A Novel Rational PROTACs Design and Validation via AI-Driven Drug Design Approach.

The rational design of novel drug candidates presents a formidable challenge in modern drug discovery. Proteolysis-targeting chimeras (PROTACs) drug design is particularly demanding due to their limited crystal structure availability and design of a viable small molecule to bridge the protein of interest (POI) and ubiquitin-protein ligase (E3). An integrated approach that combines superimposition techniques and deep neural networks is demonstrated in this study to leverage the power of deep learning and structural biology to generate structurally diverse molecules with enhanced binding affinities. The superimposition technique ensures the congruence of initial and new protein-ligand pairs, which are evaluated via subsequent comprehensive screening using the root-mean-square deviation (RMSD), binding free energy (BFE), and buried solvent-accessible surface area (SASA). The final candidates are subjected to the incorporation of molecular dynamics (MD) and free energy perturbation (FEP) simulations to provide a quantitative evaluation of relative binding energies, reinforcing the efficacy and reliability of the generated molecules. The outcomes of the generated novel PROTACs molecules exhibit comparable structural attributes while demonstrating superior binding affinities within the binding pockets when contrasted with those of the established cocrystal ternary complexes. To enhance the generalizability of the workflow, we chose the ternary structure of the cellular inhibitor of apoptosis protein 1 (cIAP1) and Bruton's Tyrosine Kinase (BTK) for validating the chemical properties generated from the processes. The new linker molecules additionally showed superior affinity from the simulations. In summary, this methodology serves as an effective workflow to align computational predictions with current limitations, thereby introducing a novel paradigm in AI-driven drug design.

Fragment Linker Prediction Using the Deep Encoder-Decoder Network for PROTACs Drug Design.

A drug discovery and development pipeline is a prolonged and complex process that remains challenging for both computational methods and medicinal chemists and has not been able to be resolved using computational methods. Deep learning has been utilized in various fields and achieved tremendous success in designing novel molecules in the pharmaceutical industry. Herein, we use state-of-the-art techniques to propose a deep neural network, AIMLinker, to rapidly design and generate meaningful drug-like proteolysis targeting chimeras (PROTACs) analogs. The model extracts the structural information from the input fragments and generates linkers to incorporate them. We integrate filters in the model to exclude nondruggable structures guided via protein-protein complexes while retaining molecules with potent chemical properties. The novel PROTACs subsequently pass through molecular docking, taking root-mean-square deviation (RMSD), relative Gibbs free energy (ΔΔGbinding), molecular dynamics (MD) simulation, and free energy perturbation (FEP) calculations as the measurement criteria for testing the robustness and feasibility of the model. The generated novel PROTACs molecules possess similar structural information with superior binding affinity to the binding pockets compared to the existing CRBN-dBET6-BRD4 ternary complexes. We demonstrate the effectiveness of the methodology of leveraging AIMLinker to design novel compounds for PROTACs molecules exhibiting better chemical properties compared to the dBET6 crystal pose.

Harnessing polyhydroxylated pyrrolidines as a stabilizer of acid alpha-glucosidase (GAA) to enhance the efficacy of enzyme replacement therapy in Pompe disease.

To discover small molecules as acid alpha-glucosidase (GAA) stabilizers for potential benefits of the exogenous enzyme treatment toward Pompe disease cells, we started from the initial screening of the unique chemical space, consisting of sixteen stereoisomers of 2-aminomethyl polyhydroxylated pyrrolidines (ADMDPs) to find out two primary stabilizers 17 and 18. Further external or internal structural modifications of 17 and 18 were performed to increase structural diversity, followed by the protein thermal shift study to evaluate the GAA stabilizing ability. Fortunately, pyrrolidine 21, possessing an l-arabino-typed configuration pattern, was identified as a specific potent rh-GAA stabilizer, enabling the suppression of rh-GAA protein denaturation. In a cell-based Pompe model, co-administration of 21 with rh-GAA protein significantly improved enzymatic activity (up to 5-fold) compared to administration of enzyme alone. Potentially, pyrrolidine 21 enables the direct increase of ERT (enzyme replacement therapy) efficacy in cellulo and in vivo.

Exploring a sulfone linker utilizing trimethyl aluminum as a cleavage reagent: solid-phase synthesis of sulfonamides and ureas.

A novel and efficient cleavage reagent, trimethyl aluminum, for traceless sulfinate-functionalized resin has been developed. The synthesis of sulfonamide and urea derivatives via a traceless solid-phase sulfone linker strategy through six synthetic steps comprising utilization of trimethyl aluminum as a novel cleavage reagent was also established. An insight of the plausible mechanism of the cleavage reaction was discussed.

Synthesis and biological evaluation of 2-amino-1-thiazolyl imidazoles as orally active anticancer agents.

Designed from a high throughput screened hit compound, novel 2-amino-1-thiazolyl imidazoles were synthesized and demonstrated cytotoxicity against human cancer cells. 1-(4-Phenylthiazol-2-yl)-4-(thiophen-2-yl)-1H-imidazol-2-amine (compound 2), a 2-amino-1-thiazolyl imidazole, inhibited tubulin polymerization, interacted with the colchicine-binding sites of tubulins, and caused cell cycle arrest at the G(2)/M phase in human gastric cancer cells. Disruption of the microtubule structure in cancer cells by compound 2 was also observed. Compound 2 concentration-dependently inhibited the proliferation of cancer cells in histocultured human gastric and colorectal tumors. Given orally, compound 2 prolonged the lifespans of leukemia mice intraperitoneally inoculated with the murine P388 leukemic cells. We report 2-amino-1-thiazolyl imidazoles as a novel class of orally active microtubule-destabilizing anticancer agents.

Synthesis and biological activities of 2-amino-1-arylidenamino imidazoles as orally active anticancer agents.

2-Amino-1-arylidenaminoimidazoles, a novel class of orally (po) active microtubule-destabilizing anticancer agents, were synthesized. The compounds were designed from a hit compound identified in a drug discovery platform by using cancer cell-based high throughput screening assay. Selective synthesized compounds exerted cell cytotoxicity against human cancer cells. The underlying mechanisms for the anticancer activity were demonstrated as interacting with the tubulins and inhibiting microtubule assembly, leading to proliferation inhibition and apoptosis induction in the human tumor cells. Furthermore, two compounds showed in vivo anticancer activities in both po and intravenously (iv) administered routes and prolonged the life spans of murine leukemic P388 cells-inoculated mice. These new po active antimitotic anticancer agents are to be further examined in preclinical studies and developed for clinical uses.

Balloon angioplasty of native coarctation and comparison of patients younger and older than 3 months.

BACKGROUND: There is a high incidence of restenosis and aneurysm formation after balloon angioplasty for discrete native coarctation in neonates and young infants, and so the techniques remains controversial in this group of patients because its clinical validity, particularly in comparison with surgery, has not been well established. METHODS AND RESULTS: From January 1999 to October 2005, group A (17 patients [8 males, 9 females] <3 months old ranging from 0.2 to 2.9 months, with a body weight of 2.5-5.5 kg) and group B (11 patients [5 males, 6 females] >3 months old ranging from 5.5 months to 6.4 years, with a body weight of 7.8-21 kg) with discrete native coarctation who underwent balloon angioplasty and were included in this study. There were 13 (76%) successes in group A, and 10 (90%) successes in group B for the initial balloon angioplasty. There was no significant difference in success rate between groups A and B (p>0.05). There were 9 (69%) cases of restenosis patients in group A, and 2 (20%) in group B, a significant difference between the 2 groups (p<0.05). In group A, 1 patient showed aneurysm formation after angioplasty, 1 (5.8%) showed femoral artery obstruction and 2 (11%) showed reduced pulses. CONCLUSIONS: Balloon angioplasty of discrete native coarctation is effective in patients both younger and older than 3 months. However, thea rates of restenosis, aneurysm formation, and approach artery injury are higher in patients younger than 3 months old when compared with patients aged over 3 months. These complications should be considered when performing balloon angioplasty in patients less than 3 months of age.

Secondary confirmation of endotracheal tube position by ultrasound image.

OBJECTIVE: Secondary confirmation of endotracheal (ET) tube position by ultrasound image. DESIGN: Prospective, randomized study. SETTING: A medical center-based tertiary pediatric intensive care unit. PATIENTS: A total of 59 patients aged from newborn to 17 yrs old underwent ET tube insertion because of cardiopulmonary arrest or impending respiratory failure. INTERVENTION: Ultrasound imaging was performed immediately before and after the ET tube placement procedure. The most frequently used ultrasonic scanning window was the subxiphoid window at the mid-upper abdominal, just beneath the xiphoid process and the lower margin of liver. The sector angle was set as wide as possible (90 degrees) so that the bilateral diaphragm could be well scanned. MEASUREMENTS AND MAIN RESULTS: Using the ultrasound imaging method, we successfully identified all of two esophageal intubations and eight incidents of initial ET tube misplacement, which had been positioned down to the right main bronchus. Finally, we successfully identified all 59 of the correct placements of ET tubes in the trachea. CONCLUSIONS: Ultrasound imaging of diaphragm motion is a useful, quick, noninvasive, portable, and direct anatomic method for assessment of ET tube position. We think it should be considered the method of choice for the secondary confirmation of the ET tube position.

Synthesis and biological evaluation of N-heterocyclic indolyl glyoxylamides as orally active anticancer agents.

A series of N-heterocyclic indolyl glyoxylamides were synthesized and evaluated for in vitro and in vivo anticancer activities. They exhibited a broad spectrum of anticancer activity not only in murine leukemic cancer cells but also in human gastric, breast, and uterus cancer cells as well as their multidrug resistant sublines with a wide range of IC(50) values. They also induced apoptosis and caused DNA fragmentation in human gastric cancer cells. Among the compounds studied, 7 showed the most potent activity of growth inhibition (IC(50) = 17-1711 nM) in several human cancer cells. Given orally, compounds 7 and 13 dose-dependently prolonged the survival of animals inoculated with P388 leukemic cancer cells. N-Heterocyclic indolyl glyoxylamides may be useful as orally active chemotherapeutic agents against cancer and refractory cancerous diseases of multidrug resistance phenotype.

First Exclusive Regioselective Fragmentation of Primary Ozonides Controlled by Remote Carbonyl Groups and a New Method for Determining the Regiochemistry of Carbonyl Oxide Formation.

The first exclusive regioselective fragmentation of primary ozonides controlled by remote carbonyl groups on ozonolysis of norbornene derivatives and reaction of final ozonides with triethylamine as a new probe for determining the regiochemistry of carbonyl oxide formation from primary ozonide fragmentation are reported. Ozonolysis of the endo adducts 3a-d and the deuterated compounds 8a and 8b in CDCl(3) at -78 degrees C gave the final ozonides 4a-d, 9a, and 9b as the sole products (>95%), respectively. No detectable amount of the isomeric final ozonides 5, 10, 11, and 12 was obtained. A mechanism is proposed to account for the exclusive regioselective fragmentation of the primary ozonides. Ozonolysis of 3a-d, 8a, and 8b in CH(2)Cl(2) at -78 degrees C followed by treatment with triethylamine exclusively gave the convex tetraquinane oxa cage compounds 16a-d, 19a, and 19b in 85-90% yields, respectively. No detectable amount of the other regioisomers 17a-d, 20a, and 20b was obtained. Ozonolysis of 3a-d, 8a, and 8b in CH(2)Cl(2) at -78 degrees C followed by reduction with dimethyl sulfide gave the tetraacetal tetraoxa cage compounds 21a-d, 23a, and 23b in 85% yields, respectively. The difference in function between triethylamine and dimethyl sulfide in reaction with final ozonide is demonstrated. Ozonolysis of the endo adducts 24a and 24b in CDCl(3) at -78 degrees C exclusively gave the final ozonides 27a and 27b, respectively. The order of the preference of various remote carbonyl groups to control the fragmentation of the primary ozonides formed by ozonolysis of norbornene derivatives is investigated. Ozonolysis of the endo esters 32a-c in CH(2)Cl(2) at -78 degrees C followed by reduction with dimethyl sulfide gave the new tetraacetal oxa cages 35a-c, with an alkoxyl group directly on the skeleton, and the novel triacetal oxa cages 36b and 36c, respectively. The structures of triacetal oxa cages are proven for the first time by X-ray analysis of the crystalline compound 36c.