively). Fibrosis significantly increased and was more apparent when a dose of 5ml of 2.5% EO or 5% EO were injected [by semi-quantitative evaluation (p=0.016 and 0.002, respectively) and morphometric measurements (p=0.016 and 0.008, respectively)]. This scarring effect was significantly associated with reduction of area of acinar cells when a dose of 1ml-5%, 5ml-2.5% or 5ml-5% EO were applied (p=0.03. 0.012 and 0.004, respectively). Moreover, ductal injury was only significant when a dose of 5ml of 5% EO was used (p=0.034). This dose and concentration (i.e. 5ml-5% EO) had a significant synergetic effect [p=0.0119]. CONCLUSION In this model, treatment with EO proved to permanently reduce the acinar area through induction of progressive, irreversible and dose dependant scarring (medical sialoadenectomy).
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Affiliation(s)
- F Abbas
- ENT Department, Faculty of Medicine, Misr University for Science and Technology, 6th of October city, Giza, Egypt
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Tran QT, Williams S, Farid R, Erdemli G, Pearlstein R. The translocation kinetics of antibiotics through porin OmpC: insights from structure-based solvation mapping using WaterMap. Proteins 2012; 81:291-9. [PMID: 23011778 DOI: 10.1002/prot.24185] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/24/2012] [Accepted: 09/13/2012] [Indexed: 11/12/2022]
Abstract
Poor permeability of the lipopolysaccharide-based outer membrane of Gram-negative bacteria is compensated by the existence of protein channels (porins) that selectively admit low molecular weight substrates, including many antibiotics. Improved understanding of the translocation mechanisms of porin substrates could help guide the design of antibiotics capable of achieving high intracellular exposure. Energy barriers to channel entry and exit govern antibiotic fluxes through porins. We have previously reported a hypothesis that the costs of transferring protein solvation to and from bulk medium underlie the barriers to protein-ligand association and dissociation, respectively, concomitant with the gain and loss of protein-ligand interactions during those processes. We have now applied this hypothesis to explain the published rates of entry (association) and exit (dissociation) of six antibiotics to/from reconstituted E. coli porin OmpC. WaterMap was used to estimate the total water transfer energies resulting from transient occupation by each antibiotic. Our results suggest that solvation within the porin cavity is highly energetically favorable, and the observed moderately fast entry rates of the antibiotics are consistent with replacement of protein-water H-bonds. The observed ultrafast exit kinetics is consistent with the lack of intrachannel solvation sites that convey unfavorable resolvation during antibiotic dissociation. These results are aligned with known general relationships between antibiotic efficacy and physicochemical properties, namely unusually low logP, reflecting an abundance of H-bond partners. We conclude that antibiotics figuratively "melt" their way through porin solvation at a rate determined by the cost of exchanging protein-solvent for protein-antibiotic H-bonds.
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Affiliation(s)
- Que-Tien Tran
- Novartis Institutes for BioMedical Research, Center for Proteomic Chemistry, Cambridge, Massachusetts 02139, USA.
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Bell JA, Ho KL, Farid R. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. Acta Crystallogr D Biol Crystallogr 2012; 68:935-52. [PMID: 22868759 PMCID: PMC3413210 DOI: 10.1107/s0907444912017453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/19/2012] [Indexed: 11/12/2022]
Abstract
All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.
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Affiliation(s)
- Jeffrey A. Bell
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Kenneth L. Ho
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Ramy Farid
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
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8
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Abstract
Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.
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Affiliation(s)
- Jianing Li
- Department of Chemistry, Columbia University, New York, NY
| | | | - Joseph Bylund
- Department of Chemistry, Columbia University, New York, NY
| | - Ramy Farid
- Schrödinger, Inc., 120 W. 45 St., New York, NY
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Zaware N, LaPorte MG, Farid R, Liu L, Wipf P, Floreancig PE. Diversity-oriented synthesis of a library of substituted tetrahydropyrones using oxidative carbon-hydrogen bond activation and click chemistry. Molecules 2011; 16:3648-62. [PMID: 21540794 PMCID: PMC6263335 DOI: 10.3390/molecules16053648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 04/12/2011] [Indexed: 11/16/2022] Open
Abstract
Eighteen (2RS,6RS)-2-(4-methoxyphenyl)-6-(substituted ethyl)dihydro-2H-pyran-4(3H)ones were synthesized via a DDQ-mediated oxidative carbon-hydrogen bond activation reaction. Fourteen of these tetrahydropyrans were substituted with triazoles readily assembled via azide-alkyne click-chemistry reactions. Examples of a linked benzotriazole and pyrazole motif were also prepared. To complement the structural diversity, the alcohol substrates were obtained from stereoselective reductions of the tetrahydropyrone. This library provides rapid access to structurally diverse non-natural compounds to be screened against a variety of biological targets.
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Affiliation(s)
- Nilesh Zaware
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Matthew G. LaPorte
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Ramy Farid
- Schrödinger, Inc., 120 West 45 Street, New York, NY 10036, USA
| | - Lei Liu
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Peter Wipf
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Paul E. Floreancig
- Department of Chemistry and Center for Chemical Methodologies & Library Development, University of Pittsburgh, Pittsburgh, PA 15260, USA
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10
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Abel R, Salam NK, Shelley J, Farid R, Friesner RA, Sherman W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases. ChemMedChem 2011; 6:1049-66. [PMID: 21506273 DOI: 10.1002/cmdc.201000533] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 03/08/2011] [Indexed: 11/12/2022]
Abstract
The prevention of blood coagulation is important in treating thromboembolic disorders, and several serine proteases involved in the coagulation cascade have been classified as pharmaceutically relevant. Whereas structure-based drug design has contributed to the development of some serine protease inhibitors, traditional computational methods have not been able to fully describe structure-activity relationships (SAR). Here, we study the SAR for a number of serine proteases by using a method that calculates the thermodynamic properties (enthalpy and entropy) of the water that solvates the active site. We show that the displacement of water from specific subpockets (such as S1-4 and the ester binding pocket) of the active site by the ligand can govern potency, especially for cases in which small chemical changes (i.e., a methyl group or halogen) result in a substantial increase in potency. Furthermore, we describe how relative binding free energies can be estimated by combining the water displacement energy with complementary terms from an implicit solvent molecular mechanics description binding.
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12
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13
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Lyman E, Higgs C, Kim B, Lupyan D, Shelley JC, Farid R, Voth GA. A role for a specific cholesterol interaction in stabilizing the Apo configuration of the human A(2A) adenosine receptor. Structure 2010; 17:1660-1668. [PMID: 20004169 DOI: 10.1016/j.str.2009.10.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Revised: 10/06/2009] [Accepted: 10/15/2009] [Indexed: 10/20/2022]
Abstract
The function of G-protein-coupled receptors is tightly modulated by the lipid environment. Long-timescale molecular dynamics simulations (totaling approximately 3 mus) of the A(2A) receptor in cholesterol-free bilayers, with and without the antagonist ZM241385 bound, demonstrate the instability of helix II in the apo receptor in cholesterol-poor membrane regions. We directly observe that the effect of cholesterol binding is to stabilize helix II against a buckling-type deformation, perhaps rationalizing the observation that the A(2A) receptor couples to G protein only in the presence of cholesterol (Zezula and Freissmuth, 2008). The results suggest a mechanism by which the A(2A) receptor may function as a coincidence detector, activating only in the presence of both cholesterol and agonist. We also observed a previously hypothesized conformation of the tryptophan "rotameric switch" on helix VI in which a phenylalanine on helix V positions the tryptophan out of the ligand binding pocket.
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Affiliation(s)
- Edward Lyman
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Chris Higgs
- Schrödinger, L.L.C., 8910 University Center Lane, Suite 270, San Diego, CA 92122, USA
| | - Byungchan Kim
- Schrödinger, L.L.C., 120 West 45(th) Street, New York, NY 10036, USA
| | - Dmitry Lupyan
- Schrödinger, L.L.C., 120 West 45(th) Street, New York, NY 10036, USA; Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - John C Shelley
- Schrodinger, L.L.C., 101 S.W. Main Street, Suite 1300 Portland, OR 97204, USA
| | - Ramy Farid
- Schrödinger, L.L.C., 120 West 45(th) Street, New York, NY 10036, USA
| | - Gregory A Voth
- Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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Abstract
PDZ domains have well known binding preferences for distinct C-terminal peptide motifs. For most PDZ domains, these motifs are of the form [S/T]-W-[I/L/V]. Although the preference for S/T has been explained by a specific hydrogen bond interaction with a histidine in the PDZ domain and the (I/L/V) is buried in a hydrophobic pocket, the mechanism for Trp specificity at the second to last position has thus far remained unknown. Here, we apply a method to compute the free energies of explicit water molecules and predict that potency gained by Trp binding is due to a favorable release of high-energy water molecules into bulk. The affinities of a series of peptides for both wild-type and mutant forms of the PDZ domain of Erbin correlate very well with the computed free energy of binding of displaced waters, suggesting a direct relationship between water displacement and peptide affinity. Finally, we show a correlation between the magnitude of the displaced water free energy and the degree of Trp-sensitivity among subtypes of the HTRA PDZ family, indicating a water-mediated mechanism for specificity of peptide binding.
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15
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Praveen P, Shah D, Farid R, Parmar S. O.455 Postoperative use of intremaxillary flxation devices. J Craniomaxillofac Surg 2008. [DOI: 10.1016/s1010-5182(08)71579-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Abstract
Understanding the underlying physics of the binding of small-molecule ligands to protein active sites is a key objective of computational chemistry and biology. It is widely believed that displacement of water molecules from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying molecular physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient descriptor of the contribution of the solvent to the binding free energy of a small molecule and its associated receptor that captures the effects of the ligand displacing the solvent from the protein active site with atomic detail. This descriptor quantitatively predicts (R(2) = 0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates physical properties of the active-site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity relationship of its inhibitors.
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Affiliation(s)
- Robert Abel
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Tom Young
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Ramy Farid
- Schrödinger, Inc, 120 West 45th Street, New York, New York 10036
| | - Bruce J. Berne
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
| | - Richard A. Friesner
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027
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17
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Hunt JF, Yu B, Ergel B, Pastore C, Liebisch G, Edstrom W, Gibney B, Friesner R, Farid R. Structural and mechanistic studies of AlkB. FASEB J 2008. [DOI: 10.1096/fasebj.22.1_supplement.526.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Rao S, Sanschagrin PC, Greenwood JR, Repasky MP, Sherman W, Farid R. Improving database enrichment through ensemble docking. J Comput Aided Mol Des 2008; 22:621-7. [PMID: 18253700 DOI: 10.1007/s10822-008-9182-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 01/15/2008] [Indexed: 10/22/2022]
Abstract
While it may seem intuitive that using an ensemble of multiple conformations of a receptor in structure-based virtual screening experiments would necessarily yield improved enrichment of actives relative to using just a single receptor, it turns out that at least in the p38 MAP kinase model system studied here, a very large majority of all possible ensembles do not yield improved enrichment of actives. However, there are combinations of receptor structures that do lead to improved enrichment results. We present here a method to select the ensembles that produce the best enrichments that does not rely on knowledge of active compounds or sophisticated analyses of the 3D receptor structures. In the system studied here, the small fraction of ensembles of up to 3 receptors that do yield good enrichments of actives were identified by selecting ensembles that have the best mean GlideScore for the top 1% of the docked ligands in a database screen of actives and drug-like "decoy" ligands. Ensembles of two receptors identified using this mean GlideScore metric generally outperform single receptors, while ensembles of three receptors identified using this metric consistently give optimal enrichment factors in which, for example, 40% of the known actives outrank all the other ligands in the database.
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Affiliation(s)
- Shashidhar Rao
- Schrödinger, Inc, 120 West 45th Street, New York, NY, 10036, USA
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19
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Tagliamonte M, Naderi H, Tornesello M, Farid R, Buonaguro F, Buonaguro L. HIV type 1 subtype A epidemic in injecting drug user (IDU) communities in Iran. AIDS Res Hum Retroviruses 2007; 23:1569-74. [PMID: 18160015 DOI: 10.1089/aid.2007.0169] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
HIV-1 C2-V3 subgenomic regions of the env gene from Iranian seropositive injecting drug users (IDUs) living in Mashhad have been analyzed to evaluate molecular and phylogenetic relationships with IDUs living in Tehran and identify possible common founder virus isolates. The results show that the viral sequences of the Iranian IDUs are strongly related and form a single cluster within the A subtype related to African Ugandan/Kenyan sub-Saharan isolates. Pairwise nucleotide alignment shows higher average divergence values within the Mashhad group than the Tehran group. Furthermore, the Mashhad sequences show much less conserved amino acid residues in the V3 loop than the Tehran sequences. These data represent the first macro-analysis of the HIV-1 molecular evolution in the Iran and Middle East epidemics and may be extremely relevant to guide the development and implementation of diagnostic as well as preventive/therapeutic approaches in this region.
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Affiliation(s)
- M. Tagliamonte
- Viral Oncogenesis and Immunotherapy and AIDS Reference Center, Istituto Nazionale Tumori “Fond. G. Pascale,” 80131 Naples, Italy
| | - H.R. Naderi
- Institute of Infectious Diseases, University of Mashhad, Mashhad, Iran
- Department of Allergy and Immunology, University of Mashhad, Mashhad, Iran
| | - M.L. Tornesello
- Viral Oncogenesis and Immunotherapy and AIDS Reference Center, Istituto Nazionale Tumori “Fond. G. Pascale,” 80131 Naples, Italy
| | - R. Farid
- Department of Allergy and Immunology, University of Mashhad, Mashhad, Iran
| | - F.M. Buonaguro
- Viral Oncogenesis and Immunotherapy and AIDS Reference Center, Istituto Nazionale Tumori “Fond. G. Pascale,” 80131 Naples, Italy
| | - L. Buonaguro
- Viral Oncogenesis and Immunotherapy and AIDS Reference Center, Istituto Nazionale Tumori “Fond. G. Pascale,” 80131 Naples, Italy
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Naderi HR, Tagliamonte M, Tornesello ML, Ciccozzi M, Rezza G, Farid R, Buonaguro FM, Buonaguro L. Molecular and phylogenetic analysis of HIV-1 variants circulating among injecting drug users in Mashhad-Iran. Infect Agent Cancer 2006; 1:4. [PMID: 17150133 PMCID: PMC1635003 DOI: 10.1186/1750-9378-1-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2006] [Accepted: 09/19/2006] [Indexed: 11/10/2022] Open
Abstract
Genetic and phylogenetic information on the HIV-1 epidemic in Middle-East Countries, and in particular in Iran, are extremely limited. By March 2004, the Iranian Ministry of Health officially reported a cumulative number of 6'532 HIV positive individuals and 214 AIDS cases in the Iranian HIV-1 epidemic. The intra-venous drug users (IDUs) represent the group at highest risk for HIV-1 infection in Iran, accounting for almost 63% of all HIV-infected population. In this regards, a molecular phylogenetic study has been performed on a sentinel cohort of HIV-1 seropositive IDUs enrolled at the end of 2005 at the University of Mashhad, the largest city North East of Tehran. The study has been performed on both gag and env subgenomic regions amplified by Polymerase Chain Reaction (PCR) from peripheral blood mononuclear cells (PBMCs) and characterized by direct DNA sequence analysis. The results reported here show that the HIV-1 subtype A is circulating in this IDUs sentinel cohort. Moreover, the single phylogenetic cluster as well as the intra-group low nucleotide divergence is indicative of a recent outbreak. Unexpectedly, the Iranian samples appear to be phylogenetically derived from African Sub-Saharan subtype A viruses, raising stirring speculations on HIV-1 introduction into the IDUs epidemic in Mashhad. This sentinel study could represent the starting point for a wider molecular survey of the HIV-1 epidemics in Iran to evaluate in detail the distribution of genetic subtypes and possible natural drug-resistant variants, which are extremely helpful information to design diagnostic and therapeutic strategies.
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Affiliation(s)
- HR Naderi
- Inst. of Infectious Diseases, Univ. of Mashhad –, Iran
- Allergy and Immunology Dept, Univ. of Mashhad –, Iran
| | - M Tagliamonte
- Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples –, Italy
| | - ML Tornesello
- Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples –, Italy
| | - M Ciccozzi
- Epidemiology Unit, Dept. Infectious Diseases, ISS, Rome –, Italy
| | - G Rezza
- Epidemiology Unit, Dept. Infectious Diseases, ISS, Rome –, Italy
| | - R Farid
- Allergy and Immunology Dept, Univ. of Mashhad –, Iran
| | - FM Buonaguro
- Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples –, Italy
| | - L Buonaguro
- Viral Oncogenesis and Immunotherapy & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples –, Italy
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Farid R, Day T, Friesner RA, Pearlstein RA. New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies. Bioorg Med Chem 2006; 14:3160-73. [PMID: 16413785 DOI: 10.1016/j.bmc.2005.12.032] [Citation(s) in RCA: 359] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 12/15/2005] [Accepted: 12/16/2005] [Indexed: 11/23/2022]
Abstract
We created a homology model of the homo-tetrameric pore domain of HERG using the crystal structure of the bacterial potassium channel, KvAP, as a template. We docked a set of known blockers with well-characterized effects on channel function into the lumen of the pore between the selectivity filter and extracellular entrance using a novel docking and refinement procedure incorporating Glide and Prime. Key aromatic groups of the blockers are predicted to form multiple simultaneous ring stacking and hydrophobic interactions among the eight aromatic residues lining the pore. Furthermore, each blocker can achieve these interactions via multiple docking configurations. To further interpret the docking results, we mapped hydrophobic and hydrophilic potentials within the lumen of each refined docked complex. Hydrophilic iso-potential contours define a 'propeller-shaped' volume at the selectivity filter entrance. Hydrophobic contours define a hollow 'crown-shaped' volume located above the 'propeller', whose hydrophobic 'rim' extends along the pore axis between Tyr652 and Phe656. Blockers adopt conformations/binding orientations that closely mimic the shapes and properties of these contours. Blocker basic groups are localized in the hydrophilic 'propeller', forming electrostatic interactions with Ser624 rather than a generally accepted pi-cation interaction with Tyr652. Terfenadine, cisapride, sertindole, ibutilide, and clofilium adopt similar docked poses, in which their N-substituents bridge radially across the hollow interior of the 'crown' (analogous to the hub and spokes of a wheel), and project aromatic/hydrophobic portions into the hydrophobic 'rim'. MK-499 docks with its longitudinal axis parallel to the axis of the pore and 'crown', and its hydrophobic groups buried within the hydrophobic 'rim'.
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Affiliation(s)
- Ramy Farid
- Schrödinger, Inc., 120 West Forty-Fifth Street, 32nd Floor, New York, NY 10036, USA.
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22
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Abstract
We present a novel protein-ligand docking method that accurately accounts for both ligand and receptor flexibility by iteratively combining rigid receptor docking (Glide) with protein structure prediction (Prime) techniques. While traditional rigid-receptor docking methods are useful when the receptor structure does not change substantially upon ligand binding, success is limited when the protein must be "induced" into the correct binding conformation for a given ligand. We provide an in-depth description of our novel methodology and present results for 21 pharmaceutically relevant examples. Traditional rigid-receptor docking for these 21 cases yields an average RMSD of 5.5 A. The average ligand RMSD for docking to a flexible receptor for the 21 pairs is 1.4 A; the RMSD is < or =1.8 A for 18 of the cases. For the three cases with RMSDs greater than 1.8 A, the core of the ligand is properly docked and all key protein/ligand interactions are captured.
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Abstract
Structured-based drug design has traditionally relied on a single receptor structure as a target for docking and screening studies. However, it has become increasingly clear that in many cases where protein flexibility is an issue, it is critical to accurately model ligand-induced receptor movement in order to obtain high enrichment factors. We present a novel protein-ligand docking method that accounts for both ligand and receptor flexibility and accurately predicts the conformation of protein-ligand binding complexes. This method can generate viable receptor ensembles that can be used in virtual database screens.
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Affiliation(s)
- Woody Sherman
- Schrödinger Inc., 120 West 45th Street, 32nd Floor, New York, NY 10036, USA
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Forouhar F, Hussain M, Farid R, Benach J, Abashidze M, Edstrom WC, Vorobiev SM, Xiao R, Acton TB, Fu Z, Kim JJP, Miziorko HM, Montelione GT, Hunt JF. Crystal structures of two bacterial 3-hydroxy-3-methylglutaryl-CoA lyases suggest a common catalytic mechanism among a family of TIM barrel metalloenzymes cleaving carbon-carbon bonds. J Biol Chem 2005; 281:7533-45. [PMID: 16330546 DOI: 10.1074/jbc.m507996200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) lyase catalyzes the terminal steps in ketone body generation and leucine degradation. Mutations in this enzyme cause a human autosomal recessive disorder called primary metabolic aciduria, which typically kills victims because of an inability to tolerate hypoglycemia. Here we present crystal structures of the HMG-CoA lyases from Bacillus subtilis and Brucella melitensis at 2.7 and 2.3 A resolution, respectively. These enzymes share greater than 45% sequence identity with the human orthologue. Although the enzyme has the anticipated triose-phosphate isomerase (TIM) barrel fold, the catalytic center contains a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel, contrary to the predictions of homology models. Surprisingly, the residues forming this cation-binding site and most of their interaction partners are shared with three other TIM barrel enzymes that catalyze diverse carbon-carbon bond cleavage reactions believed to proceed through enolate intermediates (4-hydroxy-2-ketovalerate aldolase, 2-isopropylmalate synthase, and transcarboxylase 5S). We propose the name "DRE-TIM metallolyases" for this newly identified enzyme family likely to employ a common catalytic reaction mechanism involving an invariant Asp-Arg-Glu (DRE) triplet. The Asp ligates the divalent cation, while the Arg probably stabilizes charge accumulation in the enolate intermediate, and the Glu maintains the precise structural alignment of the Asp and Arg. We propose a detailed model for the catalytic reaction mechanism of HMG-CoA lyase based on the examination of previously reported product complexes of other DRE-TIM metallolyases and induced fit substrate docking studies conducted using the crystal structure of human HMG-CoA lyase (reported in the accompanying paper by Fu, et al. (2006) J. Biol. Chem. 281, 7526-7532). Our model is consistent with extensive mutagenesis results and can guide subsequent studies directed at definitive experimental elucidation of this enzyme's reaction mechanism.
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Affiliation(s)
- Farhad Forouhar
- Department of Biological Sciences and Northeast Structural Genomics Consortium, Columbia University, New York, NY 10027, USA
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Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J Comput Chem 2005; 26:1752-80. [PMID: 16211539 PMCID: PMC2742605 DOI: 10.1002/jcc.20292] [Citation(s) in RCA: 1021] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.
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Jovanovic T, Farid R, Friesner RA, McDermott AE. Thermal Equilibrium of High- and Low-Spin Forms of Cytochrome P450 BM-3: Repositioning of the Substrate? J Am Chem Soc 2005; 127:13548-52. [PMID: 16190718 DOI: 10.1021/ja0524604] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate that cytochrome P450 BM-3 in complex with N-palmitoylglycine undergoes a spin state change between room temperature, where optimal activity is seen, and low temperatures, where X-ray diffraction characterization has been carried out. On the basis of NMR measurements of the full-length protein, this spin state change is likely to be accompanied by a general structural rearrangement in the enzyme pocket. The substrate remains bound at all temperatures. We propose that the substrate may "slide" from a position directly atop the heme (thus displacing the ligating water) to the more distant position (thus restoring the ligating water) as the temperature is lowered. This proposal is evaluated on the basis of computational modeling of the protein-ligand complex, using a novel induced fit methodology. We thereby generate a structure with the ligand in close contact with the heme, similar in energy to the experimental structure. With this combination of theory and experiment we provide a specific proposal of how ligands may be positioned for chemistry for this enzyme.
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Affiliation(s)
- Tijana Jovanovic
- Department of Chemistry, Columbia University, New York, New York 10027, USA
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27
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Farid R, Ghaffari J, Taghavi M, Rafatpanah H, Jabbari-azad F. Evaluation and association of anti-thyroid antibodies with Chronic Idiopathic Urticaria. J Allergy Clin Immunol 2005. [DOI: 10.1016/j.jaci.2004.12.718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sabouri AH, Saito M, Matsumoto W, Kodama D, Farid R, Izumo S, Usuku K, Osame M. A C77G point mutation in CD45 exon 4, which is associated with the development of multiple sclerosis and increased susceptibility to HIV-1 infection, is undetectable in Japanese population. Eur J Neurol 2003; 10:737-9. [PMID: 14641523 DOI: 10.1046/j.1468-1331.2003.00679.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) is one outcome of Human T-cell lymphotropic virus type 1 (HTLV-1) infection. It remains unknown why the majority of infected people remain healthy whereas only approximately 2-3% develop disease. Recently, heterozygous state of CD45 exon 4 mutation (C77C wild type and C77G mutant) was reported to be associated with development of multiple sclerosis in German patients and increased susceptibility to HIV-1 infection in the United Kingdom. To investigate whether this mutation is associated with the development of HAM/TSP, we studied a group of 164 HAM/TSP patients and 108 asymptomatic HTLV-1 carriers in Kagoshima (HTLV-1 endemic area in Southern Japan) by using PCR-RFLP and subsequent direct sequencing analysis. All 272 subjects showed homozygosity in the CD45 exon 4, suggesting that this mutation is absent or very rare in Japanese population.
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Affiliation(s)
- A H Sabouri
- Third Department of Internal Medicine, Faculty of Medicine, Kagoshima University, Sakuragaoka, Kagoshima, Japan
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Abstract
Asthma is characterized as a chronic inflammatory process. Pycnogenol((R)), a bioflavonoid mixture extracted from Pinus maritima, is known to scavenge free radicals while possessing antioxidant and antiinflammatory properties. The objective of this study was to evaluate the efficiency of this agent in a randomized, double-blinded, placebo-controlled, crossover study in patients with varying asthma severity. Twenty-six patients who fulfilled the American Thoracic Society criteria for asthma were enrolled in the study. Medical history, physical examination, blood sample analyses, and spirometric values were obtained at baseline, 4 weeks, and 8 weeks. The patients were randomly assigned to receive either 1 mg/lb/day (maximum 200 mg/day) Pycnogenol or placebo for the first period of 4 weeks and then crossed over to the alternate regimen for the next 4 weeks. No adverse effects were observed related to the study drug. Within the contingent of 22 patients who completed the study, almost all responded favorably to Pycnogenol in contrast to placebo. Pycnogenol treatment also significantly reduced serum leukotrienes compared with placebo. The results of this pilot study indicate that Pycnogenol may be a valuable nutraceutical in the management of chronic asthma. We recommend that further clinical trials be conducted in larger groups of asthmatics to establish its efficacy.
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Affiliation(s)
- Saeed Hosseini
- College of Public Health and School of Medicine, The University of Arizona, 1501 N. Campbell Ave., Tucson, AZ 85724
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Kunin AJ, Farid R, Johnson CE, Eisenberg R. Diastereoselection and the influence of chiraphos on metal-centered chirality in cis oxidative addition of hydrogen and triphenylsilane. J Am Chem Soc 2002. [DOI: 10.1021/ja00304a071] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Safai B, Huang JL, Boeri E, Farid R, Raafat J, Schutzer P, Ahkami R, Franchini G. Prevalence of HTLV type I infection in Iran: a serological and genetic study. AIDS Res Hum Retroviruses 1996; 12:1185-90. [PMID: 8844023 DOI: 10.1089/aid.1996.12.1185] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Several publications describe the presence of the human T cell lymphotropic virus type I (HTLV-I) in Jewish individuals born in Mash-had, Iran. We report here the results of HTLV-I serological and genetic studies in the non-Jewish population of Mash-had as well as a neighboring area: Gonbad-Kavous. Seven hundred and seven serum samples from Mash-had (694 healthy individuals and 13 patients with lymphoma) and 90 from Gonbad-Kavous were tested for HTLV antibodies by gelatin particle agglutination assay (PA) and confirmatory Western blots (WBs). Seropositive rates of 3.0% (21 of 694) in Mash-had, 0% (0 of 90) in Gonbad-Kavous, and 100% (13 of 13) in lymphoma cases were observed. HTLV-I DNA sequence were amplified by polymerase chain reaction directly from the fresh PBMCs of seropositive individuals. Phylogenetic analysis of the viral DNA sequence indicated that the HTLV-I present in Mash-had belong to the HTLV-I cosmopolitan clade. Altogether, these data indicate that Mash-had, located in northeastern Iran, is a newly recognized endemic center for HTLV-I.
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Affiliation(s)
- B Safai
- Department of Dermatology, New York Medical College, Valhalla 10595, USA
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Abstract
Many oxidoreductases are constructed from (a) local sites of strongly coupled substrate-redox cofactor partners participating in exchange of electron pairs, (b) electron pair/single electron transducing redox centers, and (c) nonadiabatic, long-distance, single-electron tunneling between weakly coupled redox centers. The latter is the subject of an expanding experimental program that seeks to manipulate, test, and apply the parameters of theory. New results from the photosynthetic reaction center protein confirm that the electronic-tunneling medium appears relatively homogeneous, with any variances evident having no impact on function, and that control of intraprotein rates and directional specificity rests on a combination of distance, free energy, and reorganization energy. Interprotein electron transfer between cytochrome c and the reaction center and in lactate dehydrogenase, a typical oxidoreductase from yeast, are examined. Rates of interprotein electron transfer appear to follow intraprotein guidelines with the added essential provision of binding forces to bring the cofactors of the reacting proteins into proximity.
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Affiliation(s)
- C C Moser
- Johnson Research Foundation, University of Pennsylvania, Philadelphia 19104, USA
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Abstract
Interethnic differences in drug responsiveness may in part be accounted for by differences in drug disposition. We investigated the reversible binding interaction by equilibrium dialysis between a representative acidic (warfarin) and basic (lignocaine) drug and drug binding proteins in 20 healthy age and sex matched Iranian and Irish (Caucasian) subjects. The unbound fraction of warfarin and its major binding protein albumin, were similar in the two groups. In contrast unbound lignocaine was higher in Iranian subjects (49.6 +/- 6.96 vs 37.7 +/- 51%, mean +/- SD, p < 0.05) and this was associated with lower plasma concentrations of alpha 1 acid glycoprotein (AAG, 48.8 +/- 10 vs. 60.5 +/- 8 mg/dl p < 0.01) Such alterations may result in differences in drug responsiveness in addition to predictable pharmacokinetic consequences. Protein binding should be included in comparative studies of drugs in subjects of different races.
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Affiliation(s)
- S J Hosseine
- Department of Pharmacology & Therapeutics, Trinity College, Dublin, Ireland
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35
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Vidal AU, Gessain A, Yoshida M, Tekaia F, Garin B, Guillemain B, Schulz T, Farid R, De Thé G. Phylogenetic classification of human T cell leukaemia/lymphoma virus type I genotypes in five major molecular and geographical subtypes. J Gen Virol 1994; 75 ( Pt 12):3655-66. [PMID: 7996161 DOI: 10.1099/0022-1317-75-12-3655] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Proviral DNA was obtained from ex vivo peripheral blood mononuclear cells of 75 human T cell leukaemia/lymphoma virus type I (HTLV-I)-infected individuals who were either asymptomatic or had adult T cell leukaemia or tropical spastic paraparesis/HTLV-I-associated myelopathy. Amplified long terminal repeats (LTRs) were analysed for restriction fragment length polymorphisms (RFLPs). The results, together with previously published LTR data (a total of 180 specimens analysed), showed the presence of 12 different RFLP profiles with four major molecular subtypes. Furthermore, a fragment of 413 bp (nucleotides 22 to 434) of the U3/R region was sequenced for 12 new HTLV-I specimens originating from Central and West Africa (8 cases), Iran (1 case), Caribbean (2 cases) and Reunion Island (1 case). Phylogenetic analysis using three different techniques (maximum parsimony, neighbour-joining and UPGMA) comparing these 12 strains (including four new African HTLV-I variants) with the 30 published partial HTLV-I LTR sequences (nt 120 to 434) showed the existence of clusters of molecular variants in discrete geographical areas. The topology of the phylogenetic trees is thought to reflect HTLV-I evolution and the migrations of virally infected populations in the recent or distant past. Furthermore, there was a nearly perfect concordance between the clustering based on the LTR sequence homologies and the LTR RFLP subtypes suggesting that this rapid and simple technique is well suited to the investigation of HTLV-I molecular epidemiology. These results allow a new phylogenetic classification of HTLV-I genotypes into five major molecular subtypes: Cosmopolitan (C) subtype widespread all over the world, Japanese (J) subtype, West African (WA) subtype. Central African (CA) subtype and Melanesian (M) subtype.
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MESH Headings
- Africa/epidemiology
- Base Sequence
- Caribbean Region/epidemiology
- Carrier State
- DNA, Viral/blood
- DNA, Viral/genetics
- Genome, Viral
- Genotype
- HTLV-I Infections/epidemiology
- HTLV-I Infections/virology
- Human T-lymphotropic virus 1/classification
- Human T-lymphotropic virus 1/genetics
- Humans
- Iran/epidemiology
- Leukemia, T-Cell/epidemiology
- Leukemia, T-Cell/virology
- Molecular Sequence Data
- Mutation/genetics
- Paraparesis, Tropical Spastic/epidemiology
- Paraparesis, Tropical Spastic/virology
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- Proviruses/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Reunion/epidemiology
- Sequence Alignment
- Sequence Analysis, DNA
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Farid R, Bahrami A, Ghorashi-al Hosseini J. Aeroallergens in northeastern Iran (Khorasan). Ann Allergy 1991; 66:235-6. [PMID: 2006772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- R Farid
- Allergy and Immunology Department, Ghaem Medical School, Mashhad University of Medical Sciences, Iran
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40
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