Ferroelectric compute-in-memory annealer for combinatorial optimization problems.

Computationally hard combinatorial optimization problems (COPs) are ubiquitous in many applications. Various digital annealers, dynamical Ising machines, and quantum/photonic systems have been developed for solving COPs, but they still suffer from the memory access issue, scalability, restricted applicability to certain types of COPs, and VLSI-incompatibility, respectively. Here we report a ferroelectric field effect transistor (FeFET) based compute-in-memory (CiM) annealer for solving larger-scale COPs efficiently. Our CiM annealer converts COPs into quadratic unconstrained binary optimization (QUBO) formulations, and uniquely accelerates in-situ the core vector-matrix-vector (VMV) multiplication operations of QUBO formulations in a single step. Specifically, the three-terminal FeFET structure allows for lossless compression of the stored QUBO matrix, achieving a remarkably 75% chip size saving when solving Max-Cut problems. A multi-epoch simulated annealing (MESA) algorithm is proposed for efficient annealing, achieving up to 27% better solution and ~ 2X speedup than conventional simulated annealing. Experimental validation is performed using the first integrated FeFET chip on 28nm HKMG CMOS technology, indicating great promise of FeFET CiM array in solving general COPs.

Feasibility of using quantitative 1H-NMR spectroscopy and ultra-microbalances for investigation of a PET microplastic reference material.

Here, we report on the feasibility of using quantitative NMR and ultra-microbalances for additional measurements of the mass of poly-ethylene terephthalate (PET) particles in a reference material (RM). The microplastic (MP) PET particles were immobilised in solid NaCl following freeze-drying of a 1-ml NaCl suspension. The particles ranged from 30 to about 200 µm (Feretmin). In a 3-day process, more than 500 such units of PET particles in the NaCl carrier were prepared and later used in a large-scale inter-laboratory comparison. The homogeneity of PET in the salt carrier over these 500 units had previously been evaluated with respect to the mass of PET using an ultra-microbalance. In addition to the original results obtained by weighing, two independent results of quantitative 1H-NMR have been obtained for further investigation of this reference material together with one additional set of weighing data. The NMR data were used for confirmation of the weighed amount of PET (as weighing is non-specific for PET). Average masses of 0.293 ± 0.04 mg and 0.286 ± 0.03 mg of PET were obtained using two different ultra-microbalances (14% RSD for n = 14 and 9% RSD for n = 4, respectively). The corresponding 1H-NMR data was 0.300 ± 0.02 mg of PET (6.7% RSD for n = 5) and 0.345 ± 0.04 mg of PET (12.5% RSD for n = 14), respectively. The average mass of PET obtained by 1H-NMR measurements was in agreement with the weighed amounts within their standard deviations. A mean value of 0.306 mg PET with an expanded uncertainty of 0.058 mg (± 19% relative) was calculated, and it is traceable to the SI system of measurements. Measurement of PET by quantitative 1H-NMR spectroscopy is also reported for a water sample. The PET contained in one RM sample was transferred to 1 L of water to mimic a drinking water sample for microplastics.

Simultaneous quantification of microplastic particles by non-deuterated (NoD) 1H-qNMR from samples comprising different polymer types.

Facing microplastic contamination and thereby its impacts on the environment and health will probably be one of the most concerning challenges in our immediate future. Yet, data on these emerging pollutants are still scarce in many aspects leading to the ongoing development and expansion of analytical procedures and approaches. In recent years, despite being used formerly only for qualitative aspects, nuclear magnetic resonance spectroscopy (NMR) was introduced for the quantification of microplastic particles. By the combination of linear regression procedures, internal standards and the integration of proton NMR, the so-called qNMR method allows mass-based quantification of microplastics in a limited amount of time and independent of particle size. Based on this approach, further optimization through the simultaneous dissolution and quantification of multiple polymers is investigated. Individual requirements, known issues and considerations will be demonstrated along with additional possibilities for five polymers: polystyrene (PS), butadiene rubber (BR), polyvinylchloride (PVC), polyethylene terephthalate (PET) and polyamide (PA). The applicability of homopolymer-based calibrations is demonstrated for both the quantification of multiple homopolymers dissolved in a shared solvent system and the quantification of copolymers; for example, a styrene-butadiene copolymer (SBR). Linearities and limits of detection and quantification as well as precision and accuracy comparable to those of solely measured microplastic particles are achieved. The improvement significantly reduces the preparation and measurement time in combination with lowered costs. In addition, enhanced reliability was achieved by implementing hexamethyldisiloxane (HMDSO) as an internal standard in NoD measurements, replacing dichloromethane (DCM).

Discovery and Development of First-in-Class ACKR3/CXCR7 Superagonists for Platelet Degranulation Modulation.

The atypical chemokine receptor 3 (ACKR3), formerly known as CXC-chemokine receptor 7 (CXCR7), has been postulated to regulate platelet function and thrombus formation. Herein, we report the discovery and development of first-in-class ACKR3 agonists, which demonstrated superagonistic properties with Emax values of up to 160% compared to the endogenous reference ligand CXCL12 in a ß-arrestin recruitment assay. Initial in silico screening using an ACKR3 homology model identified two hits, C10 (EC50 19.1 µM) and C11 (EC50 = 11.4 µM). Based on these hits, extensive structure-activity relationship studies were conducted by synthesis and testing of derivatives. It resulted in the identification of the novel thiadiazolopyrimidinone-based compounds 26 (LN5972, EC50 = 3.4 µM) and 27 (LN6023, EC50 = 3.5 µM). These compounds are selective for ACKR3 versus CXCR4 and show metabolic stability. In a platelet degranulation assay, these agonists effectively reduced P-selectin expression by up to 97%, suggesting potential candidates for the treatment of platelet-mediated thrombosis.

Design of a "Two-in-One" Mutant-Selective Epidermal Growth Factor Receptor Inhibitor That Spans the Orthosteric and Allosteric Sites.

Inhibitors targeting the epidermal growth factor receptor (EGFR) are an effective therapy for patients with non-small cell lung cancer harboring drug-sensitive activating mutations in the EGFR kinase domain. Drug resistance due to treatment-acquired mutations has motivated the development of successive generations of inhibitors that bind in the ATP site. The third-generation agent osimertinib is now a first-line treatment for this disease. Recently, allosteric inhibitors have been developed to overcome drug-resistant mutations that confer a resistance to osimertinib. Here, we present the structure-guided design and synthesis of a mutant-selective lead compound, which consists of a pyridinyl imidazole-fused benzylisoindolinedione scaffold that simultaneously occupies the orthosteric and allosteric sites. The compound potently inhibits enzymatic activity in L858R/T790M/C797S mutant EGFR (4.9 nM), with a significantly lower activity for wild-type EGFR (47 nM). Additionally, this compound achieves modest cetuximab-independent and mutant-selective cellular efficacies on the L858R (1.2 µM) and L858R/T790M (4.4 µM) variants.

Structural Basis for EGFR Mutant Inhibition by Trisubstituted Imidazole Inhibitors.

Acquired drug resistance in epidermal growth factor receptor (EGFR) mutant non-small-cell lung cancer is a persistent challenge in cancer therapy. Previous studies of trisubstituted imidazole inhibitors led to the serendipitous discovery of inhibitors that target the drug resistant EGFR(L858R/T790M/C797S) mutant with nanomolar potencies in a reversible binding mechanism. To dissect the molecular basis for their activity, we determined the binding modes of several trisubstituted imidazole inhibitors in complex with the EGFR kinase domain with X-ray crystallography. These structures reveal that the imidazole core acts as an H-bond acceptor for the catalytic lysine (K745) in the "αC-helix out" inactive state. Selective N-methylation of the H-bond accepting nitrogen ablates inhibitor potency, confirming the role of the K745 H-bond in potent, noncovalent inhibition of the C797S variant. Insights from these studies offer new strategies for developing next generation inhibitors targeting EGFR in non-small-cell lung cancer.

Synthesis and structure­activity­relationship of 3,4­Diaryl­1H­pyrrolo[2,3­b]pyridines as irreversible Inhibitors of mutant EGFR­L858R/T790M.

The epidermal growth factor receptor (EGFR) is a well­validated drug target for the treatment of non­small cell lung cancer. Here we present an optimization approach and preliminary structure­activity relationship for 1H­pyrrolo[2,3­b]pyridines as covalent irreversible mutant EGFR inhibitors. We synthesized a focused library to investigate the effect of different aromatic substituents in the 4­position of this scaffold, interacting with the gatekeeper. We determined the activity of the synthesized compounds mutant EGFR enzyme assays and determined the selectivity over the wild type.

Trisubstituted Pyridinylimidazoles as Potent Inhibitors of the Clinically Resistant L858R/T790M/C797S EGFR Mutant: Targeting of Both Hydrophobic Regions and the Phosphate Binding Site.

Inhibition of the epidermal growth factor receptor represents one of the most promising strategies in the treatment of lung cancer. Acquired resistance compromises the clinical efficacy of EGFR inhibitors during long-term treatment. The recently discovered EGFR-C797S mutation causes resistance against third-generation EGFR inhibitors. Here we present a rational approach based on extending the inhibition profile of a p38 MAP kinase inhibitor toward mutant EGFR inhibition. We used a privileged scaffold with proven cellular potency as well as in vivo efficacy and low toxicity. Guided by molecular modeling, we synthesized and studied the structure-activity relationship of 40 compounds against clinically relevant EGFR mutants. We successfully improved the cellular EGFR inhibition down to the low nanomolar range with covalently binding inhibitors against a gefitinib resistant T790M mutant cell line. We identified additional noncovalent interactions, which allowed us to develop metabolically stable inhibitors with high activities against the osimertinib resistant L858R/T790M/C797S mutant.

Trisubstituted Imidazoles with a Rigidized Hinge Binding Motif Act As Single Digit nM Inhibitors of Clinically Relevant EGFR L858R/T790M and L858R/T790M/C797S Mutants: An Example of Target Hopping.

The high genomic instability of non-small cell lung cancer tumors leads to the rapid development of resistance against promising EGFR tyrosine kinase inhibitors (TKIs). A recently detected triple mutation compromises the activity of the gold standard third-generation EGFR inhibitors. We have prepared a set of trisubstituted imidazoles with a rigidized 7-azaindole hinge binding motif as a new structural class of EGFR inhibitors by a target hopping approach from p38α MAPK inhibitor templates. On the basis of an iterative approach of docking, compound preparation, biological testing, and SAR interpretation, robust and flexible synthetic routes were established. As a result, we report two reversible inhibitors 11d and 11e of the clinically challenging triple mutant L858R/T790M/C797S with IC50 values in the low nanomolar range. Furthermore, we developed a kinome selective irreversible inhibitor 45a with an IC50 value of 1 nM against the EGFR L858R/T790M double mutant. Target binding kinetics and metabolic stability data are included. These potent mutant EGFR inhibitors may serve as a basis for the development of structurally novel EGFR probes, tools, or candidates.

Lung Cancer: EGFR Inhibitors with Low Nanomolar Activity against a Therapy-Resistant L858R/T790M/C797S Mutant.

The treatment of non-small-cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) inhibitors is made challenging by acquired resistance caused by somatic mutations. Third-generation EGFR inhibitors have been designed to overcome resistance through covalent binding to the Cys 797 residue of the enzyme, and these inhibitors are effective against most clinically relevant EGFR mutants. However, the high dependence of these recent EGFR inhibitors on this particular interaction means that additional mutation of Cys 797 results in poor inhibitory activity, which leads to tumor relapse in initially responding patients. A new generation of irreversible and reversible mutant EGFR inhibitors was developed with strong noncovalent binding properties, and these compounds show high inhibitory activities against the cysteine-mutated L858R/T790M/C797S EGFR.

Targeting the Gatekeeper MET146 of C-Jun N-Terminal Kinase 3 Induces a Bivalent Halogen/Chalcogen Bond.

We target the gatekeeper MET146 of c-Jun N-terminal kinase 3 (JNK3) to exemplify the applicability of X···S halogen bonds in molecular design using computational, synthetic, structural and biophysical techniques. In a designed series of aminopyrimidine-based inhibitors, we unexpectedly encounter a plateau of affinity. Compared to their QM-calculated interaction energies, particularly bromine and iodine fail to reach the full potential according to the size of their σ-hole. Instead, mutation of the gatekeeper residue into leucine, alanine, or threonine reveals that the heavier halides can significantly influence selectivity in the human kinome. Thus, we demonstrate that, although the choice of halogen may not always increase affinity, it can still be relevant for inducing selectivity. Determining the crystal structure of the iodine derivative in complex with JNK3 (4X21) reveals an unusual bivalent halogen/chalcogen bond donated by the ligand and the back-pocket residue MET115. Incipient repulsion from the too short halogen bond increases the flexibility of Cε of MET146, whereas the rest of the residue fails to adapt being fixed by the chalcogen bond. This effect can be useful to induce selectivity, as the necessary combination of methionine residues only occurs in 9.3% of human kinases, while methionine is the predominant gatekeeper (39%).

Fighting cancer drug resistance: Opportunities and challenges for mutation-specific EGFR inhibitors.

Multiple mutations in the EGFR gene are a major cause for the failure of Erlotinib and Gefitinib in the treatment of patients harboring non-small-cell lung cancer (NSCLC) who initially responded to this therapy. The development of these tyrosine kinase inhibitors (TKIs) is going back to the early 90s, where cancer was widely considered and fully treated as a disease of an organ. Fundamental gain of knowledge in cell biology in general and cancer genetics in particular led us to where we currently stand: cancer is a disease that originates in the genome. Fast and affordable gene sequencing paved the way and opened our eyes for the genetic instability of many cancers, particularly EGFR driven NSCLC. This might allow highly rational and personal therapies by aiming at a very particular wild type and mutant kinase pattern. However, the paradigm "one disease - one target - one drug" is currently challenged. Both activating and deactivating EGFR mutations are known to render the development of novel targeted drugs difficult. Among all lung adenocarcinomas, only 20% are driven by EGFR and only a subpopulation has an activating mutation (e.g. L858R), making them sensitive to first generation EGFR inhibitors. Unfortunately, most of them acquire second deactivating mutations (e.g. T790M) during treatment, leading to a complete loss of response. Are specific inhibitors of the double EGFR mutant L858R/T790M the magic bullet? Much scientific evidence but also high expectations justify this approach. Structural biology of EGFR mutants constitutes the basis for highly rational approaches. Second generation pan EGFR inhibitors inhibiting wild type (WT) and mutant EGFR like Afatinib suffer from dose-limiting adverse effects. Inhibition of WT EGFR is considered to be the culprit. Third generation EGFR inhibitors follow two strategies. Mutant selectivity and improved target residential time. These inhibitors display high mutant selectivity and irreversible binding patterns while sparing WT EGFR activity, hence enhancing tumor selectivity while minimizing adverse effects. Third generation EGFR inhibitors are still undergoing preclinical and clinical evaluation. The most advanced are Rociletinib and AZD9291 which displayed encouraging preliminary clinical phase II data regarding response and adverse effects. In the current review we show both a medicinal chemists' approach toward the design of third generation EGFR inhibitors as well as a detailed overview of the development of EGFR inhibitors over the last decade. High interdisciplinary approaches, such as structural biology and time-resolved tumor genetics pave the way toward the development of drugs that target EGFR mutants. This might lead to highly effective targeted and personalized therapies with enhanced response rates for a minor cohort of patients which have to undergo continuous gene sequencing, hence enabling therapies with tailor-made TKIs.

Tetra-substituted pyridinylimidazoles as dual inhibitors of p38α mitogen-activated protein kinase and c-Jun N-terminal kinase 3 for potential treatment of neurodegenerative diseases.

Tetra-substituted imidazoles were designed as dual inhibitors of c-Jun N-terminal kinase (JNK) 3 and p38α mitogen-activated protein (MAP) kinase. A library of 45 derivatives was prepared and evaluated in a kinase activity assay for their ability to inhibit both kinases, JNK3 and p38α MAP kinase. Dual inhibitors with IC50 values down to the low double-digit nanomolar range at both enzymes were identified. The best balanced dual JNK3/p38α MAP kinase inhibitors are 6m (IC50: JNK3, 18 nM; p38α, 30 nM) and 14d (IC50: JNK3, 26 nM; p38α, 34 nM) featuring both excellent solubility and metabolic stability. They may serve as useful tool compounds for preclinical proof-of-principle studies in order to validate the synergistic role of both kinases in the progression of Huntington's disease.