David A. Delgadillo

@daverdude.bsky.social

Organic-Natural Products-Medicinal-Analytical- Chemist. Postdoc in the Nelson Group @Caltech leveraging electron diffraction to discover natural products. Trying to do more with less. https://orcid.org/0000-0002-0897-4470

New paper with @barriewilks.bsky.social. There are many reports on fasamycins and formicamycins (aka accramycins, naphthacemycins, streptovertimycins). Here, we unambiguously solve their structures and stereochemistry. A great effort, led by Dr Edward Hems pubs.acs.org/doi/10.1021/...

Using X-ray Crystallography and 1,n-ADEQUATE NMR to Revise the Structures of Highly Substituted Aromatic Natural Products: The Absolute Configuration of Formicamycin Congeners

Formicamycins and their biosynthetic precursors, the fasamycins, form part of the phenylnaphthacenoid family of polyketide natural products. A recent atroposelective total synthesis of formicamycin H brought into question our original stereochemical assignment of the axially chiral linkage between C-6 and C-7. To address this, we obtained an X-ray crystal structure for formicamycin H that unambiguously confirmed our original assignment as the Sa atropisomer. X-ray structures for multiple additional fasamycins and formicamycins confirmed that this is common to all congeners. However, these studies identified a compounded error made by us whereby several structures previously reported as para-methoxy were found to have ortho-methoxy groups on the hanging E-ring. To address this for congeners that did not crystallize or gave nondiffracting crystals, we turned to the surprisingly underutilized 1,n-ADEQUATE NMR experiment. In total, we generated X-ray structures for 15 phenylnaphthacenoid metabolites and by combining these results report the corrected structures for three formicamycins, six fasamycins, and three biosynthetic lactone intermediates, noting that several revised fasamycin structures now match previously reported naphthacemycins. Our results highlight the utility of 1,n-ADEQUATE experiments for regiochemical determination in polysubstituted aromatic molecules. Moreover, our investigations uncovered a potential deracemization step during biosynthesis of the formicamycin framework.

pubs.acs.org

I’m looking for an automated way to read others’s scientific data without giving credit or acknowledgement, and also claim full credit for insights from it. And I want it to have a fitting name OAI: say no more

OpenAI {bot}@openaibot.bsky.social · 4mo ago

Introducing GPT-Rosalind, our frontier reasoning model built to support research across biology, drug discovery, and translational medicine. Video: https://twitter.com/openai/status/2044861690911850863

My quote of the day Science is the search for truth, that is the effort to understand the world: it involves the rejection of bias, of dogma, of revelation, but not the rejection of morality. Linus Pauling

“The enormous diversity of fungal genomes...offers catalogs of enzymes, secondary metabolites & other parts lists for biotechnology, bioenergy & biomaterials."—Igor Grigoriev, Fungal & Algal Program Head. 🖥️🧬🍄🍄‍🟫 https://jgi.doe.gov/user-science/science-stories/mapping-earths-hidden-fungal-kingdom

Mapping the Earth’s Hidden Fungal Kingdom | Joint Genome Institute

Leveraging massive comparative genomics to decode millions of mystery genes and lay a future-ready foundation

jgi.doe.gov

@dmeremin.bsky.social Absolutely crushed it with this automated workflow! It ain’t about the size of your crystals, nor the way that they look, that matters…it’s all about how they diffract! Cheers to the whole team!

Dmitry Eremin@dmeremin.bsky.social · 9mo ago

🚨Hot off the press @jacs.acspublications.org! Your TEM can now solve crystal structures on its own. Small molecules, materials, proteins—all with one platform: REyes, the first end-to-end autonomous electron diffraction suite doi.org/10.1021/jacs... @caltechcce.bsky.social @uclacb.bsky.social

📢 New preprint: Experiment-guided AlphaFold3 resolves accurate protein ensembles. doi.org/10.1101/2025... AlphaFold3 is incredible, but has crucial limitations: it typically collapses to a single conformation, ignoring the inherent dynamics of proteins. And it can be wrong. Here's a solution. 🧵👇

Structures from AlphaFold3 - while often impressively good - tend to fail representing the dynamic ensembles accurately. And often parts of the structure are not correct.
Adding experimental data, directly in AlphaFold's diffusion step, provides physically realistic protein ensembles. This image shows two cases where AlphaFold3-only structures were largely improved by guiding with experimental data.

❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology

bioRxiv Biophysics@biorxiv-biophys.bsky.social · 11mo ago

Overcoming Preferred Orientation in Cryo-EM With Ultrasonic Excitation During Vitrification https://www.biorxiv.org/content/10.1101/2025.09.14.676144v1

Scientists’ role in defending democracy www.science.org/doi/10.1126/... Let's all support this vital need: the ability to tell the truth. 💪 "Those in the science community who are willing & able to be more visible can step up. Acting together will be more impactful than going it alone."

Scientists’ role in defending democracy

The United States’ democratic leadership, commitment to freedom of expression, and investment in the pursuit of knowledge have long enabled its preeminence in science and technology. Yet today we are ...

science.org