Re: [GRG] Alternatives, and supplements, to mouse testing in drug discovery

Here is your answer, Edouard:

1. PCBA – This is an acronym for PubChem BioAssay Database.

Ref: http://ift.tt/1xMV54e

How to Access PCBA: You can access PCBA for free!  Just go to:  http://ift.tt/18M7HgQ

Hot tips for using PCBA in searches – 

Summary: PCBA was set up by the the US NIH and contains over 500,000 descriptions of assay

protocols covering 5,000 protein targets , 30,000 gene targets, and over 130,000

million bioactivity compounds.  This by far is the biggest database of molecules, and

far outstrips ChEMBL (1.3 million bioactivity compounds) and Kaggle (164,000 compounds). 

ChEMBL has 5,000 drug targes and Kaggle has 15 drug targets. Google only looked

at 128 experiments from this database.  They found only 1.8% of the molecules were

active compounds. 

Molecules included in PCBA:  small molecules (synthetic and natural) and RNAi reagents.

What it does not cover:  PCBA does not cover large molecules (anti-bodies, hormones, etc.)

and does not cover any of the non-coding target genes that are now thought to 

account for > 50% of aging, 90% of autoimmune diseases, and 93% of

variations in human diseases.  In other words, the protein targets and

protein-coding gene targets in PCBA do not cover the largest component

of aging and human disease which involve non-coding portion of the genome

(See references below and Science article from May, 2011 – below)

Ref: http://ift.tt/1xMV54g

http://ift.tt/1xMV2Fr

http://ift.tt/1LHjdAK

http://ift.tt/1xMV2Fv

http://ift.tt/1LHjbc6

http://ift.tt/1xMV5ky

2. DUD-E – This is an acronym for Directory of Useful Decoys, Enhanced.

Ref: http://ift.tt/1LHjbc9

How to access DUD-E: Go to the following site: http://dude.docking.org

From there, you can just browse the DUD-E targets or download the software package.

To generate decoys, go here:  http://ift.tt/1xMV2Fz

Summary:  This is a database that was set up by the Dept. of Pharmacology at the University of

California, San Francisco (UCSF) and is designed to predict molecular docking of 

various compounds.  It is an enhanced and rebuilt version of DUD, which was the old

molecular docking program. It includes 22,886 active compounds and their affinities 

against 102 targets (proteins). It includes 50 decoys.  It is free and can be easily accessed 

by anyone.  The Googe authors looked at 102 datasets (protein targets) and found 1.6%

of these to be active. 

What it does not cover:  DUD-E does not look at assays (such as assay artifacts).  It also does not

cover decoys that are large molecules (such as antibodies, cytokines, hormones, etc.)

It also does not cover RNA (such as RNAi, lncRNA, etc.)

Ref: http://ift.tt/1LHjbc9

3. MUV – This is an acronym for Maximum Unbiased Validation.

Ref: http://ift.tt/1LHjbca

How to Access MUV:  First go to the main page for the virtual drug screening site:

http://ift.tt/1xMV2FF

Then download the MUV datasets from the following site:

http://ift.tt/1LHjbcc

Summary: This is a virtual drug screening database that was set up by the University of Technology,

Carolo-Wilehlmina, in Braunschweig, Germany.  It uses a concept called “nearest neighbor 

analysis” to design benchmark data sets, based on PubChem bioactivity data.  The computer

program first removes assay artifacts (Hill slop filter, Frequency of hits filter, autoflourescence

filter, and Luciferase inhibitor filter), then it removes activities not embedded in decoys (Ex:

chemical space embedding filter), then it designs datasets of actives (common spread), then

it designs datasets of decoys (common separation).   The 1st MUV version contained 17 datasets

and corresponding decoys.  Further datasets can be generated yourself, where you create

your own MUVs.  The Google paper authors only looked at 17 datasets using MUV. 

Molecules included: Inhibitors, Agonists, Antagonists, Alloersteric modulators, and allosteric inhibitors

for virtually any protein target.  (Ex: GPCRs, Kinases, Nuclear receptors, RNases, Chaperones,

PPIs, Proteases, Receptors for Tyrosine Kinases, etc.)

Molecules included in MUV:  http://ift.tt/1xMV2FF

4. Tox21 – This is an abbreviation for “Toxicology in the 21st Century”.  It was actually a contest

where there were applicants, registration, and winners.  The winners were announced

on January 26,  2015. 

Ref: http://ift.tt/1xMV5kC

How to access Tox21:  First go to the main page for this toxicology database:

http://ift.tt/1xMV5kC

Summary:  This is one of the first scientific contests to use “crowdsource” data from independent

researchers to reveal how well they can predict compounds interference in biochemical

pathways, using only chemical structure data.  The contest was set up by the NIH’s

National Center for Advancing Translational Sciences (NIH-NCAT), by the EPA, and

by the FDA.   The contest had competitors from 18 countries.  The winners included the

following teams:

1. Team Bioinf from Johannes Kepler University in Linz, Austria.  They won the Grand

Challenge, the Nuclear Receptor Panel award, and the Stress response panel award.

Team Bioinf accurately predicted their compounds in all 12 assays.  

Their challenge assays included the following:

a) stress  response panel,  which the aryl hydrocarbon receptor, the nuclear factor 

     (Erythroid-derived 2) like 2 antioxidant response element (aka Nrf2ARE);

b) the estrogen receptor alpha and the Heat Shock Factor response element (HSFRE);

c) the androgen receptor ligand binding domain;

d) the nuclear receptor signaling panel, including the PPARgamma receptor

2. Team AMAZIZ – This team from the Technical University of Munich.

They wind the award for “Best Balanced Accuracy”

Team AMAZIZ  figured out two assays:

– ATAD5 and one for the Mitochondrial membrane potential (MtP)

3. Team Dmlab – This team from Budapest University of Technology figured out three assays:

– Androgen receptor, aromatase, and p53

4. Team Microsomes – This team from Meiji Pharmaceutical University figured out one assay:

– Estrogen receptor alpha ligand binding domain

Ref: http://ift.tt/1G35iOn

http://ift.tt/1Goq7rh

http://ift.tt/1LHjbce

Advertisements

About Johnny Adams

My full-time commitment is to slow and ultimately reverse age related functional decline to increase healthy years of life. I’ve been active in this area since the 1970s, steadily building skills and accomplishments. I have a good basic understanding of the science of aging, and have many skills that complement those of scientists so they can focus on science to advance our shared mission. Broad experience Top skills: administration, management, information technology (data and programming), communications, writing, marketing, market research and analysis, public speaking, forging ethical win-win outcomes among stakeholders (i.e. high level "selling"). Knowledge in grant writing, fundraising, finance. Like most skilled professionals, I’m best described as a guy who defines an end point, then figures out how to get there. I enjoy the conception, design, execution and successful completion of a grand plan. Executive Director Gerontology Research Group (GRG). Manages Email discussion forum, web site, meetings and oversees supercentenarian (oldest humans, 110+ years) research. CEO / Executive Director Carl I. Bourhenne Medical Research Foundation (Aging Intervention Foundation), an IRS approved 501(c)(3) nonprofit. http://www.AgingIntervention.org Early contributor to Supercentenarian Research Foundation. Co-Founder Geroscience Healthspan Forum. Active contributor to numerous initiatives to increase healthy years of life. Co-authored book on conventional, practical methods available today to slow the processes of aging – nutrition, exercise, behavior modification and motivation, stress reduction, proper supplementation, damage caused by improper programs, risk reduction and others. Fundamental understanding of, and experience in the genomics of longevity (internship analyzing and curating longevity gene papers). Biological and technical includes information technology, software development and computer programming, bioinformatics and protein informatics, online education, training programs, regulatory, clinical trials software, medical devices (CAT scanners and related), hospital electrical equipment testing program. Interpersonal skills – good communication, honest, well liked, works well in teams or alone. Real world experience collaborating in interdisciplinary teams in fast paced organizations. Uses technology to advance our shared mission. Education: MBA 1985 University of Southern California -- Deans List, Albert Quon Community Service Award (for volunteering with the American Longevity Association and helping an elderly lady every other week), George S. May Scholarship, CA State Fellowship. BA psychology, psychobiology emphasis 1983 California State University Fullerton Physiological courses as well as core courses (developmental, abnormal etc). UCLA Psychobiology 1978, one brief but fast moving and fulfilling quarter. Main interest was the electrochemical basis of consciousness. Also seminars at the NeuroPsychiatric Institute. Other: Ongoing conferences, meetings and continuing education. Aging, computer software and information technology. Some molecular biology, biotech, bio and protein informatics, computer aided drug design, clinical medical devices, electronics, HIPAA, fundraising through the Assoc. of Fundraising Professionals. Previous careers include: Marketing Increasing skill set and successes in virtually all phases, with valuable experience in locating people and companies with the greatest need and interest in a product or service, and sitting across the table with decision makers and working out agreements favorable to all. Information Technology: Management, data analysis and programming in commercial and clinical trials systems, and bioinformatics and protein informatics. As IT Director at Newport Beach, CA based technology organization Success Family of Continuing Education Companies, provided online software solutions for insurance and financial professionals in small to Fortune 500 size companies. We were successful with lean team organization (the slower moving competition was unable to create similar software systems). Medical devices: At Omnimedical in Paramount CA developed and managed quality assurance dept. and training depts. for engineers, physicians and technicians. Designed hospital equipment testing program for hospital services division. In my early 20’s I was a musician, and studied psychology and music. Interned with the intention of becoming a music therapist. These experiences helped develop valuable skills used today to advance our shared mission of creating aging solutions.
This entry was posted in Uncategorized and tagged , , , . Bookmark the permalink.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s