1
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Carney DW, Leffler AE, Bell JA, Chandrasinghe AS, Cheng C, Chang E, Dornford A, Dougan DR, Frye LL, Grimes ME, Knehans T, Knight JL, Komandla M, Lane W, Li H, Newman SR, Phimister K, Saikatendu KS, Silverstein H, Vafaei S. Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity. Bioorg Med Chem 2024; 103:117577. [PMID: 38518735 DOI: 10.1016/j.bmc.2023.117577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 03/24/2024]
Abstract
Small-molecule antivirals that prevent the replication of the SARS-CoV-2 virus by blocking the enzymatic activity of its main protease (Mpro) are and will be a tenet of pandemic preparedness. However, the peptidic nature of such compounds often precludes the design of compounds within favorable physical property ranges, limiting cellular activity. Here we describe the discovery of peptide aldehyde Mpro inhibitors with potent enzymatic and cellular antiviral activity. This structure-activity relationship (SAR) exploration was guided by the use of calculated hydration site thermodynamic maps (WaterMap) to drive potency via displacement of waters from high-energy sites. Thousands of diverse compounds were designed to target these high-energy hydration sites and then prioritized for synthesis by physics- and structure-based Free-Energy Perturbation (FEP+) simulations, which accurately predicted biochemical potencies. This approach ultimately led to the rapid discovery of lead compounds with unique SAR that exhibited potent enzymatic and cellular activity with excellent pan-coronavirus coverage.
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Affiliation(s)
- Daniel W Carney
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States.
| | - Abba E Leffler
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States.
| | - Jeffrey A Bell
- Schrödinger, Inc, 1540 Broadway, New York, NY 10036, United States
| | | | - Cecilia Cheng
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Adam Dornford
- Schrödinger, Inc, 1 Main St, 11th Floor, Cambridge, MA 02142, United States
| | - Douglas R Dougan
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Leah L Frye
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Mary E Grimes
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Tim Knehans
- Schrödinger GmbH, Glücksteinallee 25, 68163 Mannheim, Germany
| | | | - Mallareddy Komandla
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Weston Lane
- Treeline Biosciences, 500 Arsenal Way, Watertown, MA 02472, United States
| | - Hubert Li
- Schrödinger, Inc, 9868 Scranton Road, Suite 3200, San Diego, CA 92121, United States
| | - Sophia R Newman
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
| | - Katalin Phimister
- Schrödinger Technologies Limited, 1st Floor West, Davidson House, Forbury Square, Reading RG1 3EU, United Kingdom
| | - Kumar S Saikatendu
- Takeda Development Center Americas, Inc, 9625 Towne Centre Drive, San Diego, CA 92121, United States
| | - Hercules Silverstein
- Schrödinger, Inc, 101 SW Main Street, Suite 1300, Portland, OR 97204, United States
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2
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Sun S, Silvergleid S, Gerasyuto AI, Wang J, Pelletier RD, Placzek A, Knight JL, Clark A, Wright H, Yin W, Elk JC, Bell J, Bos PH, Boyles NA, Therrien E, Jensen K, Akinsanya K. Abstract 2570: Discovery of potent, selective, and orally available WEE1 inhibitors that demonstrate increased DNA damage and mitosis in tumor cells leading to tumor regression in vivo. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
WEE1 inhibits the activation of both CDK1 and CDK2 through phosphorylation of Tyr15, allowing DNA damage repair before entering mitosis, thereby regulating the cell cycle in S and G2/M phases. Inhibition of WEE1 could result in premature progression through the G2/M cell cycle checkpoint with unresolved DNA damage, leading to mitotic catastrophe and cell death. Small molecule WEE1 inhibitors, such as AZD1775 and Zn-C3, are currently being evaluated in the clinic and have demonstrated promising efficacy in solid tumors including ovarian, colon, and uterine carcinoma.
By applying Schrödinger’s computational platform including Free Energy Perturbation (FEP) and Protein FEP, we have identified novel, potent, and highly selective WEE1 inhibitors with IC50 values in the low nanomolar range in a biochemical kinase activity assay and cellular target engagement (CDK1 pTyr15) IC50s of 100 - 300 nM in A427 and OVCAR3 cell lines. The compounds also show potent anti-proliferative activity in over 20 breast and ovarian tumor cell lines, including cell lines insensitive to PARP inhibitors. The compounds demonstrate superior kinase selectivity compared to AZD1775 and Zn-C3 in a broad kinase panel with >450 kinases (ScanMAX). In addition, the compounds show desirable ADME properties and PK profiles in preclinical species. Based on in vitro CYP3A4 TDI assay performance (kinact/KI), we have reduced the potential for drug-drug interaction liabilities compared to AZD1775. In the A427 xenograft model, our WEE1 inhibitors demonstrate dose-dependent tumor growth inhibition and tumor regression at high doses. Anti-tumor activity is also demonstrated in additional tumor models, including OVCAR3 and HCC1806 xenograft models. The established PK-PD relationship shows sustained target engagement (pCDK1), increased DNA damage (gH2AX) and mitosis (pHH3). We demonstrate that hematological adverse effects can be mitigated by dosing holidays in xenograft tumor models while maintaining anti-tumor activity. Notably, our compound shows more sustained anti-tumor activity with dosing holidays compared to AZD1775, which we believe is attributable to the prolonged and higher exposure in tumor and plasma with our compound. In the A427 non small-cell lung cancer xenograft model, following 3 dosing holiday cycles at high doses, tumor eradication was maintained after treatment was stopped. In summary, we have identified novel, potent and exquisitely selective WEE1 kinase inhibitors that demonstrate robust anti-tumor activity and sustained target engagement in tumor models. The compound’s anti-tumor effects are maintained with dosing holidays while allowing full recovery of mechanism-based hematological effects.
Citation Format: Shaoxian Sun, Sarah Silvergleid, Aleksey I. Gerasyuto, Jiashi Wang, Robert D. Pelletier, Andrew Placzek, Jennifer L. Knight, Anthony Clark, Hamish Wright, Wu Yin, Jackson Chief Elk, Jeff Bell, Pieter H. Bos, Nicholas A. Boyles, Eric Therrien, Kristian Jensen, Karen Akinsanya. Discovery of potent, selective, and orally available WEE1 inhibitors that demonstrate increased DNA damage and mitosis in tumor cells leading to tumor regression in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2570.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wu Yin
- 1Schrödinger, Inc., New York, NY
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Knight JL, Hebl MR, Foster JB, Mannix LM. Out of Role? Out of Luck: The Influence of Race and Leadership Status on Performance Appraisals. Journal of Leadership & Organizational Studies 2016. [DOI: 10.1177/107179190300900308] [Citation(s) in RCA: 28] [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] [Indexed: 11/17/2022]
Abstract
Although the American workforce is becoming more diverse, Black managers continue to face obstacles to success. One of the greatest challenges facing Black leaders is aversive racism, a subtle but insidious form of prejudice that emerges when people can justify their negative feelings towards Blacks based on factors other than race. The present study (N = 156) revealed that participants gave negative ratings to Black leaders and White subordinates and positive ratings to Black subordinates and White leaders, thus affirming these workers in their stereotypical societal positions. Furthermore, participants used even innocuous past mistakes of Black leaders to justify their negative evaluations of them. The theoretical and practical implications for leadership theories, performance appraisals, and organizational policy are discussed.
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4
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Knight JL, Krilov G, Borrelli KW, Williams J, Gunn JR, Clowes A, Cheng L, Friesner RA, Abel R. Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods. J Chem Theory Comput 2015; 10:3207-20. [PMID: 26588291 DOI: 10.1021/ct500189s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico modeling during the lead optimization phase of a drug discovery campaign. Here, we present a large-scale study of the efficacy of data fusion strategies to leverage results from end-point MM/GBSA calculations in multiple receptors to identify potent inhibitors among an ensemble of congeneric ligands. The retrospective analysis of 13 congeneric ligand series curated from publicly available data across seven biological targets demonstrates that in 90% of the individual receptor structures MM/GBSA scores successfully identify subsets of inhibitors that are more potent than a random selection, and data fusion strategies that combine MM/GBSA scores from each of the receptors significantly increase the robustness of the predictions. Among nine different data fusion metrics based on consensus scores or receptor rankings, the SumZScore (i.e., converting MM/GBSA scores into standardized Z-Scores within a receptor and computing the sum of the Z-Scores for a given ligand across the ensemble of receptors) is found to be a robust and physically meaningful metric for combining results across multiple receptors. Perhaps most surprisingly, even with relatively low to modest overall correlations between SumZScore and experimental binding affinities, SumZScore tends to reliably prioritize subsets of inhibitors that are at least as potent as those that are prioritized from a "best" single receptor identified from known compounds within the congeneric series.
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Affiliation(s)
- Jennifer L Knight
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Goran Krilov
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Kenneth W Borrelli
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Joshua Williams
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - John R Gunn
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Alec Clowes
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Luciano Cheng
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
| | - Richard A Friesner
- Columbia University , Department of Chemistry, 3000 Broadway, MC 3110, New York, New York 10027, United States
| | - Robert Abel
- Schrödinger, 120 West 45th Street, 17th Floor, Tower 45, New York, New York 10036-4041, United States
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5
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Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput 2015; 12:281-96. [PMID: 26584231 DOI: 10.1021/acs.jctc.5b00864] [Citation(s) in RCA: 1978] [Impact Index Per Article: 219.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The parametrization and validation of the OPLS3 force field for small molecules and proteins are reported. Enhancements with respect to the previous version (OPLS2.1) include the addition of off-atom charge sites to represent halogen bonding and aryl nitrogen lone pairs as well as a complete refit of peptide dihedral parameters to better model the native structure of proteins. To adequately cover medicinal chemical space, OPLS3 employs over an order of magnitude more reference data and associated parameter types relative to other commonly used small molecule force fields (e.g., MMFF and OPLS_2005). As a consequence, OPLS3 achieves a high level of accuracy across performance benchmarks that assess small molecule conformational propensities and solvation. The newly fitted peptide dihedrals lead to significant improvements in the representation of secondary structure elements in simulated peptides and native structure stability over a number of proteins. Together, the improvements made to both the small molecule and protein force field lead to a high level of accuracy in predicting protein-ligand binding measured over a wide range of targets and ligands (less than 1 kcal/mol RMS error) representing a 30% improvement over earlier variants of the OPLS force field.
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Affiliation(s)
- Edward Harder
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Wolfgang Damm
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jon Maple
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Chuanjie Wu
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Mark Reboul
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jin Yu Xiang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Lingle Wang
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Dmitry Lupyan
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Markus K Dahlgren
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Jennifer L Knight
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Joseph W Kaus
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - David S Cerutti
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Goran Krilov
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Robert Abel
- Schrodinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A Friesner
- Department of Chemistry, Columbia University , 3000 Broadway, New York, New York 10027, United States
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6
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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: 766] [Impact Index Per Article: 85.1] [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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7
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Abstract
Activation of class-A G-protein-coupled receptors (GPCRs) involves large-scale reorganization of the H3/H6 interhelical network. In rhodopsin (Rh), this process is coupled to a change in the protonation state of a key residue, E134, whose exact role in activation is not well understood. Capturing this millisecond pH-dependent process is a well-appreciated challenge. We have developed a scheme combining the harmonic Fourier beads (HFB) method and constant-pH molecular dynamics with pH-based replica exchange (pH-REX) to gain insight into the structural changes that occur along the activation pathway as a function of the protonation state of E134. Our results indicate that E134 is protonated as a consequence of tilting of H6 by ca. 4.0° with respect to its initial position and simultaneous rotation by ca. 23° along its principal axis. The movement of H6 is associated with breakage of the E247-R135 and R135-E134 salt bridges and concomitant release of the E134 side chain, which results in an increase in its pKa value above physiological pH. An increase in the hydrophobicity of the environment surrounding E134 leads to further tilting and rotation of H6 and upshift of the E134 pKa. Such atomic-level information, which is not accessible through experiments, refines the earlier proposed sequential model of Rh activation (see: Zaitseva, E.; et al. Sequential Rearrangement of Interhelical Networks Upon Rhodopsin Activation in Membranes: The Meta IIa Conformational Substate . J. Am. Chem. Soc. 2010, 132, 4815) and argues that the E134 protonation switch is both a cause and a consequence of the H6 motion.
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Affiliation(s)
- Elena N. Laricheva
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Karunesh Arora
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer L. Knight
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Charles L. Brooks
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
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8
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Knight JL, Yesselman JD, Brooks CL. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J Comput Chem 2013; 34:893-903. [PMID: 23292859 PMCID: PMC4402937 DOI: 10.1002/jcc.23199] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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] [Received: 09/05/2012] [Revised: 11/14/2012] [Accepted: 11/14/2012] [Indexed: 11/06/2022]
Abstract
Multipurpose atom-typer for CHARMM (MATCH), an atom-typing toolset for molecular mechanics force fields, was recently developed in our laboratory. Here, we assess the ability of MATCH-generated parameters and partial atomic charges to reproduce experimental absolute hydration free energies for a series of 457 small neutral molecules in GBMV2, Generalized Born with a smooth SWitching (GBSW), and fast analytical continuum treatment of solvation (FACTS) implicit solvent models. The quality of hydration free energies associated with small molecule parameters obtained from ParamChem, SwissParam, and Antechamber are compared. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, these automated parameterization schemes with GBMV2 and GBSW demonstrate reasonable agreement with experimental hydration free energies (average unsigned errors of 0.9-1.5 kcal/mol and R(2) of 0.63-0.87). GBMV2 and GBSW consistently provide slightly more accurate estimates than FACTS, whereas Antechamber parameters yield marginally more accurate estimates than the current generation of MATCH, ParamChem, and SwissParam parameterization strategies. Modeling with MATCH libraries that are derived from different CHARMM topology and parameter files highlights the importance of having sufficient coverage of chemical space within the underlying databases of these automated schemes and the benefit of targeting specific functional groups for parameterization efforts to maximize both the breadth and the depth of the parameterized space.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry & Department of Biophysics University of Michigan, 930 N. University Ave. Ann Arbor, MI 48109 USA
| | - Joseph D Yesselman
- Department of Chemistry & Department of Biophysics University of Michigan, 930 N. University Ave. Ann Arbor, MI 48109 USA
| | - Charles L Brooks
- Department of Chemistry & Department of Biophysics University of Michigan, 930 N. University Ave. Ann Arbor, MI 48109 USA
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9
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Abstract
The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMDMSλD) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMDMSλD framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa unit. Lastly, we show that pH-REX CPHMDMSλD simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMDMSλD simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles, and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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10
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Abstract
The role of pH-dependent protonation equilibrium in modulating RNA dynamics and function is one of the key unanswered questions in RNA biology. Molecular dynamics (MD) simulations can provide insight into the mechanistic roles of protonated nucleotides, but it is only capable of modeling fixed protonation states and requires prior knowledge of the key residue's protonation state. Recently, we developed a framework for constant pH molecular dynamics simulations (CPHMDMSλD) of nucleic acids, where the nucleotides' protonation states are modeled as dynamic variables that are coupled to the structural dynamics of the RNA. In the present study, we demonstrate the application of CPHMDMSλD to the lead-dependent ribozyme; establishing the validity of this approach for modeling complex RNA structures. We show that CPHMDMSλD accurately predicts the direction of the pKa shifts and reproduces experimentally-measured microscopic pKa values with an average unsigned error of 1.3 pKa units. The effects of coupled titration states in RNA structures are modeled, and the importance of conformation sampling is highlighted. The general accuracy of CPHMDMSλD simulations in reproducing pH-dependent observables reported in this work demonstrates that constant pH simulations provides a powerful tool to investigate pH-dependent processes in nucleic acids.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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11
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Wang L, Deng Y, Knight JL, Wu Y, Kim B, Sherman W, Shelley JC, Lin T, Abel R. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors. J Chem Theory Comput 2013; 9:1282-93. [PMID: 26588769 DOI: 10.1021/ct300911a] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Lingle Wang
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Yuqing Deng
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Jennifer L. Knight
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Yujie Wu
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Byungchan Kim
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Woody Sherman
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - John C. Shelley
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Teng Lin
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
| | - Robert Abel
- Schrodinger, 120 West 45st Street, New York, New York
10036, United States
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12
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Abstract
The nucleosides of adenine and cytosine have pKa values of 3.50 and 4.08, respectively, and are assumed to be unprotonated under physiological conditions. However, evidence from recent NMR and X-Ray crystallography studies has revealed the prevalence of protonated adenine and cytosine in RNA macromolecules. Such nucleotides with elevated pKa values may play a role in stabilizing RNA structure and participate in the mechanism of ribozyme catalysis. With the work presented here, we establish the framework and demonstrate the first constant pH MD simulations (CPHMD) for nucleic acids in explicit solvent in which the protonation state is coupled to the dynamical evolution of the RNA system via λ-dynamics. We adopt the new functional form λ(Nexp) for λ that was recently developed for Multi-Site λ-Dynamics (MSλD) and demonstrate good sampling characteristics in which rapid and frequent transitions between the protonated and unprotonated states at pH = pKa are achieved. Our calculated pKa values of simple nucleotides are in a good agreement with experimentally measured values, with a mean absolute error of 0.24 pKa units. This work demonstrates that CPHMD can be used as a powerful tool to investigate pH-dependent biological properties of RNA macromolecules.
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Affiliation(s)
- Garrett B Goh
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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13
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Knight JL, Brooks CL. Applying efficient implicit nongeometric constraints in alchemical free energy simulations. J Comput Chem 2011; 32:3423-32. [PMID: 21919014 PMCID: PMC3196384 DOI: 10.1002/jcc.21921] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [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] [Received: 06/23/2011] [Accepted: 07/29/2011] [Indexed: 11/08/2022]
Abstract
Several strategies have been developed for satisfying bond lengths, angle, and other geometric constraints in molecular dynamics simulations. Advanced variations of alchemical free energy perturbation simulations, however, also require nongeometric constraints. In our recently developed multisite λ-dynamics simulation method, the conventional λ parameters that are associated with the progress variables in alchemical transformations are treated as dynamic variables and are constrained such that: 0 ≤ λ(i) ≤ 1 and Σ(i = 1)(N) λ(i) = 1. Here, we present four functional forms of λ that implicitly satisfy these nongeometric constraints, whose values and forces are facile to compute and that yield stable simulations using a 2 fs integration timestep. Using model systems, we present the sampling characteristics of these functional forms and demonstrate the enhanced sampling profiles and improved convergence rates that are achieved by the functional form: λ(i) = e(c sinθ(i))/Σ(j = 1)(N) e(c sinθ(j)) that oscillates between λ(i) = 0 and λ(i) = 1 and has relatively steep transitions between these endpoints.
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Affiliation(s)
- Jennifer L. Knight
- Department of Chemistry & Department of Biophysics. University of Michigan. 930 N. University Ave. Ann Arbor, MI 48109 USA
| | - Charles L. Brooks
- Department of Chemistry & Department of Biophysics. University of Michigan. 930 N. University Ave. Ann Arbor, MI 48109 USA
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Yesselman JD, Price DJ, Knight JL, Brooks CL. MATCH: an atom-typing toolset for molecular mechanics force fields. J Comput Chem 2011; 33:189-202. [PMID: 22042689 DOI: 10.1002/jcc.21963] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 09/09/2011] [Accepted: 09/12/2011] [Indexed: 11/08/2022]
Abstract
We introduce a toolset of program libraries collectively titled multipurpose atom-typer for CHARMM (MATCH) for the automated assignment of atom types and force field parameters for molecular mechanics simulation of organic molecules. The toolset includes utilities for the conversion of multiple chemical structure file formats into a molecular graph. A general chemical pattern-matching engine using this graph has been implemented whereby assignment of molecular mechanics atom types, charges, and force field parameters are achieved by comparison against a customizable list of chemical fragments. While initially designed to complement the CHARMM simulation package and force fields by generating the necessary input topology and atom-type data files, MATCH can be expanded to any force field and program, and has core functionality that makes it extendable to other applications such as fragment-based property prediction. In this work, we demonstrate the accurate construction of atomic parameters of molecules within each force field included in CHARMM36 through exhaustive cross validation studies illustrating that bond charge increment rules derived from one force field can be transferred to another. In addition, using leave-one-out substitution it is shown that it is also possible to substitute missing intra and intermolecular parameters with ones included in a force field to complete the parameterization of novel molecules. Finally, to demonstrate the robustness of MATCH and the coverage of chemical space offered by the recent CHARMM general force field (Vanommeslaeghe, et al., J Comput Chem 2010, 31, 671), one million molecules from the PubChem database of small molecules are typed, parameterized, and minimized.
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Affiliation(s)
- Joseph D Yesselman
- Department of Chemistry and Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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Knight JL, Brooks CL. Surveying implicit solvent models for estimating small molecule absolute hydration free energies. J Comput Chem 2011; 32:2909-23. [PMID: 21735452 PMCID: PMC3142295 DOI: 10.1002/jcc.21876] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [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] [Received: 03/13/2011] [Revised: 05/25/2011] [Accepted: 06/01/2011] [Indexed: 11/11/2022]
Abstract
Implicit solvent models are powerful tools in accounting for the aqueous environment at a fraction of the computational expense of explicit solvent representations. Here, we compare the ability of common implicit solvent models (TC, OBC, OBC2, GBMV, GBMV2, GBSW, GBSW/MS, GBSW/MS2 and FACTS) to reproduce experimental absolute hydration free energies for a series of 499 small neutral molecules that are modeled using AMBER/GAFF parameters and AM1-BCC charges. Given optimized surface tension coefficients for scaling the surface area term in the nonpolar contribution, most implicit solvent models demonstrate reasonable agreement with extensive explicit solvent simulations (average difference 1.0-1.7 kcal/mol and R(2)=0.81-0.91) and with experimental hydration free energies (average unsigned errors=1.1-1.4 kcal/mol and R(2)=0.66-0.81). Chemical classes of compounds are identified that need further optimization of their ligand force field parameters and others that require improvement in the physical parameters of the implicit solvent models themselves. More sophisticated nonpolar models are also likely necessary to more effectively represent the underlying physics of solvation and take the quality of hydration free energies estimated from implicit solvent models to the next level.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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Abstract
Multi-Site λ-dynamics (MSλD) is a new free energy simulation method that is based on λ-dynamics. It has been developed to enable multiple substituents at multiple sites on a common ligand core to be modeled simultaneously and their free energies assessed. The efficacy of MSλD for estimating relative hydration free energies and relative binding affinties is demonstrated using three test systems. Model compounds representing multiple identical benzene, dihydroxybenzene and dimethoxybenzene molecules show total combined MSλD trajectory lengths of ~1.5 ns are sufficient to reliably achieve relative hydration free energy estimates within 0.2 kcal/mol and are less sensitive to the number of trajectories that are used to generate these estimates for hybrid ligands that contain up to ten substituents modeled at a single site or five substituents modeled at each of two sites. Relative hydration free energies among six benzene derivatives calculated from MSλD simulations are in very good agreement with those from alchemical free energy simulations (with average unsigned differences of 0.23 kcal/mol and R(2)=0.991) and experiment (with average unsigned errors of 1.8 kcal/mol and R(2)=0.959). Estimates of the relative binding affinities among 14 inhibitors of HIV-1 reverse transcriptase obtained from MSλD simulations are in reasonable agreement with those from traditional free energy simulations and experiment (average unsigned errors of 0.9 kcal/mol and R(2)=0.402). For the same level of accuracy and precision MSλD simulations are achieved ~20-50 times faster than traditional free energy simulations and thus with reliable force field parameters can be used effectively to screen tens to hundreds of compounds in structure-based drug design applications.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry & Department of Biophysics. University of Michigan. 930 N. University Ave. Ann Arbor, MI 48109 USA
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Abstract
The phase-selective crystallization of acetaminophen (ACM) using insoluble polymers as heteronuclei was investigated in a combined experimental and computational effort to elucidate the mechanism of polymer-induced heteronucleation (PIHn). ACM heteronucleates from supersaturated aqueous solution in its most thermodynamically stable monoclinic form on poly(n-butyl methacrylate), whereas the metastable orthorhombic form is observed on poly(methyl methacrylate). When ACM crystals were grown through vapor deposition, only the monoclinic polymorph was observed on each polymer. Each crystallization condition leads to a unique powder X-ray diffraction pattern with the major preferred orientation corresponding to the crystallographic faces in which these crystal phases nucleate from surfaces of the polymers. The molecular recognition events leading to these outcomes are elucidated with the aid of computed polymer-crystal binding energies using docking simulations. This investigation illuminates the mechanism by which phase selection occurs during the crystallization of ACM using polymers as heteronuclei, paving the way for the improvement of methods for polymorph selection and discovery based on heterogeneous nucleation promoters.
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Affiliation(s)
- Vilmalí López-Mejías
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA
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Knight JL, Giuliano TA, Sanchez-Ross MG. Famous or Infamous? The Influence of Celebrity Status and Race on Perceptions of Responsibility for Rape. Basic and Applied Social Psychology 2010. [DOI: 10.1207/s15324834basp2303_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Abstract
Free energy calculations are fundamental to obtaining accurate theoretical estimates of many important biological phenomena including hydration energies, protein-ligand binding affinities and energetics of conformational changes. Unlike traditional free energy perturbation and thermodynamic integration methods, lambda-dynamics treats the conventional "lambda" as a dynamic variable in free energy simulations and simultaneously evaluates thermodynamic properties for multiple states in a single simulation. In the present article, we provide an overview of the theory of lambda-dynamics, including the use of biasing and restraining potentials to facilitate conformational sampling. We review how lambda-dynamics has been used to rapidly and reliably compute relative hydration free energies and binding affinities for series of ligands, to accurately identify crystallographically observed binding modes starting from incorrect orientations, and to model the effects of mutations upon protein stability. Finally, we suggest how lambda-dynamics may be extended to facilitate modeling efforts in structure-based drug design.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry, University of Michigan, 930 N. University Ann Arbor, Michigan 48109, USA
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20
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Abstract
Using an extensive series of TIBO compounds that are non-nucleoside inhibitors of HIV-1 reverse transcriptase, we have systematically evaluated the quality of recently developed ligand parameters that are consistent with the CHARMM22 force field. Thermodynamic integration simulations for 44 pairs of TIBO compounds achieve a high level of success with an overall average unsigned error (AUE) in the relative binding affinities of 1.3 kcal/mol; however, the accuracy is strongly dependent on the size differential between the substituents sampled as well as the class of functional group. Low errors are observed among the alkyl, allyl, aldehyde, nitrile, trifluorinated methyl, and halide TIBO derivatives and large systematic errors among thioether derivatives. We have also investigated how different charge assignment schemes for small molecules impact the quality of computed binding affinities for a subset of this series. This study demonstrates the advantage of using model compounds to derive physically meaningful charge distributions and bond-charge increments for rapidly expanding fragment libraries for drug development applications. Specifically, in the absence of a bond-charge increment for a given pair of atom types, the strategy of adopting CHELPG charges from localized regions of model compounds provides reliable results when modeling with the CHARMM force field.
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Affiliation(s)
- Jennifer L. Knight
- Department of Chemistry & Department of Biophysics. University of Michigan., 930 N. University Ave. Ann Arbor, MI 48109 USA
| | - Charles L. Brooks
- Department of Chemistry & Department of Biophysics. University of Michigan., 930 N. University Ave. Ann Arbor, MI 48109 USA
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Knight JL, Zhou Z, Gallicchio E, Himmel DM, Friesner RA, Arnold E, Levy RM. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling. Acta Crystallogr D Biol Crystallogr 2008; 64:383-96. [PMID: 18391405 PMCID: PMC2631124 DOI: 10.1107/s090744490800070x] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Accepted: 01/08/2008] [Indexed: 11/10/2022]
Abstract
Modeling structural variability is critical for understanding protein function and for modeling reliable targets for in silico docking experiments. Because of the time-intensive nature of manual X-ray crystallographic refinement, automated refinement methods that thoroughly explore conformational space are essential for the systematic construction of structurally variable models. Using five proteins spanning resolutions of 1.0-2.8 A, it is demonstrated how torsion-angle sampling of backbone and side-chain libraries with filtering against both the chemical energy, using a modern effective potential, and the electron density, coupled with minimization of a reciprocal-space X-ray target function, can generate multiple structurally variable models which fit the X-ray data well. Torsion-angle sampling as implemented in the Protein Local Optimization Program (PLOP) has been used in this work. Models with the lowest R(free) values are obtained when electrostatic and implicit solvation terms are included in the effective potential. HIV-1 protease, calmodulin and SUMO-conjugating enzyme illustrate how variability in the ensemble of structures captures structural variability that is observed across multiple crystal structures and is linked to functional flexibility at hinge regions and binding interfaces. An ensemble-refinement procedure is proposed to differentiate between variability that is a consequence of physical conformational heterogeneity and that which reflects uncertainty in the atomic coordinates.
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Affiliation(s)
| | | | - Emilio Gallicchio
- Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Daniel M. Himmel
- Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Eddy Arnold
- Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ronald M. Levy
- Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Himmel DM, Sarafianos SG, Dharmasena S, Hossain MM, McCoy-Simandle K, Ilina T, Clark AD, Knight JL, Julias JG, Clark PK, Krogh-Jespersen K, Levy RM, Hughes SH, Parniak MA, Arnold E. HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. ACS Chem Biol 2006; 1:702-12. [PMID: 17184135 PMCID: PMC2963427 DOI: 10.1021/cb600303y] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [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: 11/28/2022]
Abstract
The rapid emergence of drug-resistant variants of human immunodeficiency virus, type 1 (HIV-1), has limited the efficacy of anti-acquired immune deficiency syndrome (AIDS) treatments, and new lead compounds that target novel binding sites are needed. We have determined the 3.15 A resolution crystal structure of HIV-1 reverse transcriptase (RT) complexed with dihydroxy benzoyl naphthyl hydrazone (DHBNH), an HIV-1 RT RNase H (RNH) inhibitor (RNHI). DHBNH is effective against a variety of drug-resistant HIV-1 RT mutants. While DHBNH has little effect on most aspects of RT-catalyzed DNA synthesis, at relatively high concentrations it does inhibit the initiation of RNA-primed DNA synthesis. Although primarily an RNHI, DHBNH binds >50 A away from the RNH active site, at a novel site near both the polymerase active site and the non-nucleoside RT inhibitor (NNRTI) binding pocket. When DHBNH binds, both Tyr181 and Tyr188 remain in the conformations seen in unliganded HIV-1 RT. DHBNH interacts with conserved residues (Asp186, Trp229) and has substantial interactions with the backbones of several less well-conserved residues. On the basis of this structure, we designed substituted DHBNH derivatives that interact with the NNRTI-binding pocket. These compounds inhibit both the polymerase and RNH activities of RT.
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Affiliation(s)
- Daniel M. Himmel
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
| | - Stefan G. Sarafianos
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
| | - Sanjeewa Dharmasena
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Mohammed M. Hossain
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Kessler McCoy-Simandle
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Tatiana Ilina
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Arthur D. Clark
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
| | - Jennifer L. Knight
- Department of Chemistry and Chemical Biology and BIOMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854-8066
| | - John G. Julias
- Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702-1201
| | - Patrick K. Clark
- Basic Research Program, SAIC-Frederick, Inc., Frederick, Maryland 21702-1201
| | - Karsten Krogh-Jespersen
- Department of Chemistry and Chemical Biology and BIOMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854-8066
| | - Ronald M. Levy
- Department of Chemistry and Chemical Biology and BIOMAPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854-8066
| | - Stephen H. Hughes
- HIV Drug Resistance Program, NCI-Frederick, Building 539, Frederick, Maryland 21702-1201
| | - Michael A. Parniak
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261-0001
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-5627
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King EB, Mendoza SA, Madera JM, Hebl MR, Knight JL. What's in a Name? A Multiracial Investigation of the Role of Occupational Stereotypes in Selection Decisions. J Appl Social Pyschol 2006. [DOI: 10.1111/j.0021-9029.2006.00035.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Baker RA, Knight JL. The OXICAB trial: cerebral oximetry in adult cardiac surgical patients. J Extra Corpor Technol 2006; 38:77. [PMID: 16637536 PMCID: PMC4680778] [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: 05/08/2023]
Affiliation(s)
- R A Baker
- Depart of Cardiac and Thoracic Surgery, Flinders Medical Centre and Flinders University, Bedford Park, Adelaide, South Australia, Australia
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Abstract
BACKGROUND Studies of neuropsychological outcome following coronary artery bypass graft surgery (CABG) have traditionally dichotomised patients as "impaired" or "unimpaired". This conceals the potential heterogeneity of deficits due to different mechanisms and sites of brain injury. OBJECTIVES To explore neuropsychological outcome following CABG and determine to what extent it conforms to prototypic cortical and/or subcortical neurobehavioral syndromes and whether different intraoperative physiologic measures are associated with different subtypes of neuropsychological outcome. METHODS Neuropsychological tests were administered to 85 patients before and after elective CABG and to 50 matched normal control subjects. Pre- to postoperative change scores were computed using standardised regression based norms. Change scores on selected memory measures were subjected to cluster analysis to identify qualitatively distinct subtypes of memory outcome. Emergent clusters were compared on non-memory measures, intraoperative physiologic measures, and demographic variables. RESULTS Three subtypes of memory outcome were identified: memory spared (48% of patients), retrieval deficit (35%), and encoding/storage deficit (17%). Contrary to expectation, the subgroups were indistinguishable on measures of confrontation naming and manual dexterity and on intraoperative cardiac surgical physiologic measures and demographic variables. The encoding/storage deficit subgroup exhibited executive dysfunction. CONCLUSIONS Heterogeneous profiles of neuropsychological dysfunction were found following CABG although they did not tightly conform to prototypic cortical and subcortical neurobehavioral syndromes. This challenges the value and appropriateness of the common practice of collapsing individual test scores to arrive at a single figure to define "impairment". Whether different subtypes of neuropsychological outcome are caused by different pathophysiologic mechanisms remains unknown.
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Affiliation(s)
- A C Kneebone
- Department of Psychological Medicine, Flinders Medical Centre, Bedford Park 5042, Australia.
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Knight JL, Mekler V, Mukhopadhyay J, Ebright RH, Levy RM. Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys J 2004; 88:925-38. [PMID: 15542547 PMCID: PMC1305165 DOI: 10.1529/biophysj.104.050187] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [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: 01/22/2023] Open
Abstract
We are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (FRET) measurements. In this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. Using simulated FRET data, we have generated a series of benchmarks that permit estimation of model accuracy based on the quantity and quality of FRET-derived distance restraints, including the number, random error, systematic error, distance distribution, and radial distribution of FRET-derived distance restraints. We find that expected model accuracy is 10 A or better for models based on: i), > or =20 restraints with up to 15% random error and no systematic error, or ii), > or =20 restraints with up to 15% random error, up to 10% systematic error, and a symmetric radial distribution of restraints. Model accuracies can be improved to 5 A or better by increasing the number of restraints to > or =40 and/or by optimizing the distance distribution of restraints. Using experimental FRET data, we have defined the positions of the binding sites within bacterial RNA polymerase of the small-molecule inhibitors rifampicin (Rif) and rifamycin SV (Rif SV). The inferred binding sites for Rif and Rif SV were located with accuracies of, respectively, 7 and 10 A relative to the crystallographically defined binding site for Rif. These accuracies agree with expectations from the benchmark simulations and suffice to indicate that the binding sites for Rif and Rif SV are located within the RNA polymerase active-center cleft, overlapping the binding site for the RNA-DNA hybrid.
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Affiliation(s)
- Jennifer L Knight
- Department of Chemistry and Chemical Biology and the BioMaPS Institute for Quantitative Biology, and Howard Hughes Medical Institute, Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
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Abstract
The safety and efficacy of off-pump coronary artery bypass surgery with the aid of the Octopus Tissue Stabilizer (Octopus OPCAB), in comparison to conventional on-pump coronary artery bypass surgery (CPB-CABG), was examined by a systematic assessment of the peer-reviewed literature. The limited comparative data suggested that there was no difference in safety outcomes between Octopus OPCAB and CPB-CABG. The paucity of efficacy data reported in the higher level comparative studies meant that it was impossible to assess whether Octopus OPCAB was more efficacious than CPB-CABG. The evidence base for the procedure was deemed inadequate and an audit of the procedure was recommended.
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Affiliation(s)
- N A Scott
- ASERNIP-S, Royal Australasian College of Surgeons, Box 688 North Adelaide, SA 5006, Australia
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Bennetts JS, Arnolda LF, Cullen HC, Knight JL, Baker RA, McKitrick DJ. Coronary artery baroreceptor-mediated changes in arterial pressure: a pilot study in conscious and anaesthetized sheep. Clin Exp Pharmacol Physiol 2001; 28:768-72. [PMID: 11560126 DOI: 10.1046/j.1440-1681.2001.03522.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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
1. Evidence suggesting the presence of coronary artery baroreceptors on coronary arteries has existed for over 30 years. 2. Evidence that activation of ventricular mechanoreceptors can elicit cardiovascular changes has been challenged, with those changes now thought to be due to coronary artery mechanoreceptors. 3. Studies have suggested that coronary artery mechanoreceptors act as coronary baroreceptors with a role in cardiovascular regulation. However, all evidence to date has been obtained in anaesthetized animal models in physiologically compromised intra-operative states. 4. The purpose of the present study was to design an ovine model that would allow the discrete stretch of coronary arteries without causing ischaemia or changing flow or intra-arterial pressure and that would confirm results seen in previous studies. In addition, the possibility that the technique could be used for studies of coronary artery baroreflexes in conscious sheep was investigated. 5. Controlled stretch of the proximal left anterior descending coronary artery elicited decreases in arterial pressure without changes in heart rate or electrocardiographic activity in halothane-anaesthetized sheep. Similar results were demonstrated in conscious sheep after surgical recovery of up to 2 weeks. 6. The present study supports the possibility that coronary artery baroreceptors exist and likely have a role in cardiovascular regulation. The results of the present study in anaesthetized sheep are in agreement with previous results in anaesthetized animals, but also provide the first demonstration of coronary baroreceptor activity in a conscious animal model, underscoring the potential use of the model in the study of coronary artery baroreceptors in the intact animal.
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Affiliation(s)
- J S Bennetts
- Department of Cardiac Surgery Research, Flinders Medical Centre, Bedford Park, South Australia
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Baker RA, Andrew MJ, Ross IK, Knight JL. The Octopus II stabilizing system: biochemical and neuropsychological outcomes in coronary artery bypass surgery. Heart Surg Forum 2001; 4 Suppl 1:S19-23. [PMID: 11178303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2000] [Indexed: 02/18/2023]
Abstract
INTRODUCTION The aim of this study was to determine if coronary artery bypass graft (CABG) surgery performed utilizing the Octopus II stabilizing system provides myocardial and cerebral protection comparable to traditional CABG surgery utilizing cardiopulmonary bypass (CPB). METHODS Elective patients requiring surgery for double or triple vessel disease were randomized to receive either conventional CABG with CPB (n = 14) or OPCAB using the Octopus II stabilizing system (n = 12), after receiving institutional approval and written consent. Exclusion criteria included previous cardiac surgery, recent myocardial infarction, and previous cerebrovascular disease. Troponin T (TnT) was measured preoperatively and at 2, 4, 6, 8, 10, 12, 24, and 72 hours after initiation of grafting. Neuropsychological assessments (10 measures) were performed in the week prior to surgery, one week, and six months after surgery. RESULTS Troponin T release was reduced in the OPCAB patients at all time points (repeated measures ANOVA p = 0.043), reaching significance at 8, 10 and 12 hours (p = 0.033, 0.038, 0.019). Other factors (composite clinical end point (prolonged LOS or ICU stay or 30-day mortality), infarction, and intubation time) did not show any significant differences between the two groups. The incidence of neuropsychological deficits was not different between the two groups at both seven-day and six-month follow-up assessments. CONCLUSIONS Decreased TnT release suggests a myocardial benefit for the OPCAB procedure. A neuropsychological benefit remains to be demonstrated.
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Affiliation(s)
- R A Baker
- Cardiac Surgical Research Group, Department of Cardiothoracic Surgery, Division of Medicine, Flinders Medical Centre, Bedford Park, South Australia 5042, Australia.
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31
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Abstract
It is well recognized that cardiac surgery with cardiopulmonary bypass can potentially induce a wide spectrum of central nervous system (CNS) sequelae. Our awareness of the prevalence of these CNS complications is dependent on the validity of the available diagnostic methods. Current assessment methods designed to detect both focal and diffuse cerebral ischemia include neurologic examination, imaging techniques, biochemical markers, neuropsychologic assessment, and patient perceived outcomes. These techniques vary in their sensitivity and specificity, as well as feasibility for use in everyday clinical practice. There are currently only limited standardized methodologic guidelines for the assessment of CNS complications after cardiac surgery, which has resulted in considerable interstudy variability in the identification and reporting of outcomes. The application of clearly definable endpoints for reporting of CNS outcomes would be beneficial. The wealth of available data suggests that the incidence of overt CNS injury such as stroke has declined since the 1980s and is now approximately 2%, whereas evidence suggests that up to one third of cardiac surgery patients experience postoperative cognitive deficits. One of the clear strengths of the current era is the recognition of CNS injury associated with cardiac surgery, and the quest to improve our understanding of these outcomes. The application of more uniform assessment and reporting practices is surely vital to the continued advancement of cardiac surgery.
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Affiliation(s)
- R A Baker
- Cardiac Surgical Research Group, Flinders Medical Centre Adelaide, South Australia.
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Abstract
BACKGROUND There is convincing evidence to suggest that depression significantly increases the risk of mortality following myocardial infarction. There are few data concerning depression as a risk factor for mortality following cardiac surgery. The aim of the present observational study was to determine if preoperative depressive symptoms resulted in an increased risk of late mortality following cardiac surgery. METHODS Preoperative assessments of depressive symptoms were performed on 158 patients undergoing coronary artery bypass surgery. Elevated preoperative depression symptoms were defined as a depression anxiety stress scale score of > or = 10. RESULTS Twenty-four of the 158 patients ( 15.2%) were classified as having elevated preoperative depressive symptoms. Patients were followed for a median of 25 months (range: 4-38 months). Three of the 24 patients (12.5%) with preoperative depressive symptoms died within the follow-up period, compared with three of the 134 (2.2%) non-depressed patients (odds ratio: 6.24; 95% CI: 1.18-32.98; P = 0.046). There were no other group differences on variables including population demographics, medical risk factors, surgical parameters, and indices of postoperative morbidity. CONCLUSIONS Elevated depressive symptoms before coronary bypass surgery may be a significant predictor of late death. Prospective studies evaluating the prevalence of depressive symptoms in cardiac surgical patients and their effect on long-term outcome must be undertaken.
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Affiliation(s)
- R A Baker
- Cardiac Surgical Research Unit, Flinders Medical Centre, Queen Elizabeth Hospital, Adelaide, South Australia.
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Abstract
OBJECTIVE To compare the incidence of neuropsychologic deficits 1 week and 6 months after coronary artery bypass graft (CABG) surgery (extracardiac) and valve surgery with or without CABG surgery (intracardiac) using reliable change indices to define the incidence of neuropsychologic deficits. DESIGN Prospective study. SETTING Cardiac surgical unit in a university teaching hospital. PARTICIPANTS Patients scheduled for elective multiple-graft (> or =3 grafts) CABG surgery (n = 59), or elective valve surgery (with or without concomitant CABG surgery) (n = 50) and a matched sample of nonsurgical controls (n = 53). INTERVENTIONS Neuropsychologic assessments were performed 1 day before surgery, 7 days and 6 months after surgery. MEASUREMENTS AND MAIN RESULTS The 7-day assessment showed no significant differences between valve surgery patients and CABG surgery patients in the incidence of neuropsychologic deficits. When reassessed 6 months postoperatively, the valve group displayed a significantly higher incidence of deficits on the digit symbol test compared with the CABG group (valve 26.7% v CABG 6.8%). In the CABG group, there was a significant change in the incidence of deficits per patient from 7 days to 6 months (p = 0.03) that was not evident in the valve group. CONCLUSION There are some differences in the neuropsychologic outcome of extracardiac and intracardiac surgery. Patients undergoing isolated CABG surgery showed a greater reduction in the incidence of persisting deficits at 6 months than patients undergoing valve surgery with or without CABG surgery. This finding warrants further investigation, with particular attention to patients undergoing combined valve and coronary artery procedures.
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Affiliation(s)
- M J Andrew
- Department of Surgery, Flinders Medical Centre and Flinders University of South Australia, Adelaide
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35
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Abstract
OBJECTIVES mood disorders and neuropsychological deficits are both commonly reported occurrences after cardiac surgery. We examined the relationship between mood state and postoperative cognitive deficits in this population. METHODS assessments of neuropsychological functions and mood state (depression, anxiety, stress scales; DASS) were performed preoperatively and postoperatively on 147 patients undergoing cardiac surgery. RESULTS the incidence of preoperative depression, anxiety, and stress symptomatology was 16%, 27%, and 16%, respectively. The incidence of postoperative anxiety symptomatology significantly increased to 45% (p<0.001), while the incidence of depression and stress symptomatology remained stable (19% and 15%, respectively; ns). Changes in mood state did not influence changes in neuropsychological performance. Preoperative mood was a strong predictor of postoperative mood, and was related to postoperative deficits on measures of attention and memory. CONCLUSIONS an assessment of preoperative mood is critical in identifying patients at risk of postoperative mood disorders and neuropsychological deficits. Measures assessing somatic manifestations of anxiety may not be suitable for a surgical population.
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Affiliation(s)
- M J Andrew
- Cardiac Surgical Research Group, Department of Medicine, Flinders Medical Centre and Flinders University of South Australia, Bedford Park, South Australia 5042, Adelaide, Australia
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36
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Knight JL, Helming C. Collarless polished tapered impaction grafting of the femur during revision total hip arthroplasty: pitfalls of the surgical technique and follow-up in 31 cases. J Arthroplasty 2000; 15:159-65. [PMID: 10708079 DOI: 10.1016/s0883-5403(00)90088-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.5] [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] [Indexed: 02/01/2023] Open
Abstract
Impacting morcellized allograft bone into the femur during revision total hip arthroplasty is a simple concept with the goal of rebuilding femoral bone stock and providing secure fixation to the femoral stem. Using the collarless polished tapered (CPT, Zimmer, Warsaw, IN) stem impaction grafting system, we became concerned about the discrepancy between the straightforward concept and precise execution of the technique. In this study, we examined 31 consecutive procedures to determine intraoperative difficulties and report on the clinical outcome of 30 cases at an average follow-up of 31 months. Modified Harris Hip Scores averaged 41 points preoperatively and improved to 86 points at follow-up. Nineteen cases were performed on intact femora, whereas 12 cases had disrupted femoral integrity, either extended trochanteric osteotomy or periprosthetic fracture. Successful outcome was seen in all cases with an intact femur, and restoration of femoral integrity was key to successful outcome in cases with compromised femoral integrity. Among cases with disrupted femoral integrity, 3 distal fractures occurred as a result of the rigid CPT cement plug, and 2 complete femoral fractures occurred as a result of bone impaction, for a technique-related fracture rate of 16%. Difficulty packing bone distally occurred in 94% of cases and was associated with varus and valgus stem alignment and medial and lateral stem displacement. Complete cement mantles were seen in 77% of cases. No stem subsidence was seen in 15 of 30 cases (50%). Stem subsidence of <5 mm was seen in 10 of 30, stem subsidence of 6 to 8 mm was seen in 4 of 30, and stem subsidence of >10 mm was seen in 1 patient (4%). Of the patients, 87% thought the procedure improved their function, and 97% would recommend it to a friend with a failed femoral component. Although we hope that the instruments for this procedure can improve, we endorse the concept of impaction grafting with the CPT stem as a successful way of dealing with revision femoral surgery.
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Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Redmond, Washington 98052, USA
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37
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38
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Abstract
Manually operated injection systems are routinely used to deliver polymethyl methacrylate during cemented femoral component primary total hip arthroplasty (THA). The goal of cement delivery is to achieve sufficient intrusion of cement into the trabecular bone of the prepared femur so that the femoral component is securely bonded to the femur. We have observed posterior distal cement extrusion (PDCE), which appears to be secondary to too-successful pressurization. We sought to quantify and offer a possible explanation for this phenomenon. Eight patients with PDCE were identified, with an estimated incidence range of 0.90%, to 1.6% of primary cemented femoral component THA. All occurred in female patients of small stature. Endosteal canal diameters were also small, averaging 11 mm, 10 cm from the lesser trochanter. The PDCE occurred at an average distance of 9.8 cm from the midpoint of the lesser trochanter, and was most easily visualized on the lateral radiograph where it resided in the posterior soft tissues. Examination of 49 human femora showed 1 or more vascular channels in the posterior aspect of the femur in all specimens. The most proximal vascular channel averaged 10.1 cm distal to the lesser trochanter and had an average lumen diameter of 1 mm. The vascular channel contained an artery and 2 veins by histologic examination. We postulate that PDCE represents the escape of low-viscosity cement out of the vascular channel, and laboratory simulation supports this possibility. Because this finding has not previously been reported, we hoped that other centers will look closely for this phenomenon.
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Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Redmond, Washington 98052, USA
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39
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Abstract
With an increasingly aging population, heart failure is a major health issue, affecting more than 10% of the population over 65 years of age, and costing hundreds of millions of dollars per year for ongoing care. Even with maximal medical therapy, annual mortality rates of in excess of 25% are commonly reported. Over the last three decades, various surgical approaches have been examined in the hope of improving the outcome of congestive cardiac failure. These procedures range from simple coronary revascularisation to left ventricular reduction surgery and cardiac transplantation. Although of value in selected situations, no surgical approach, beyond transplantation, has had significant impact on the outcome of heart failure. In the last decade, development in the area of mechanical support for the failing heart has continued to expand at a rapid rate. Strong evidence now exists to show that in many patients with advanced heart failure, prolonged mechanical support results in significant myocardial recovery. There are currently several mechanical support devices available for clinical use, although most are considered experimental in this country. These devices are expensive and are not without significant complications, but early results of their use as either a bridge to transplantation or as a stand alone treatment, have been very encouraging. Currently available mechanical assist devices are described, with discussion of indications for implantation, complications and results of their use.
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Affiliation(s)
- J L Knight
- Cardiac Surgery, Flinders Medical Centre, Adelaide, SA
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40
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Abstract
BACKGROUND We compared postoperative neuropsychological dysfunction after minimally invasive direct coronary artery bypass grafting (MIDCAB) operation with coronary artery bypass graft operations using cardiopulmonary bypass. METHODS Neuropsychological assessment was performed preoperatively and before discharge on 7 patients undergoing MIDCAB procedures, 9 patients undergoing single-graft cardiopulmonary bypass operation, and 27 patients undergoing multiple-graft cardiopulmonary bypass operation. From a matched control group of 40 normal subjects reliable change indices were derived for each measure and used to determine the incidence of postoperative decline. RESULTS There was little difference between the MIDCAB and single-graft cardiopulmonary bypass groups on the incidence of neuropsychologic decline. However, the multiple-graft cardiopulmonary bypass group had a significantly higher incidence of decline than the MIDCAB and single-graft cardiopulmonary bypass groups on specific neuropsychologic measures, coupled with a significantly greater number of postoperative deteriorations per patient. CONCLUSIONS The elimination of cardiopulmonary bypass does not prevent neuropsychological dysfunction after cardiac operation as patients undergoing MIDCAB and single-graft cardiopulmonary bypass experience similar deteriorations in performance. However, the deterioration is markedly worsened when the number of surgical grafts is increased.
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Affiliation(s)
- M J Andrew
- Department of Surgery, Flinders Medical Centre and Flinders University of South Australia, Adelaide, Australia
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41
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Knight JL, Weaver DF. A computational quantitative structure-activity relationship study of carbamate anticonvulsants using quantum pharmacological methods. Seizure 1998; 7:347-54. [PMID: 9808108 DOI: 10.1016/s1059-1311(05)80001-9] [Citation(s) in RCA: 5] [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: 02/09/2023] Open
Abstract
A pattern recognition quantitative structure-activity relationship (QSAR) study has been performed to determine the molecular features of carbamate anticonvulsants which influence biological activity. Although carbamates, such as felbamate, have been used to treat epilepsy, their mechanisms of efficacy and toxicity are not completely understood. Quantum and classical mechanics calculations have been exploited to describe 46 carbamate drugs. Employing a principal component analysis and multiple linear regression calculations, five crucial structural descriptors were identified which directly relate to the bioactivity of the carbamate family. With the resulting mathematical model, the biological activity of carbamate analogues can be predicted with 85-90% accuracy.
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Affiliation(s)
- J L Knight
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
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42
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Knight JL, Atwater RD, Guo J. Clinical results of the midstem porous-coated anatomic uncemented femoral stem in primary total hip arthroplasty: a five- to nine-year prospective study. J Arthroplasty 1998; 13:535-45. [PMID: 9726319 DOI: 10.1016/s0883-5403(98)90053-5] [Citation(s) in RCA: 10] [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] [Indexed: 02/01/2023] Open
Abstract
The clinical and radiologic results of an inclusive series of 60 patients (70 hips) who had primary total hip arthroplasty using the porous-coated anatomic (PCA) midstem femoral prosthesis was prospectively studied. The midstem component features a proximal circumferential porous bead coating similar to the PCA primary stem; but increased proximal thickness, increased length, and a distal anterior curve for additional rotational stability. The mean Harris Hip Score rose from 39.5 points before surgery to 91.3 points at a minimum follow-up of 5 years (average, 69 months); 88% were good or excellent. Moderate or severe thigh pain on a visual analogue scale was reported by 30% of cases, and was more common in women. Radiographic analysis indicated preservation of proximal bone stock and bony ingrowth in 87%, but stem subsidence in 9%. One stem has been revised for subsidence and thigh pain (1.4%), and one stem is radiographically loose, but the patient refuses surgical revision. Endosteal osteolysis was rarely seen (2.8%) and was benign in appearance. Acetabular components used included 63 nonmodular PCA metal-backed cups and 7 hemispherical porous ingrowth cups fixed with screws. One PCA cup was revised for loosening (1.4%), and one is radiographically loose but stable (1.4%). Only one cup exhibited an area of osteolysis. At this intermediate follow-up the clinical outcome of the midstem component is stable and excellent. The radiographic results appear superior to the PCA primary stem, with a lower incidence of stem subsidence and osteolysis. The prevalence of thigh pain is a concern and we recommend regular follow-up of patients with the midstem femoral implant, and the use of a visual analogue thigh pain scale when any femoral prosthesis is evaluated.
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Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Redmond, Washington 98052, USA
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43
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Knight JL. Genu recurvatum deformity secondary to partial proximal tibial epiphyseal arrest: case report. Am J Knee Surg 1998; 11:111-5. [PMID: 9586741] [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: 02/07/2023]
Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Eastside Specialty Center, Redmond, Washington 98052, USA
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44
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Abstract
BACKGROUND A method of defining change in neuropsychologic test scores that accounts for test reliability and practice effects was applied to determine accurately the incidence of acquired neuropsychologic deficits after coronary artery bypass grafting. METHODS Neuropsychologic assessment was performed on 50 patients before and at 7 days after either hypothermic or normothermic coronary artery bypass grafting. From a matched control group of 24 normal subjects who were examined twice over a similar interval, reliable change indices that controlled for measurement error and practice effects were calculated for each neuropsychologic measure. With the use of these indices, the incidence of postoperative decline among the study patients was determined. For comparison, the incidence of decline using the "one standard deviation" criterion also was calculated. RESULTS Comparing the reliable change and standard deviation methods, statistically significant differences in the incidence of decline were observed in 5 of 11 neuropsychologic measures. The reliable change method identified more patients with neuropsychologic deficits on most measures. CONCLUSIONS The control of measurement error and practice effects can alter significantly the calculated incidence of neuropsychologic impairment after coronary artery bypass grafting.
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Affiliation(s)
- A C Kneebone
- Department of Health Psychology, Flinders Medical Centre, Adelaide, South Australia, Australia
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45
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Knight JL, Sherer D, Guo J. Blood transfusion strategies for total knee arthroplasty: minimizing autologous blood wastage, risk of homologous blood transfusion, and transfusion cost. J Arthroplasty 1998; 13:70-6. [PMID: 9493540 DOI: 10.1016/s0883-5403(98)90077-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [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] [Indexed: 02/06/2023] Open
Abstract
In this nonrandomized study, alternative strategies were suggested to 10 orthopaedic surgeons to minimize autologous blood wastage, the risk of homologous blood transfusion, and cost associated with blood product usage after total knee arthroplasty (TKA). One hundred fifty-five patients with 177 consecutive TKAs over a 2-year period were studied. Group 1 patients had undergone unilateral TKA and did not predonate; 1A patients (n = 19) were drained with a Hemovac, and 1B patients (n = 28) with a postoperative blood recovery system. Group 2 patients (n = 47) predonated one packed red blood cell (pRBC) unit. Group 3 patients (n = 20) predonated 2 pRBC units. Group 4 patients had undergone bilateral sequential TKAs (n = 21) and had predonated 2 pRBC units. Group 5 patients (n = 14) had undergone revision TKA procedures and their blood requirements were individualized. Group 6 patients (n = 6) had preexisting anemia and were excluded from the study. There was no significant difference in total blood loss (909 mL) between groups. Female sex was associated with significantly lower admission hematocrit. Homologous blood was required for 4% of patients in the entire study and the percentage was not statistically different between groups. Twenty-five percent of patients who predonated autologous pRBCs did not use all or some of it. In group 1, the postoperative blood recovery system had a significant effect on reducing postoperative hematocrit drop (P = .0001), but it was not a significant factor if autologous pRBCs were available. The costs associated with group 1A were significantly less (P = .0001) compared with the other groups; group 1A had the highest admission hematocrit (43.2). Transfusion with autologous pRBCs was related to lower admission hematocrit rather than to increased postoperative blood loss. An algorithm is presented to provide cost-effective management of blood products after TKA.
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Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Eastside Specialty Center, Redmond, Washington 98052, USA
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46
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Abstract
Our study examines the clinical, radiographic, and patient satisfaction outcome of the cemented Modular Porous-Coated Anatomic (PCA) total knee arthroplasty with a minimum 5-year follow up. All data were gathered prospectively and consecutively. Patient satisfaction was assessed with a self-administered survey. Statistical analysis examined the effect of 17 patient factors, 19 surgical factors, and postoperative continuous passive motion use on range of motion (ROM) and HSS scores at 2 years. Seventy-eight Modular PCA arthroplasties performed by 9 orthopedic surgeons on 71 patients between January 1988 and November 1989 are reported in this study. Preoperative HSS scores averaged 51.2 and improved to an average of 89 at 1 and 2 years, and 86 at 5 years after surgery (90% good or excellent). ROM changed after surgery through improvement in preoperative knee flexion contracture, but not in increased knee flexion. One patient underwent reoperation for patellar instability, and one patient's arthroplasty was revised at 53 months for late instability. The total reoperation rate for any reason was 7.7%. Zonal analysis for progressive radiolucency at the bone-cement interface showed increasing frequency of narrow (< 1 mm) radiolucencies concentrated on the anterior and medial aspect of the tibial tray. Ninety-eight percent of patients responded to an outcome questionnaire, and 96% rated themselves improved. The Kaplan-Meier probability of an implant surviving without loosening at 5 years was 100%. The Modular PCA TKA has a low incidence of patellofemoral problems, is clinically successful, and results are stable at a minimum 5-year follow-up examination.
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Affiliation(s)
- J L Knight
- Department of Orthopedics, Eastside Specialty Center, Redmond, WA 98052, USA
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47
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Knight JL, Au K, Whitley MA. Popliteal aneurysm presenting as chronic exertional compartment syndrome. Orthopedics 1997; 20:166-9. [PMID: 9048394 DOI: 10.3928/0147-7447-19970201-16] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- J L Knight
- Department of Orthopedics, Group Health Cooperative of Puget Sound, Eastside Specialty Center, Redmond, WA 98052, USA
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48
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Abstract
Unicompartmental knee arthroplasty (UKA) is performed less frequently than total (tricompartmental) knee arthroplasty (TKA). This study examined the range of presenting symptoms and usefulness of diagnostic tests to determine the failure mode; the outcome of surgical revision of failed UKA is also reported. From a consecutive prospective series of 43 Porous Coated Anatomic (Howmedica, Rutherford, NJ) UKAs performed between 1985 and 1992 and followed for an average of 64 months, 12 cases have come to revision surgery (28%). The average time to failure was 37 months. Symptoms preceded revision surgery by an average of 10 months. The most common presenting symptom was pain (100%), followed by swelling (92%), reduced range of motion (42%), instability (42%), and clicking (17%). Failure was caused by polyethylene wear in 50%, loosening of the femoral component in 42%, and progression of patellofemoral arthritis in one patient. The combination of single leg standing anteroposterior radiographs and supine lateral radiographs detected most causes of UKA failure. A bone scan was confirmatory in every case of suspected loosening of the femoral component. Arthroscopy diagnosed polyethylene wear in two cases and progression of joint arthritis in one case and was not helpful in one case. Revision surgery was done with primary TKA components, and follow-up periods averaged 27 months. Bone stock deficiency was found in 58%, but required bone-grafting in only one case. Revision surgery successfully restored pain-free function and range of motion in all cases. Two-year postrevision Hospital for Special Surgery scores are equal to those for primary TKA. Survivorship analysis showed a 33% failure rate at 57 months after Porous Coated Anatomic UKA when revision was the endpoint and a 41% failure rate when unsatisfactory clinical status was the endpoint. Regular follow-up evaluation is suggested for the Porous Coated Anatomic UKA.
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Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Eastside Specialty Center, Redmond, Washington 98052, USA
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49
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Knight JL, Gorai PA, Atwater RD, Grothaus L. Tibial polyethylene failure after primary porous-coated anatomic total knee arthroplasty. Aids to diagnosis and revision. J Arthroplasty 1995; 10:748-57. [PMID: 8749756 DOI: 10.1016/s0883-5403(05)80070-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [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] [Indexed: 02/02/2023] Open
Abstract
Recognizing and providing effective treatment for polyethylene failure after total knee arthroplasty (TKA) are challenging problems. The range of presenting symptoms and the usefulness of diagnostic tests are examined, and the outcome of surgical treatment of patients with tibial polyethylene failure is reported. From a consecutive series of 209 Primary Porous-Coated Anatomic (Howmedica, Rutherford, NJ) TKAs performed between 1984 and 1987, 18 cases (9%) required revision surgery. No patient experienced polyethylene failure prior to 48 months, and the average time to revision was 81 months after index TKA. The follow-up period after revision surgery averaged 24 months. Symptoms began after a period of good function, and preceded revision by an average of 8 months. The most common presenting symptom was swelling (89%), followed by stiffness (72%), pain (67%), and clicking (38%) or instability (22%). Single leg standing anteroposterior radiographs were most effective, demonstrating polyethylene failure by a change to increasing varus and narrowing of the polyethylene space in 16 of 18 cases. Arthroscopic evaluation confirmed the diagnosis in two cases. Five cases required tibial tubercle osteotomy for exposure, and 15 required complete synovectomy. Exchange of the damaged heat-pressed polyethylene insert with a machined insert was performed in 14 cases, exchange plus tibial tray revision in 3 cases, and complete knee revision in 1 case. Revision surgery successfully restored pain-free function and improved range of motion in 16 of 18 cases. Survivorship analysis showed an 11% failure rate at 8 years after index procedure. Regular follow-up evaluation for the Primary Porous-Coated Anatomic TKA is suggested.
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Affiliation(s)
- J L Knight
- Department of Orthopaedics, Group Health Cooperative of Puget Sound, Redmond, Washington 98052, USA
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50
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Geiger-Dow JE, Knight JL, Sanfilippo AJ. Aortic ring abscess and mitral valve aneurysm in aortic valvular endocarditis: enhanced diagnosis with transesophageal echocardiography. Can J Cardiol 1995; 11:239-42. [PMID: 7889443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Aortic ring abscess and mitral valve aneurysms complicating infective endocarditis have previously been described as surgical or autopsy findings. More recently, transesophageal echocardiography has been shown to be more sensitive than standard transthoracic echocardiography or other imaging modalities in detecting each of these complications. Since aortic ring abscess and mitral valve aneurysms virtually mandate surgical intervention, their early detection may be crucial. This report describes a 35-year-old male with congenitally abnormal aortic valve which became infected and in whom both an aortic ring abscess and mitral valve aneurysm occurred. These findings are discussed and the pertinent literature is reviewed.
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Affiliation(s)
- J E Geiger-Dow
- Division of Cardiology and Cardiothoracic Surgery, Queen's University, Kingston, Ontario
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