Joe Olechno - Academia.edu (original) (raw)
Papers by Joe Olechno
Analytical Chemistry, 2019
Green Chemistry, 2019
Miniaturized and automated nanomole synthesis using acoustic dispensing technology dramatically a... more Miniaturized and automated nanomole synthesis using acoustic dispensing technology dramatically accelerated the production of diverse libraries of three small molecule scaffolds.
Journal of laboratory automation, 2016
Phytochemistry, 1984
... NANDININ: AN'ACYLATED FREE CYANOHYDRIN FROM NANDINA DOMESTICA JOSEPH D. OLECHNO, JONATHA... more ... NANDININ: AN'ACYLATED FREE CYANOHYDRIN FROM NANDINA DOMESTICA JOSEPH D. OLECHNO, JONATHAN E. POULTON* and ERIC E. CONN Department of Biochemistry ... 2.Harborne, J. and Williams, C. (1982) in The Flavonoids (Harborne, J. and Mabry, T., eds). ...
ACS Central Science, 2019
Dispensing and dilution processes may profoundly influence estimates of biological activity of co... more Dispensing and dilution processes may profoundly influence estimates of biological activity of compounds. Published data show Ephrin type-B receptor 4 IC50 values obtained via tip-based serial dilution and dispensing versus acoustic dispensing with direct dilution differ by orders of magnitude with no correlation or ranking of datasets. We generated computational 3D pharmacophores based on data derived by both acoustic and tip-based transfer. The computed pharmacophores differ significantly depending upon dispensing and dilution methods. The acoustic dispensing-derived pharmacophore correctly identified active compounds in a subsequent test set where the tip-based method failed. Data from acoustic dispensing generates a pharmacophore containing two hydrophobic features, one hydrogen bond donor and one hydrogen bond acceptor. This is consistent with X-ray crystallography studies of ligand-protein interactions and automatically generated pharmacophores derived from this structural dat...
Science Advances
The compatibility of free boronic acid building blocks in multicomponent reactions to readily cre... more The compatibility of free boronic acid building blocks in multicomponent reactions to readily create large libraries of diverse and complex small molecules was investigated. Traditionally, boronic acid synthesis is sequential, synthetically demanding, and time-consuming, which leads to high target synthesis times and low coverage of the boronic acid chemical space. We have performed the synthesis of large libraries of boronic acid derivatives based on multiple chemistries and building blocks using acoustic dispensing technology. The synthesis was performed on a nanomole scale with high synthesis success rates. The discovery of a protease inhibitor underscores the usefulness of the approach. Our acoustic dispensing–enabled chemistry paves the way to highly accelerated synthesis and miniaturized reaction scouting, allowing access to unprecedented boronic acid libraries.
ASSAY and Drug Development Technologies, 2005
Acoustic auditing is a non-destructive, non-invasive technique to monitor the composition and vol... more Acoustic auditing is a non-destructive, non-invasive technique to monitor the composition and volume of fluids in open or sealed microplates and storage tubes. When acoustic energy encounters an interface between two materials, some of the energy passes through the interface, while the remainder is reflected. Acoustic energy applied to the bottom of a multi-well plate or a storage tube is reflected by the fluid contents of the microplate or tube. The amplitude of these reflections or echoes correlates directly with properties of the fluid, including the speed of sound and the concentration of water in the fluid. Once the speed of sound in the solution is known from the analysis of these echoes, it is easy to determine the depth of liquid and, thereby, the volume by monitoring how long it takes for sound energy to reflect off the fluid meniscus. This technique is rapid (>100,000 samples per day), precise (<1% coefficient of variation for hydration measurements, <4% coefficient of variation for volume measurements), and robust. It does not require uncapping tubes or unsealing or unlidding microplates. The sound energy is extremely gentle and has no deleterious impact upon the fluid or compounds dissolved in it.
American biotechnology laboratory
X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular ... more X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.
The introduction of new pharmaceutical drugs has slowed while money and effort expended by the in... more The introduction of new pharmaceutical drugs has slowed while money and effort expended by the industry has dramatically increased. We suggest that some of that effort may be inadvertently wasted in drug screening and quantitative structure-activity relationship studies where results can be strongly skewed by the method of liquid handling and the protocol used. Recent work has demonstrated that dispensing processes have a profound influence on estimates of IC50. What appear to be minor modifications in the design of concentration gradients coupled with long-standing liquid handling procedures have generated a 1.5 to 1,000-fold difference in IC50 showing no correlation or ranking between competing processes. Importantly when such data are used for computational modeling, the computed pharmacophores for each dataset are different and lead to the development of compounds with significantly different structures and chemico-physical properties. Dispensing processes are therefore an impor...
WIGGLESWORTH:SAMPLE MGMT. O-BK, 2012
ABSTRACT
PLoS ONE, 2013
Dispensing and dilution processes may profoundly influence estimates of biological activity of co... more Dispensing and dilution processes may profoundly influence estimates of biological activity of compounds. Published data show Ephrin type-B receptor 4 IC 50 values obtained via tip-based serial dilution and dispensing versus acoustic dispensing with direct dilution differ by orders of magnitude with no correlation or ranking of datasets. We generated computational 3D pharmacophores based on data derived by both acoustic and tip-based transfer. The computed pharmacophores differ significantly depending upon dispensing and dilution methods. The acoustic dispensing-derived pharmacophore correctly identified active compounds in a subsequent test set where the tip-based method failed. Data from acoustic dispensing generates a pharmacophore containing two hydrophobic features, one hydrogen bond donor and one hydrogen bond acceptor. This is consistent with X-ray crystallography studies of ligand-protein interactions and automatically generated pharmacophores derived from this structural data. In contrast, the tip-based data suggest a pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and no hydrophobic features. This pharmacophore is inconsistent with the X-ray crystallographic studies and automatically generated pharmacophores. In short, traditional dispensing processes are another important source of error in high-throughput screening that impacts computational and statistical analyses. These findings have far-reaching implications in biological research.
Journal of the Association for Laboratory Automation, 2006
Journal of the Association for Laboratory Automation, 2006
Journal of Synchrotron Radiation, 2013
To take full advantage of advanced data collection techniques and high beam flux at next-generati... more To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide 'conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.
Analytical Chemistry, 2019
Green Chemistry, 2019
Miniaturized and automated nanomole synthesis using acoustic dispensing technology dramatically a... more Miniaturized and automated nanomole synthesis using acoustic dispensing technology dramatically accelerated the production of diverse libraries of three small molecule scaffolds.
Journal of laboratory automation, 2016
Phytochemistry, 1984
... NANDININ: AN'ACYLATED FREE CYANOHYDRIN FROM NANDINA DOMESTICA JOSEPH D. OLECHNO, JONATHA... more ... NANDININ: AN'ACYLATED FREE CYANOHYDRIN FROM NANDINA DOMESTICA JOSEPH D. OLECHNO, JONATHAN E. POULTON* and ERIC E. CONN Department of Biochemistry ... 2.Harborne, J. and Williams, C. (1982) in The Flavonoids (Harborne, J. and Mabry, T., eds). ...
ACS Central Science, 2019
Dispensing and dilution processes may profoundly influence estimates of biological activity of co... more Dispensing and dilution processes may profoundly influence estimates of biological activity of compounds. Published data show Ephrin type-B receptor 4 IC50 values obtained via tip-based serial dilution and dispensing versus acoustic dispensing with direct dilution differ by orders of magnitude with no correlation or ranking of datasets. We generated computational 3D pharmacophores based on data derived by both acoustic and tip-based transfer. The computed pharmacophores differ significantly depending upon dispensing and dilution methods. The acoustic dispensing-derived pharmacophore correctly identified active compounds in a subsequent test set where the tip-based method failed. Data from acoustic dispensing generates a pharmacophore containing two hydrophobic features, one hydrogen bond donor and one hydrogen bond acceptor. This is consistent with X-ray crystallography studies of ligand-protein interactions and automatically generated pharmacophores derived from this structural dat...
Science Advances
The compatibility of free boronic acid building blocks in multicomponent reactions to readily cre... more The compatibility of free boronic acid building blocks in multicomponent reactions to readily create large libraries of diverse and complex small molecules was investigated. Traditionally, boronic acid synthesis is sequential, synthetically demanding, and time-consuming, which leads to high target synthesis times and low coverage of the boronic acid chemical space. We have performed the synthesis of large libraries of boronic acid derivatives based on multiple chemistries and building blocks using acoustic dispensing technology. The synthesis was performed on a nanomole scale with high synthesis success rates. The discovery of a protease inhibitor underscores the usefulness of the approach. Our acoustic dispensing–enabled chemistry paves the way to highly accelerated synthesis and miniaturized reaction scouting, allowing access to unprecedented boronic acid libraries.
ASSAY and Drug Development Technologies, 2005
Acoustic auditing is a non-destructive, non-invasive technique to monitor the composition and vol... more Acoustic auditing is a non-destructive, non-invasive technique to monitor the composition and volume of fluids in open or sealed microplates and storage tubes. When acoustic energy encounters an interface between two materials, some of the energy passes through the interface, while the remainder is reflected. Acoustic energy applied to the bottom of a multi-well plate or a storage tube is reflected by the fluid contents of the microplate or tube. The amplitude of these reflections or echoes correlates directly with properties of the fluid, including the speed of sound and the concentration of water in the fluid. Once the speed of sound in the solution is known from the analysis of these echoes, it is easy to determine the depth of liquid and, thereby, the volume by monitoring how long it takes for sound energy to reflect off the fluid meniscus. This technique is rapid (>100,000 samples per day), precise (<1% coefficient of variation for hydration measurements, <4% coefficient of variation for volume measurements), and robust. It does not require uncapping tubes or unsealing or unlidding microplates. The sound energy is extremely gentle and has no deleterious impact upon the fluid or compounds dissolved in it.
American biotechnology laboratory
X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular ... more X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.
The introduction of new pharmaceutical drugs has slowed while money and effort expended by the in... more The introduction of new pharmaceutical drugs has slowed while money and effort expended by the industry has dramatically increased. We suggest that some of that effort may be inadvertently wasted in drug screening and quantitative structure-activity relationship studies where results can be strongly skewed by the method of liquid handling and the protocol used. Recent work has demonstrated that dispensing processes have a profound influence on estimates of IC50. What appear to be minor modifications in the design of concentration gradients coupled with long-standing liquid handling procedures have generated a 1.5 to 1,000-fold difference in IC50 showing no correlation or ranking between competing processes. Importantly when such data are used for computational modeling, the computed pharmacophores for each dataset are different and lead to the development of compounds with significantly different structures and chemico-physical properties. Dispensing processes are therefore an impor...
WIGGLESWORTH:SAMPLE MGMT. O-BK, 2012
ABSTRACT
PLoS ONE, 2013
Dispensing and dilution processes may profoundly influence estimates of biological activity of co... more Dispensing and dilution processes may profoundly influence estimates of biological activity of compounds. Published data show Ephrin type-B receptor 4 IC 50 values obtained via tip-based serial dilution and dispensing versus acoustic dispensing with direct dilution differ by orders of magnitude with no correlation or ranking of datasets. We generated computational 3D pharmacophores based on data derived by both acoustic and tip-based transfer. The computed pharmacophores differ significantly depending upon dispensing and dilution methods. The acoustic dispensing-derived pharmacophore correctly identified active compounds in a subsequent test set where the tip-based method failed. Data from acoustic dispensing generates a pharmacophore containing two hydrophobic features, one hydrogen bond donor and one hydrogen bond acceptor. This is consistent with X-ray crystallography studies of ligand-protein interactions and automatically generated pharmacophores derived from this structural data. In contrast, the tip-based data suggest a pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and no hydrophobic features. This pharmacophore is inconsistent with the X-ray crystallographic studies and automatically generated pharmacophores. In short, traditional dispensing processes are another important source of error in high-throughput screening that impacts computational and statistical analyses. These findings have far-reaching implications in biological research.
Journal of the Association for Laboratory Automation, 2006
Journal of the Association for Laboratory Automation, 2006
Journal of Synchrotron Radiation, 2013
To take full advantage of advanced data collection techniques and high beam flux at next-generati... more To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide 'conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.