Illuminating protein space with a programmable generative model

Three billion years of evolution has produced a tremendous diversity of protein molecules1, but the full potential of proteins is likely to be much greater. Accessing this potential has been challenging for both computation and experiments because the space of possible protein molecules is much larger than the space of those likely to have functions. Here we introduce Chroma, a generative model for proteins and protein complexes that can directly sample novel protein structures and sequences, and that can be conditioned to steer the generative process towards desired properties and functions. To enable this, we introduce a diffusion process that respects the conformational statistics of polymer ensembles, an efficient neural architecture for molecular systems that enables long-range reasoning with sub-quadratic scaling, layers for efficiently synthesizing three-dimensional structures of proteins from predicted inter-residue geometries and a general low-temperature sampling algorithm for diffusion models. Chroma achieves protein design as Bayesian inference under external constraints, which can involve symmetries, substructure, shape, semantics and even natural-language prompts. The experimental characterization of 310 proteins shows that sampling from Chroma results in proteins that are highly expressed, fold and have favourable biophysical properties. The crystal structures of two designed proteins exhibit atomistic agreement with Chroma samples (a backbone root-mean-square deviation of around 1.0 Å). With this unified approach to protein design, we hope to accelerate the programming of protein matter to benefit human health, materials science and synthetic biology.

In-hospital and long-term outcomes of percutaneous coronary interventions for chronic total occlusions in patients with contrast-associated acute kidney injury

Background

The prognostic impact on in-hospital and long-term outcomes of contrast-associated acute kidney injury (CA-AKI) in patients undergoing chronic total occlusion (CTO) percutaneous coronary intervention (PCI) has been limitedly studied.

Methods

We examined 2707 consecutive procedures performed in a referral CTO center between 2015 and 2019. CA-AKI was defined as an increase in serum creatinine ≥0.3 mg/dl or ≥50% within 48 h post-PCI†. Primary endpoints were major adverse cardiac and cerebrovascular events (MACCE) in-hospital (composite of all-cause death, myocardial infarction [MI], target vessel revascularization [TVR], stroke) and at 1-year of follow-up.

Results

The overall incidence of CA-AKI was 11.5%, respectively. Patients with CA-AKI (n=312) had more severe comorbidities in comparison with patients without CA-AKI (n=2,395). Technical success was similar across the groups (87.2% vs. 90.5%, p=0.056), whereas procedural success was lower in the CA-AKI group (84.3% vs. 89.7%, p=0.004). In-hospital MACCE was 1.3%, respectively, and were comparable in patients with and without CA-AKI (1.6% vs. 1.3%, p=0.655), however, pericardial tamponade requiring pericardiocentesis occurred more commonly in patients with renal function impairment (2.2% vs. 0.5%, p=0.001). In multivariate analysis, CA-AKI was not associated with higher risk for in-hospital MACCE (adjusted odds ratio [OR] 1.34, confidence intervals [CI] 0.45–3.19, p=0.563). At median follow-up time of 14 months (interquartile range [IQR], 11 to 35 months), the cumulative incidence of 1-year MACCE was significantly higher in patients with versus without CA-AKI (20.8% vs. 12.8%, p<0.001), and CA-AKI was independently associated with an increased risk for 1-year MACCE (adjusted hazard ratio [HR] 1.52, CI 1.05–2.15, p=0.029) following CTO PCI. Patients with CA-AKI had inferior MACCE-free (log-rank p<0.001) survival on Kaplan-Meier analysis (Figure 1), mostly driven by higher rate of target vessel failure (log-rank p<0.001), mortality (log-rank p=0.001), and myocardial infarction (log-rank p=0.042) over time. MACCE-free survivals significantly differed both in successful (Figure 2, Panel A) versus failed (Figure 2, Panel B) CTO PCI, with less favourable outcomes in patients developing CA-AKI post-PCI.

Conclusions

Contrast-associated acute kidney injury commonly occurs in patients undergoing CTO PCI, that may lead to an increased risk for MACCE 1-year post-PCI, but not immediately after the procedure.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only.

Design, Synthesis, and Characterization of a Fluorescence Polarization Pan-BET Bromodomain Probe

Several chemical probes have been developed for use in fluorescence polarization screening assays to aid in drug discovery for the bromodomain and extra-terminal domain (BET) proteins. However, few of those have been characterized in the literature. We have designed, synthesized, and thoroughly characterized a novel fluorescence polarization pan-BET chemical probe suitable for high-throughput screening, structure-activity relationships, and hit-to-lead potency and selectivity assays to identify and characterize BET bromodomain inhibitors.

Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2'-Deoxyzebularine Analogues

APOBEC3 enzymes form part of the innate immune system by deaminating cytosine to uracil in single-stranded DNA (ssDNA) and thereby preventing the spread of pathogenic genetic information. However, APOBEC mutagenesis is also exploited by viruses and cancer cells to increase rates of evolution, escape adaptive immune responses, and resist drugs. This raises the possibility of APOBEC3 inhibition as a strategy for augmenting existing antiviral and anticancer therapies. Here we show that, upon incorporation into short ssDNAs, the cytidine nucleoside analogue 2'-deoxyzebularine (dZ) becomes capable of inhibiting the catalytic activity of selected APOBEC variants derived from APOBEC3A, APOBEC3B, and APOBEC3G, supporting a mechanism in which ssDNA delivers dZ to the active site. Multiple experimental approaches, including isothermal titration calorimetry, fluorescence polarization, protein thermal shift, and nuclear magnetic resonance spectroscopy assays, demonstrate nanomolar dissociation constants and low micromolar inhibition constants. These dZ-containing ssDNAs constitute the first substrate-like APOBEC3 inhibitors and, together, comprise a platform for developing nucleic acid-based inhibitors with cellular activity.

Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain Inhibitor

As regulators of transcription, epigenetic proteins that interpret post-translational modifications to N-terminal histone tails are essential for maintaining cellular homeostasis. When dysregulated, "reader" proteins become drivers of disease. In the case of bromodomains, which recognize N-ε-acetylated lysine, selective inhibition of individual bromodomain-and-extra-terminal (BET)-family bromodomains has proven challenging. We describe the >55-fold N-terminal-BET bromodomain selectivity of 1,4,5-trisubstituted-imidazole dual kinase-bromodomain inhibitors. Selectivity for the BRD4 N-terminal bromodomain (BRD4(1)) over its second bromodomain (BRD4(2)) arises from the displacement of ordered waters and the conformational flexibility of lysine-141 in BRD4(1). Cellular efficacy was demonstrated via reduction of c-Myc expression, inhibition of NF-κB signaling, and suppression of IL-8 production through potential synergistic inhibition of BRD4(1) and p38α. These dual inhibitors provide a new scaffold for domain-selective inhibition of BRD4, the aberrant function of which plays a key role in cancer and inflammatory signaling.

BET Bromodomain Inhibitors with One-Step Synthesis Discovered from Virtual Screen

Chemical inhibition of epigenetic regulatory proteins BrdT and Brd4 is emerging as a promising therapeutic strategy in contraception, cancer, and heart disease. We report an easily synthesized dihydropyridopyrimidine pan-BET inhibitor scaffold, which was uncovered via a virtual screen followed by testing in a fluorescence anisotropy assay. Dihydropyridopyimidine 3 was subjected to further characterization and is highly selective for the BET family of bromodomains. Structure-activity relationship data and ligand deconstruction highlight the importance of the substitution of the uracil moiety for potency and selectivity. Compound 3 was also cocrystallized with Brd4 for determining the ligand binding pose and rationalizing subsequent structure-activity data. An additional series of dihydropyridopyrimidines was synthesized to exploit the proximity of a channel near the ZA loop of Brd4, leading to compounds with submicromolar affinity and cellular target engagement. Given these findings, novel and easily synthesized inhibitors are being introduced to the growing field of bromodomain inhibitor development.

Suture-supported posterior chamber intraocular lens implantation

This article describes a new technique for secondary implantation of posterior chamber intraocular lenses in the absence of capsular support. In this technique, the intraocular lens is supported by a simple net, consisting of two mattress sutures that pass across the eye at the most anterior area of the pars plana ciliaris, 3 mm from the limbus. Both sutures have limbs 3 to 4 mm apart that intersect at 90 degrees angles in the pupillary area. The main advantage of this technique is that the sutures are placed prior to the opening of the globe, thereby reducing the time that the eye must be open for the insertion of the intraocular lens. Because the exposure time and the intraocular manipulations are decreased, the consequent vitreous disturbances and the risk of infection, cystoid macular edema, and retinal detachment are likewise reduced. Another advantage of this technique is the additional support for the intraocular lens, which reduces the incidence of decentration and tilt. Moreover, because the sutures are placed in the most anterior part of the pars plana ciliaris, which is avascular, the incidence of bleeding is decreased.