CDD Vault Update (February #2 2025): Advanced Macromolecules - Modified Bioconjugates Support in CDD Vault
Collaborative Drug
FEBRUARY 21, 2025
CDD Update February 2025 #2 New Macromolecule Mode Edit DNA, RNA & Peptides with Bioconjugate Support
Case study: gget’s new Open Target module
The Open Targets Blog
JANUARY 30, 2025
This blog post is part of a series that will explore applications and expansions of the Open Targets informatics ecosystem, particularly the Open Targets Platform and Open Targets Genetics through conversations with our users. The gget opentargets module has many applications.
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Reinventing the small molecule toolbox: from proteins to RNA
Dark Matter Blog
APRIL 4, 2023
Prior to 2015, I had a casual relationship, at best, with targeting RNA. Targeting RNA is a Whole New World Then in 2015, I became smitten and eloped with RNA, setting out to build a company devoted to bringing to bear industrial drug discovery concepts and methods on a new problem of drugging RNA with small molecules.
Reaching cruising altitude: New discovery tools to target RNA
Dark Matter Blog
AUGUST 31, 2020
Our overall mission at Arrakis is to expand the set of “druggable” targets for small-molecule medicines to include RNA. Today, we are pleased to announce that our article describing one such platform: “ PEARL-seq, A Photoaffinity Platform for the Analysis of Small Molecule-RNA Interactions ” was published in ACS Chemical Biology.
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A new drug approval for the vanguard of RNA-targeted small molecules
Dark Matter Blog
AUGUST 27, 2020
A few years ago, at Arrakis Therapeutics, we set out to conquer a strange new territory, drugging RNA structures with small molecules. In fact, it was these early pharmaceutical successes that gave us the confidence that we would ultimately succeed in systematically drugging a wide range of RNA structures.
Build Your CRISPR Vocabulary
addgene Blog
JULY 2, 2024
We’ll cover the common terminology for the proteins, DNA, and RNA used in CRISPR. CRISPR is an elegant bacterial immune system and an efficient gene editing tool… but boy does it have a lot of parts! If you’re still a bit confused by CRISPR acronyms, this post is for you.
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A Needle in a Base-Stack: Cas9 Structural Biology
addgene Blog
JUNE 4, 2024
Have you ever designed a CRISPR guide RNA and wondered why it is limited to only 20 bases, or why it’s so important to choose a target sequence with a nearby protospacer-adjacent motif (PAM) ?
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PRIDICT: Predicting Efficiencies of Prime Editing Guide RNAs
addgene Blog
JUNE 25, 2024
This method uses a prime editor (typically a Cas9 H840A nickase fused to a reverse transcriptase) together with a prime editing guide RNA (pegRNA). 2019; Chen & Liu, 2023).
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A Protein Printer
Codon
JULY 11, 2023
All cells make proteins in two steps: DNA is transcribed into messenger RNA, which is then translated into protein. It moves along RNA and reads three letters at a time, called codons, to build the amino acid sequence of a protein. Blueprints The first step is to build a loop of RNA that encodes all the different codons.
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Fearlessly Forward to our Destination
Dark Matter Blog
JANUARY 16, 2023
We are moving rapidly toward escape velocity in our RNA expedition at Arrakis. We want to mark this progress with some updates and perspectives in the Dark Matter blog. Moreover, there is an even vaster universe of biology contained in non-coding transcripts that can only be reached by directly targeting RNA.
Fast Biology
Codon
FEBRUARY 20, 2024
At any given moment, thousands of messenger RNAs are being translated into proteins by ribosomes, which are protein-making machines that are, themselves, made from a mixture of proteins and RNA. As scientists devise more experiments and take more measurements, they often make them available in papers, pre-prints, websites and blogs.
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Navigating the partnering galaxy
Dark Matter Blog
JUNE 21, 2023
Since our company’s founding in 2015, we have taken the long view and been singularly focused on building an extremely flexible and broadly applicable platform that can develop a host of RNA‑targeted small molecules (rSMs) to deliver precision medicines for dozens of targets that have been out of reach for conventional approaches.
Cave Coronavirus in Wuhan Lab Seeded COVID – The Truth Has Always Been Out There, in the Genetics
PLOS: DNA Science
JUNE 13, 2024
The most compelling evidence for the origin lies in the RNA genome sequence similarities between RaTG13 and SARS-CoV-2 – specifically, a part that encodes the “furin binding site” of the spike protein with which the virus adheres to host cells. ” So ended my 2021 blog post a month later.
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High-Content Imaging siRNA Screens Identify Trafficking Factors in Alphavirus Infection
PerkinElmer
JULY 13, 2020
Imaging Modalities Help Visualize and Confirm Findings An emerging method of studying viruses is by using high-content imaging solutions to visualize the activity of small interfering RNA (siRNA), also known as short interfering RNA or “silencing” RNA.
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A Protein Printer
Codon
JULY 11, 2023
All cells make proteins in two steps: DNA is transcribed into messenger RNA, which is then translated into protein. It moves along RNA and reads three letters at a time, called codons, to build the amino acid sequence of a protein. Blueprints The first step is to build a loop of RNA that encodes all the different codons.
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A Look Back
Dark Matter Blog
JULY 16, 2021
As soon as I learned about DNA and RNA, I wanted to be a molecular biologist. Last stops at RNA My last roles in biotech were where my original passion began: DNA and RNA. My last stop at Arrakis Therapeutics is with a company targeting RNA with small molecules. I wanted to use molecular biology to create drugs.
Atlas XIV And Reflections On The VC Math Problem
LifeSciVC
DECEMBER 5, 2024
combinatorial chemistry, human genetics, functional genomics, mRNA, I/O, CRISPR, RNA editing, and many others). This is why when I started this blog the tag line was “ a biotech optimist fighting gravity.” Thankfully he’s not actually going anywhere anytime soon, and will continue contributing to the firm in countless ways.
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EIDD-2173, ATI-2173, Fosclevudine alafenamide
New Drug Approvals
AUGUST 22, 2023
The cccDNA is then transcribed by RNA polymerase II, a host DNA-dependent RNA polymerase, to produce pregenomic RNA (pgRNA). HBV possesses a 3.2- kb relaxed circular DNA (rcDNA) genome that is used to form covalently closed circular DNA (cccDNA) in a host cell. The results are shown below in Tables 8 and 9.
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Following our pole star to a transformative collaboration
Dark Matter Blog
APRIL 8, 2020
Most people, and in particular most investors we spoke to in those early days, thought we were nuts – that RNA lacked the structural and molecular complexity that medicinal chemistry exploits with such great effect for proteins. One is that molecular recognition is purely a matter of physics and RNA has to play by the same rules.
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Want A Great Team? Pick Great Leaders.
Dark Matter Blog
JULY 19, 2021
However, in June I happened to attend the Gordon Research Conference on Chemical Biology and High-throughput Chemistry where I saw a session on small molecules and RNA. Making small-molecule drugs against RNA structures looked like a really cool problem – I want to do THAT! This is a thing? I did NOT get the email.
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Breaking Down Biomarker Discovery: 5 Points
PerkinElmer
AUGUST 12, 2020
The steps taken during the analytical phase are dependent on the type of biomarker, which can range from DNA, RNA, protein, peptide, biomolecular modification(s), or biochemical pathway(s). The post Breaking Down Biomarker Discovery: 5 Points first appeared on PerkinElmer Blog.
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Codon Digest: Discovering Antibiotics with Deep Learning
Codon
MAY 30, 2023
The researchers first compared the editing efficiency of different versions of IscB when coupled with 'ωRNA,' which guides the enzyme to the right spot on the DNA. A particular variant, named IscB*-ωRNA*, had the highest editing efficiency across multiple different sites in the genome. Read more in Nature Methods.
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Codon Digest: Discovering Antibiotics with Deep Learning
Codon
MAY 30, 2023
The researchers first compared the editing efficiency of different versions of IscB when coupled with 'ωRNA,' which guides the enzyme to the right spot on the DNA. A particular variant, named IscB*-ωRNA*, had the highest editing efficiency across multiple different sites in the genome. Read more in Nature Methods.
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Optical density and absorbance measurements | BMG LABTECH
BMG Labtech
DECEMBER 20, 2024
In this blog, we examine the utility of absorbance and optical density measurements, including examples where microplate readers can help. Further tips on how to select the best method are described in the BMG LABTECH blog Protein measurement: find a suitable method. But how do they relate to each other?
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Next Generation Sequencing (NGS): why is quantifying nucleic acids important? | BMG LABTECH
BMG Labtech
OCTOBER 4, 2023
In this blog, we examine how quality control of nucleic acids on microplates before sequencing can facilitate next-generation sequencing and look at some of the emerging next-generation sequencing solutions available to researchers. If RNA is being sequenced it is first converted to cDNA by reverse transcription.
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Antidepressant Shows Potential for Treating COVID-19
PerkinElmer
JUNE 14, 2021
After three days, viral replication supernatants were collected, and viral RNA was extracted. link] The post Antidepressant Shows Potential for Treating COVID-19 first appeared on PerkinElmer Blog. Cell growth was determined using a PerkinElmer EnSight ® multimode plate reader. Viral replication was quantified by real-time RTqPCR.
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Metabolism of 2022 FDA approved small molecule drugs PART 1
Metabolite Tales Blog
JANUARY 26, 2023
Nonetheless, there are some interesting facets to discover, a selection of which we take a look at in a two-part blog on “Metabolism of 2022 FDA approved small molecule drugs.” link] Take a look at our other blogs The post Metabolism of 2022 FDA approved small molecule drugs PART 1 appeared first on Hypha Discovery.
Codon Digest: Seeing Colors After Gene Therapy
Codon
JULY 27, 2023
A LEGO robot , made by undergraduate students at Arizona State University, pours sucrose gradients (a tube with dense liquid at the bottom, and less dense liquid at the top), which are used to separate, say, proteins from RNA by spinning them really fast in centrifuges. How do transcription factors couple up with the correct RNA molecule?
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Codon Digest: Seeing Colors After Gene Therapy
Codon
JULY 27, 2023
A LEGO robot , made by undergraduate students at Arizona State University, pours sucrose gradients (a tube with dense liquid at the bottom, and less dense liquid at the top), which are used to separate, say, proteins from RNA by spinning them really fast in centrifuges. How do transcription factors couple up with the correct RNA molecule?
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How Ana Cvejic built an immune atlas of lung cancer
The Open Targets Blog
MAY 23, 2024
In a paper published today in Nature Communications , Open Targets researchers and collaborators used single-cell RNA sequencing to create a high resolution molecular map of immune cells in NSCLC tumours, to better understand the role of these cells in disease progression. This could then pave the way for subtype-specific therapies.
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Genomic Sequencing Paves the Way for Better Antiviral Treatments
PerkinElmer
JULY 13, 2020
Sequencing viral genome isolates and creating phylogenetic trees Sequencing a viral genome requires isolating the viral RNA, reverse transcribing it into DNA, and then performing multiple amplification steps using primers. The post Genomic Sequencing Paves the Way for Better Antiviral Treatments first appeared on PerkinElmer Blog.
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If I Only Had a Brain? Tissue Chips Predict Neurotoxicity
NIH Director's Blog: Drug Development
SEPTEMBER 29, 2015
Next, to see how their tiny models of the human brain respond to various chemicals, the researchers exposed the neural tissue chips to 60 compounds—about half with known neurotoxic effects, and the rest considered harmless to the brain—and measured the activity of 19,000 genes in each organoid by RNA sequencing.
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From hibernation to neurodegeneration: how a cold-resistance protein is paving the way to dementia treatments
The Open Targets Blog
AUGUST 15, 2023
These results were corroborated by an RNA sequencing analysis we carried out in parallel, which revealed that depending on the temperature, RBM3 had different isoforms created by differential self-splicing. RBM3 is an RNA-binding protein, and we needed an RNA biologist, which is when Deepak joined the project.
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Codon Digest: Injected Gene Editors
Codon
APRIL 2, 2023
Read A new DNA polymerase variant, called RT-KTq I614Y, can directly detect RNA modifications, including pseudouridine (Ψ) and queuosine (Q). By combining this new variant with standard sequencing methods, it’s possible to identify RNA modifications in a really simple way. Nucleic Acids Research. Communications Biology.
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Codon Digest: CAR-T Therapy for Neuroblastoma
Codon
APRIL 9, 2023
Small snippets of double-stranded RNA were sprayed onto hot pepper plants to control a pest, called Frankliniella occidentalis. The RNA strands shut down a specific gene in the insects, and killed half after 7 days. RNA may offer a safer form of pest control in the future. The new sequences might help de-extinction efforts.
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Oditrasertib,
New Drug Approvals
JANUARY 31, 2024
2-NTP , an analog of ATP, inhibits the SARS-CoV-2 RNA-dependent RNA polymerase replication and transcription of viral RNA. Strong clinical results for 1 have prompted interest in oral approaches to generate 2-NTP. The collected fractions were concentrated to give Intermediate 2. Hz, 1H), 2.56 (p, J = 7.0 Tchesnokov, E.
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A Molecular Biologist’s Advice For Life
LifeSciVC
JULY 1, 2024
The central dogma of molecular biology is that information generally (with few exceptions) flows from DNA to RNA to Protein. In my own career, starting to write a blog was one of my most impactful “Friday afternoon experiments” – I even called it an experiment in my very first blogpost back in March 2011. Remember life’s Central Dogma.
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Top Ten Reasons to Attend the SLAS International Conference & Exhibition
PerkinElmer
JANUARY 19, 2020
We will present a fully automated end-to-end solution inclusive of automation and reagents optimized for miniaturized NGS that is guaranteed to generate high-quality libraries.
Discovery Solutions with Alpha, HTRF by Cisbio and Multi-mode Microplate Readers for Viral Therapeutics
PerkinElmer
AUGUST 18, 2020
The technology can be applied to a number of different types of antibody-based assays, which are used to characterize GPCR signaling, activity of various protein kinases and other cytokines, and the interactions of certain singular proteins with each other or DNA and RNA. – [link] Wen et al.
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Accelerating Riboswitch Engineering for the Development of Human Performance Biosensors - A Preview of Strateos’ Presentation at SynBioBeta 2021
The Strateos Blog: Drug Discovery
DECEMBER 13, 2021
Learn how Strateos’ automated synthetic biology modules supported rapid, iterative screening of RNA sequences in modular pbuE expression system and E. Owing to their modular organization, riboswitches are ideal for engineering de novo sensing elements for use in synthetic biology. coli extract-based cell-free protein expression assays.
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Present Treatments & Hopeful Future Directions for ALS Pharmacotherapies
Conversations in Drug Development Trends
MAY 30, 2024
This approach is facilitated by developing ASOs and RNA interference (RNAi) therapies, which target the various molecular and genetic mechanisms contributing to ALS pathophysiology and disease progression. For a more in-depth discussion on challenges and solutions to ALS research, read our blog.
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Codon Digest: Vaccine Printer Go Brrrrr!
Codon
APRIL 30, 2023
Read Ribosomes are able to build proteins because they contain a strand of RNA that imbues them with their catalytic power. Read An automated platform to make riboswitches (RNA strands that bind to small molecules and then quickly switch their structure) that can sense specific proteins. Synthetic Biology. Cell Systems.
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Codon Digest: Vaccine Printer Go Brrrrr!
Codon
APRIL 30, 2023
Read Ribosomes are able to build proteins because they contain a strand of RNA that imbues them with their catalytic power. Read An automated platform to make riboswitches (RNA strands that bind to small molecules and then quickly switch their structure) that can sense specific proteins. Synthetic Biology. Cell Systems.
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To the Builders Blazing our Path to Amazing Medicines
Dark Matter Blog
JULY 19, 2021
Or should I say back to retirement, as he was comfortably relaxing at home back in 2016 when Jen Petter lured him back into the fray with the siren call of developing a new class of RNA-targeted small-molecule medicines here at Arrakis. I won’t dwell on Jim’s many accomplishments here.
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