The high throughput screening is the first step of the docking or computational method of drug discovery. This slide will help you to understand the basic things in HTVS.
molecular docking its types and de novo drug design and application and softw...GAUTAM KHUNE
This ppt deals with all the aspects related to molecular docking ,its types(rigid ,flexible and manual) and screening based on it and also deals with de novo drug design , various softwares available for docking methodologies and applications for molecular docking in new drug design
molecular docking its types and de novo drug design and application and softw...GAUTAM KHUNE
This ppt deals with all the aspects related to molecular docking ,its types(rigid ,flexible and manual) and screening based on it and also deals with de novo drug design , various softwares available for docking methodologies and applications for molecular docking in new drug design
High throughput screening is a type of assay. By this assay we can identified the target or binding site of drugs. Its mainly performed during the drug discovery process.
Lead Optimization is an important technique in new drug development. It encompasses several fields such as synthetic chemistry, phytochemistry, analysis, pharmacology and microbiology.
The basic aspects of drug discovery starts from target discovery and validation further going to lead identification and optimization. In this particular slide discussion is regarding the target discovery and the tools that have been utilized in this process.
SAR versus QSAR, History and development of QSAR, Types of physicochemical
parameters, experimental and theoretical approaches for the determination of
physicochemical parameters such as Partition coefficient, Hammet’s substituent
constant and Taft’s steric constant. Hansch analysis, Free Wilson analysis, 3D-QSAR
approaches like COMFA and COMSIA.
Back Rapid lead compounds discovery through high-throughput screeningrita martin
High-throughput screening process are used by today most of the drug discovery industries, this process helps pharmaceutical researches to make drug discovery process faster and also increase the quality and quantity of drugs production. This process in combination with robotics, data processing and control software, liquid handling devices and sensitive detectors allows a researcher to quickly conduct millions of chemical, genetic or pharmacological tests
High throughput screening is a type of assay. By this assay we can identified the target or binding site of drugs. Its mainly performed during the drug discovery process.
Lead Optimization is an important technique in new drug development. It encompasses several fields such as synthetic chemistry, phytochemistry, analysis, pharmacology and microbiology.
The basic aspects of drug discovery starts from target discovery and validation further going to lead identification and optimization. In this particular slide discussion is regarding the target discovery and the tools that have been utilized in this process.
SAR versus QSAR, History and development of QSAR, Types of physicochemical
parameters, experimental and theoretical approaches for the determination of
physicochemical parameters such as Partition coefficient, Hammet’s substituent
constant and Taft’s steric constant. Hansch analysis, Free Wilson analysis, 3D-QSAR
approaches like COMFA and COMSIA.
Back Rapid lead compounds discovery through high-throughput screeningrita martin
High-throughput screening process are used by today most of the drug discovery industries, this process helps pharmaceutical researches to make drug discovery process faster and also increase the quality and quantity of drugs production. This process in combination with robotics, data processing and control software, liquid handling devices and sensitive detectors allows a researcher to quickly conduct millions of chemical, genetic or pharmacological tests
HTS is a high-tech way to hasten the drug discovery process, allowing quick and efficient screening of large compound libraries at a rate of a few thousand compounds per day or per week.
There are tens of thousands of man-made chemicals to which humans are exposed, but only a fraction of these have the extensive in vivo toxicity data used in most traditional risk assessments. This lack of data, coupled with concerns about testing costs and animal use, are driving the development of new methods for assessing the risk of toxicity. These methods include the use of in vitro high-throughput screening assays and computational models.
This presentation by Dr. Richard Judson reviewed a variety of high-throughput, non-animal methods being used at the U.S. EPA to screen chemicals for a variety of toxicity endpoints, including methods for providing mechanistic data like the Adverse Outcome Pathway.
EPA is committed to sound science, and we are proud to have some of the world's best scientists, many of whom are internationally recognized as leaders in their fields. Not only are EPA's scientific experts vital to achieving our mission, but they are dedicated to sharing knowledge and contributing to their the scientific communities, which helps further advance the science that protects human health and the environment. Part of this includes giving presentations to other members of the scientific community. We have posted some of these presentations here so that more people have access.
Learn more about Dr. Richard Judson - https://www.epa.gov/sciencematters/meet-epa-researcher-richard-judson
Learn more about EPA's Chemical Safety Research - https://www.epa.gov/chemical-research
This is the presentation on Role of advancement in instrumentation in pharmacodynamic evaluation of drugs
in clinical trials.
CONTENTS
Concept of medical instrument and instrumentation
Centrifuge
PCR
HPLC
Flow cytometry
Mass SPECTROMETRY
Minimally invasive technologies in PD
Conclusion
Enabling HTS Hit follow up via Chemo informatics, File Enrichment, and Outsou...Graham Smith
Enabling HTS Hit follow up via Chemo informatics, File Enrichment, and Outsourcing The history of parallel chemistry for lead discovery at Pfizer Sandwich from begining to outsourcing
An Integrated Approach To Drug Discovery Using Parallel SynthesisGraham Smith
An Integrated Approach To Drug Discovery Using Parallel Synthesis. The history of parallel chemistry for lead discovery at Pfizer Sandwich from begining to outsourcing
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
1. HIGH THROUGHPUT SCREENING
FOR LEAD DISCOVERY
Ajeesh. V
Department of Pharmacy
School of chemical sciences and pharmacy
Central University of Rajasthan
2. Introduction
A lead compound is a representative of a compound series with sufficient
potential (as measured by potency, selectivity, pharmacokinetics,
physicochemical properties, toxicity and novelty) to progress to a full drug
development programme.
High Throughput Screening (HTS) is a method that uses automation and
large data set processing to quickly assay the biological or biochemical
activity of large numbers of compounds, proteins or genes.
HTS is an approach to drug discovery that has gained widespread
popularity over the last two decades and has become a standard method
for drug discovery in the pharmaceutical industry.
3. Usually first step in Drug discovery
It helps to rapidly identify active compounds, antibodies, or genes that
modulate a particular biomolecular pathway.
HTS assays are used for screening of different types of libraries,
including combinatorial chemistry, genomics, protein, and peptide
libraries.
It is basically a process of screening and assaying a large number of
biological modulators and effectors against selected and specific
targets.
4. Screening Collection
Screening libraries
(a) Diversity Libraries
(b) Focused Libraries
Ligand-Based Approaches
Structure-Based Approaches
Compound acquisition
Purchasing commercially available compounds is an
important aspect of screening collection enhancement
5. Libraries
siRNA libraries
providing the best available RNA interference technology with
maximum flexibility
The mouse whole genome contain about 16872 gene targets and the
Human whole-genome contains 18120 gene targets
microRNA libraries
Human libraries of synthetic microRNA mimics and microRNA inhibitors
Small Compound libraries
A library of 640 FDA approved drugs (Screen-Well FDA Approved Drug
Library, Enzo Life Sciences) is also available for screening.
The library contains clinically-relevant pharmacophores.
6. Steps in HTS
1st stage screening
Test optical clarity, abrasion resistance, and adhesion
Eliminates ~ 90% of samples
2nd stage screening
Test weather ability, integrity, gloss, and surface smoothness
~10% of the samples
Rapidly identify coating samples with desired properties
Candidates for scale up
Test according to the customer’s specifications
7. Screening Strategies
Mixtures versus Single Compound Screening
In the early 1990s, the strategy adopted was to synthesize and test compounds
as mixtures
Full Deck Screening
All compounds in the screening collection are subjected to HTS.
Focused Screening
Only a subset of the compound collection would be screened. The selection
method could be based on structural diversity, target knowledge, or a
combination of the two.
Sequential Screening
This consists of either an initial diversity-based or focused screen, followed by
one or more subsequent screens enriched with analogues of the hits.
8. Anatomy of HTS
It contains
1. Robotic handling systems
2. Liquid handling systems
3. Sensor systems and
4. Control software
Microplates, each of which consists of an array of wells, are
moved through the system by robotic handling. The wells in the
microplates are filled via the liquid handling systems, and sensors
are used to evaluate the samples in the microplate.
Control software choreographs the entire process, ensuring
accuracy within the process and repeatability between processes.
10. The introduction of 96-well plates and reduced assay
volumes (50–100 mL) increased screening throughput
from 50 to 7200 compounds per week by end of 1980s
Then 384-well-plate format, enabling screening
capacities of 10–100,000 compounds per day
Recently 1536-well format provides throughput of over
100,000 compounds per day (ultra-HTS)
Latest is 3456-well microplates with a total assay
volume of 1–2 mL per well
11. Detection Methods in HTS
Spectroscopy
Mass Spectrometry
Chromatography
Calorimetry
X-ray diffraction
Microscopy
Radioactive methods
Chromatography
Gas chromatography (GC)
Thin layer chromatography
HPLC
1st stage
•100-200 samples per day
2nd stage
•~10% of the samples
Rapidly identified materials
Candidates for scale up
1st stage
•100-200 samples per day
2nd stage
•~10% of the samples
Rapidly identified materials
Candidates for scale up
16. Newer method in HTS
High-Throughput, Fluorescence-Based Screening
(a) For screening, expressed proteins are labelled either as
fusions with green fluorescent protein (GFP) or through
translational incorporation of a fluorescent amino acid
derivative, BODIPY-FL-Lysine.
(b) Using fluorescence detection, the entire procedure can
be carried out in approximately 8 h.
17. Applications
In drug discovery
Systematic Study of Mitochondrial Toxicity of
Environmental Chemicals
High-Throughput Screening of Dendrimer-Binding
Drugs
To Fractionate Plant Natural Products for Drug
Discovery
18. Summary
Since its beginnings in the early 1990s, lead discovery by HTS has
evolved into a mature scientific discipline. Early HTS strategies based on
compound numbers alone have been firmly replaced by an emphasis on
quality and scientific rationale
The number of HTS-derived drugs has been steadily increasing in recent
years.
Despite the current limitations and the fact that the overall success of
the HTS paradigm is still debatable, there is no doubt that this is the
most widely applicable lead discovery approach capable of providing a
wide choice of novel chemical entities for a broad range of biological
targets.
HTS is likely to retain a central role in drug discovery and continue to
provide a focus for major scientific and technological efforts for many
years to come.
19. References
Text book of Lead Generation Approaches In Drug Discovery
by Zoran Rankovic and Richard Morphy
Text book of High-Throughput Screening in Drug Discovery
R. Mannhold, H. Kubinyi, and G. Folkers
Leach AR, Hann MM. The in silico world of virtual libraries.
Drug Discov Today 2000; 5:326–336.
J. AM. CHEM. SOC. 2010, 132, 13182–13184
Journal of Natural Products, 2010, Vol. 73, No. 4 753