1/4 A Perspective on proximity-inducing
#molecularglues
and bifunctional compounds in relation to hot-spot-associated missense mutations enshrined by natural selection and posttranslational modifications (PTMs).
Without love and encouragement from my wife Mimi, this would have remained a personal diary for the two of us. The response from so many of you has warmed my heart. I am profoundly grateful.
On behalf of his loving family, and with a heavy heart, I’m sad to report the passing of Yoshito Kishi, a towering figure in organic chemistry. In addition to his transformative research, Yoshi will be forever remembered for his warmth, generosity, and deep sense of humanity.
1/2. Molecular glues, with and without linkers, are being used to stabilize, degrade, alter cellular locations and bind otherwise featureless therapeutic targets. (Images by
@moscienceart
)
In our open letter, we scientists are standing up for
@Harvard
professor Charles Lieber. We also are speaking out against the harm that the prosecution of Charles and other scientists has inflicted on academic freedom and scholarly collaboration.
This is synthetic biology at its best – from the Pete Schultz lab at Scripps. Having made a bacterium with non-natural cross links in its cell wall, the role of this biophysical feature can now be explored in highly novel ways.
Today, humanity has a big aching hole in its heart. We lost a giant – Bob Williams, organic chemist extraordinaire, super-dad to his kids, loving husband to his wife and mentor to many. Bob was my mentor in life. I loved him and loved telling him so.
Next time drug-hunter gurus tell you your idea won't work because your target is essential, have them look up this paper relating successful drug targets to "human knock-out" genes, among others. Great work by
@EricMinikel
and team.
1/N. Missing, but mostly appreciating, Dave Evans (Jan 11, 1941-Apr 29, 2022). I'd like to share one remembrance. Dave was fond of saying that his first chemistry meeting in June 13-17, 1965 "changed my life". Judging from the speakers, you can easily imagine why.
On the heels of the repurposing of FKBP12-rapamycin with a novel synthetic molecular glue (left), we now have the repurposing of cyclophilin–CsA (center) to target KRAS G12C with another synthetic glue (right)
Half-way through my doctoral studies when my adviser passed suddenly and unexpectedly, I was rescued by a generous and outstanding mentor Yoshi Kishi. It kept me grounded and changed my life. We should all be prepared to pay forward.
When a lab shuts down in the middle of your training, it can feel like the end of your career. I'm forever grateful to my mentors who were there for me in the most concrete ways. I wish trainees hit by today's news the same support and care and that they, too, land on their feet.
1/4. Molecular glues and bifunctional compounds induce protein–protein associations. In open-source collaboration with Novartis, we first used DEL screening to discover bifunctional compounds in one step using preselected presenter and target proteins
Screening preselected presenter (FKBP12) and target (mTOR) proteins to discover molecular glues exemplified by the discovery of a synthetic mimic of rapamycin
Taking "induction of proximity" to a new level, Arena BioWorks, a Biomedical Research Institute that just launched in Boston, is bringing academic inquiry and biotech creation under one roof.
Well deserved – not only for transformative science but also mentorship, leadership and guidance for the nation through the pandemic under times when scientists' voices are being muted.
Congratulations to David R. Liu, elected into the
@theNAMedicine
today for the development of base editing and prime editing to modify genomes with unprecedented precision (among other inventions):
@davidrliu
This post from
@cureffi
provides an illuminating analysis of the challenges of drug discovery, but also a strong argument for publishing scientific research that did not achieve its original aim. Even "failure" can advance science.
Priscilla and Nathanael are two crown jewels of Harvard – Stanford's huge gain is a painful loss for those of us who benefited greatly from them and their awesome labs. But we love them both and wish them the very best! ❤️
I am excited to announce that Nathanael Gray and Priscilla Yang are moving to
@Stanford
!!Nathanael will join us
@Stanford_ChEMH
and Dept of Chem & Sys Biol and Priscilla will join Dept of Micro & Immunol, supercharging chem bio on The Farm🔥
What a pleasure to read.
@SchreiberStuart
writes a conversational history of molecular glues, emphasizing the questions being posed at each juncture of discovery.
Excited to share our new preprint describing intracellular ubiquitination of a small molecule, BRD1732, a molecule that has remained a mystery since identification in early 2010s by Enrique Garcia-Rivera,
@micahmaetani
,
@SchreiberStuart
and
@CKadoch
. 🧵
1/2. Once thought to be rare, stabilizers of protein–protein interactions now seem to be common. Two new reports of small-molecular stabilizers of specific ternary PP2A complexes and their striking effects on cell function
@CellCellPress
.
Congratulations to Carly Zeigler, a physician–scientist in training who gave a brilliant and inspiring lecture after receiving the inaugural 2021 Stuart L. Schreiber Award in Scientific Excellence for Graduate Students!
A brilliant example of modern drug discovery – a small-molecule binder functioning as a molecular prosthetic to fix a disease-causing mutation (
@nchembio
). Wow!
COVID-associated loss of germinal centers, responsible for long-lasting B-cell memory, suggests an additional hurdle for herd immunity and the need for avoiding SARS-CoV2 infection during attempted vaccination.
Congratulations to Mike Rosen, co-discover of biomolecular condensates (liquid–liquid phase separation) as a widespread phenomenon in biology, for his election to the National Academy of Sciences.
Arena follows a basic principle from physical organic chemistry: increase the effective molarity of some of the brightest minds in biomedical science, and anticipate rate acceleration
We're proud to unveil Arena BioWorks, a biomedical research institute with a mission to uncover mechanisms of disease by engaging in basic biological research that will be translated into lifesaving
#biotech
therapeutics. Learn more:
Postdoctoral training opportunity in my lab for synthetic chemists or chemical biologists to discover molecular glues and bifunctional compounds using DNA-barcoded compounds. If interested, please read and respond here:
My sense is that protein–small molecule hybrids offer vast opportunities in medicine beyond cancer cell-killing drugs. Principles arising from bifunctional compounds, including molecular glues, can be applied to hybrids in important and novel ways. Bravo Bart Roman &
@Dereklowe
Harvard and Eisai scientists, led by Yoshi Kishi, have extended the limits of synthetic organic chemistry in drug discovery. A completely synthetic halichondrin analog E7130 is now in entering a clinical trial as a novel cancer treatment.
Lots of love for Chris Walsh today at a special event at Harvard (
#CTWalsh75
). Chris has revealed to us the rules of chemical logic in metabolism and the nature of chemical transformations in organisms. He has transformed our field.
Especially for organic chemists of my generation, I hope you'll recognize the outsized yet likely underappreciated impact of a giant in our field, W. Clark Still.
Thanks to
@dylanvneel
for this interview.
1/2. "During a meeting with the goal of proposing a Ph.D. project, one of us (S.L.S.) had the occasion to discuss with Professor R. B. Woodward the transformation of eq 1, citing an article published in J. Org. Chem."
Can you surmise the mechanism? Andy Myers did:
Albert Eschenmoser taught us whole new ways to think about organic chemistry – from orbitals, to mechanisms, to syntheses, to life processes, and eventually even to the origins of life. His passing marks the end of an era defined by his intellectual brilliance. 💔
In deepest grief, the Laboratory of Organic Chemistry at
@ETH_DCHAB
at
@ETH_en
announces that our friend and colleague, Prof. em. Albert Eschenmoser passed away peacefully, at the age of 97, on July 14, 2023.
Albert
#Eschenmoser
shaped organic chemistry as did few others. 1/3
So many words of wisdom from Chris Walsh during his remarkable career – like this one: Chris sharing his conversation with Albert Eschenmoser regarding his reasoning of research directions during the evolution of his career: "think chemically, act biologically"
Christopher Walsh: 1944-2023
A giant indeed: the impact of his work is staggering. But Chris was even more impressive as a mentor. He was immeasurably devoted to, & loved by, his trainees. Nothing made him happier than doling out his wisdom. Superhuman & human at the same time.
Physician–scientist in training Ally Freedy after receiving the second annual Award in Scientific Excellence at the 2022 Broad Retreat. In recognition of her discoveries chromatin biology and their potential for novel medicines. Bravo!
Brilliant work from Brian Liau lab at Harvard showing more surprises coming from small-molecule binders – in this case from seemingly simple (they're not!) enzyme inhibitors. Follow link to must-read NCB paper. )
From FKBP12-binding natural molecular glues FK506 (calcineurin) and rapamycin (mTOR), to synthetic ones like Jun Liu's rapadocin (ENT1), PROTACs and many others, we've come full circle – a new FKBP12-binding natural molecular glue WDB002 (CEP250).
1/5. In times like these, our country has proven time and time again that we can come together and unite against a common foe (although there was never anything secretive about this particular plan).
Justice League of Science Nerds (aka Scientists to Stop COVID) member "The Flash" (aka
@michaelzlin
)* offers insights to an alarming feature of molnupiravir – its potential to accelerate selection of harmful SARS-CoV2 variants.
Non-natural amino acids now encoded in human hematopoietic stem cells that give rise to the entire hematopoietic system following transplantation – the Pete Schultz lab
@scrippsresearch
continues to advance this frontier.
New street murals to go with older favorites in South End–Roxbury. Exploring city art by bike with love-of-my-life Mimi is awesome therapy for a distressing 2020
The universe of immune-cell proteins targeted by small molecules has just been expanded dramatically. Lots of exciting future directions for immune regulation.
With Karin Briner, Frederic Zecri, Frederic Berst,
@jaybradner
and colleagues
@Novartis
, research is underway to extend the capabilities of organic synthesis used for DNA-encoded libraries. Work led by Matthias Westphal is our most recent example. 1/n
We knew melanoma resists targeted therapy and immunotherapy by adopting a high-PUFA, GPX4-dependent and ferroptosis-vulnerable cell state. Now work from
@SJMorrison_
illuminates the complex role of this state (lymph vs blood) in metastasizing melanoma.
For your work-from-home reading list – a Perspective on the principle of high effective molarity in biology and the broad generality of bifunctional compounds that co-localize signaling proteins (molecular glues; CIPs):
How do you uncover convergent evolution in distantly related organisms? Use small-molecule phenotypic screening of course. Ben Cravatt and team use extended lifetime to uncover connections between non-orthologous FAAH and MAGL in distant organisms.
A tweetorial on bifunctional compounds that enable targeted protein localization with consequential rewiring of transcriptional circuitry from
@Sadagopan_A
and
@wgibson
. See also
What if small molecules could allow you to alter protein localization at will?
What if they could allow you to turn on specific transcription factors?
Our new manuscript reveals bifunctional molecules to do just that. 🧵
Nice summary
@NatureNews
on mechanisms enabling novel phage genomes to have an alternative genetic alphabet – what commentator Steve Benner colorfully describes as “a shadow biosphere”.
We are thrilled to announce that the 5th IKCOC prize goes to the pioneer of chemical biology, Professor Stuart L. Schreiber !
@SchreiberStuart
#ikcoc15
When Ono recognized that Opdivo (nivolumab) was becoming a blockbuster, instead of searching for profit-expanding devices, they created the Ono Pharma Foundation and its Breakthrough Science Initiative Awards. Proud to have helped identify next-generation chemical biology stars
Dr. Stuart Schreiber
@SchreiberStuart
, Chair of Science Advisory Board, has stepped down from his role. We want to express our heartfelt gratitude for his invaluable contributions and unwavering dedication. 1/5
12/N. The elegance of Dave and his research is embodied in ChemDraw, which he and his wife Sally helped envision and create, and his recognition that combined with the Macintosh computer the way we teach organic chemistry would be forever changed. ❤️
Dear E.J.,
"May your hands always be busy
May your feet always be swift
May you have a strong foundation
When the winds of changes shift
May your heart always be joyful
May your song always be sung
May you stay forever young"
Bob Dylan, 1973
Happy Birthday!
Love, Stuart
🎁HBT
#chemistry
#NobelLaureate
1990 E. J. Corey turning 95 today. PhD with J. C. Sheehan
@MITin
1951; faculty member
@UofIllinois
, full professor at age 27. In 1959 he moved to
@HarvardCCB
where he has been ever since, still active prof. em. He educated over 700 group members,
"I fear I’m going to take this ML210 mystery to my grave’,” but “Like peeling the many layers of an onion, Jake has revealed, the fascinating sequence of chemical reactions that cells confer on ML210. It was a brilliant job of molecular sleuthing by Jake.”
Boston has many hidden gems. Across from Faneuil Hall is a nondescript gate on North St labeled Scott's Alley. The alley was built in 1654 by Joshua Scottow to connect to his eponymous Dock, a harbor to park ships. The misnamed alley is still standing with little alteration.
Deeply inspired by Herbert Waldmann at the MIT-Broad Chemical Biology Lecture Series. Creative synthetic chemistry combined with innovative phenotypic screening yielding novel probes. And our learning continued late into the night!
1/6. A true and illuminating testimonial of a remarkable scientist and citizen, Charles Lieber, who has dedicated his life to fundamental academic research in the fields of chemistry and nanotechnology, and to teaching students from around the world.
Conformational analysis of ten-membered rings in the context of drug discovery. This is at the heart of what brought many of us to the beautiful science of organic chemistry.
Years ago, the birth of a biotech might be chronicled in a book – such as Vertex in the "The Billion-Dollar Molecule". Today, young entrepreneurs can gain insights via Podcasts. This is an illuminating series telling the story of the birth of Belharra Tx.
Now, even our scientific journals fail to provide an honest, truthful narrative – instead we see misogynistic and racist rants. Shame on the journal and the author. Thanks to
@MJCliffe
for preserving a link:
Meet freshly minted Harvard Ph.D., Dr. Bruce Hua. Bruce earned his degree by executing on his brilliant insights into organic synthesis and chemical biology. What emerged was a doctoral thesis for the ages. Bravo!
1/2. Lots of mysteries surrounding glue mechanisms, so its nice to see hydrophobic shielding of hydrogen bonds highlighted here by
@Dereklowe
. I'll bet there will be other surprises uncovered in the future.
Keep an eye on applications of this promising tool compound from Brian Liau
@HarvardCCB
for mapping ribosome positions on mRNA genome-wide (ribosome profiling) and other chemical biology applications underway
@liaulab
.
1/n. Many of us in the scientific community are heartbroken by the sudden and tragic loss of Daniela Gerhard, a brilliant and inspirational scientist at the National Cancer Institute. But Daniela was much more than that, as I hope to share in this thread.
The world mourns with you and your family
@barneygrubbs
. Your dad was an inspiration to many – for his profound impact on chemistry but even more for his warmth, natural kindness and humanity. 💙
Fox anchor: Can you tell me your thoughts on the drug that is used normally to treat malaria.
Dr. Haseltine: It's sad to me that people are promoting that drug.
Anchor: But what about the anecdotal evidence?
Haseltine: That's complete and utter nonsense. Irresponsible.
Human genetic evidence for target relevancy increases the probability of success in clinical trials, and there is still more room for improvement in the future – insights from Eric Minikel et al.
Published today, our reasons for optimism that success rates in drug discovery can be improved by picking the right targets using human genetics:
I break the key findings down panel by panel in this thread:
As we approach the cold winter months in the Northern Hemisphere, I want to share these movies of mucociliary clearance (MCC) in the trachea of mice housed at 10% vs. 50% relative humidity (RH). Captured by
@ericsongg
(1/n)
This is MCC at 50% RH 👇🏽
Presenting my 20 year progress on enantio CH activation in front of my mentor Professor Corey, and teacher Eric Jacobsen who taught me organometallic class then. Photo 1 siting next to my mentor getting ready; photo 2 feeling spoiled when Eric presented the Tishler Prize medal.
Finally – we got the answer to the obvious question: Why not solve our University's financial woes by dipping into its massive endowment (rather than undertaking painful layoffs and hiring freezes)? Thanks
@StearnsLab
for the enlightenment.
2/2. I hope the history and future promise are captured in a readable way here, especially for students who want a glimpse into the pre-Internet era! (P.S. my second attempt at providing a paywall-free link – sorry for my previous failure)
🎧 Listen: In today's episode of The Journal podcast,
@realrobcopeland
explains how some of America’s top scientists are working to come up with ideas to combat the pandemic and collaborating with investors to get those ideas to the White House
I meant to include this photo in my "1980s Camelot" tribute to Sam Danishefsky () but was unable to locate it. Well, here it is, better late than never (how many faces can you recognize?).
Great to see the structural capstone of Dan Kahne's brilliant biochemical dissection of bacterial export of LPS to the outer membrane – confirming his membrane-to-membrane Pez model. Seeing is believing!
Celebrating Ben Cravatt as the 6th Wolf Prize winner at
@scrippsresearch
chemistry. He and his team turned ‘dirty’ covalent compounds into transformative tools e.g. activity based protein profiling. Party coincides with grad recruit dinner-Ben was a Scripps grad student! 😉
Today we embrace Dr. Damian Young, who is a medicinal chemist, and the Assistant Professor of Pharmacology and Chemical Biology at Baylor College of Medicine where his lab focuses on fragment based drug discovery.
#Blackinchem
#chemistry
#blackchemists
#STEM
#blackandstem
Made my weekly visit to my sweet Cajun Mom's paver in the Rose Kennedy Parkway. Lots of tears, lots of joy. "I miss you Mom, my angel and protector. For you, the well of love in my heart is endless. Happy Mother's Day.❤️"
Small-molecule regulation of phase separation is a promising mode of therapeutic intervention, and this new role for the druggable HDAC6
@nchembio
appears to provide at least one avenue forward.
@JSheltzer
Trikafta: a combination of three intramolecular glues that stitch domains together synergistically to complement missing biophysical and cellular functions in disease alleles (Karol Fiedorczuk, Jue Chen, et. al, Science 2022).
Cells can adopt stable cell states that avoid apoptotic death (e.g., drug-resistant cancers; fibrotic tissues; activated immune cells), but the mechanism for doing so creates a ferroptotic vulnerability. Kojin is addressing this gap in current pharmacopeia.
Bifunctional, proximity-inducing small molecules facilitate the study of an increasingly wide range of complex biological phenomena. Now, in 2 reports, they enter the KRAS arena – 1) reanalysis of previously reported binders: