Computational drug discovery for castration-resistant prostate cancers through in vitro drug response modeling.

Prostate cancer (PC) is the most frequently diagnosed malignancy and a leading cause of cancer deaths in US men. Many PC cases metastasize and develop resistance to systemic hormonal therapy, a stage known as castration-resistant prostate cancer (CRPC). Therefore, there is an urgent need to develop effective therapeutic strategies for CRPC. Traditional drug discovery pipelines require significant time and capital input, which highlights a need for novel methods to evaluate the repositioning potential of existing drugs. Here, we present a computational framework to predict drug sensitivities of clinical CRPC tumors to various existing compounds and identify treatment options with high potential for clinical impact. We applied this method to a CRPC patient cohort and nominated drugs to combat resistance to hormonal therapies including abiraterone and enzalutamide. The utility of this method was demonstrated by nomination of multiple drugs that are currently undergoing clinical trials for CRPC. Additionally, this method identified the tetracycline derivative COL-3, for which we validated higher efficacy in an isogenic cell line model of enzalutamide-resistant vs. enzalutamide-sensitive CRPC. In enzalutamide-resistant CRPC cells, COL-3 displayed higher activity for inhibiting cell growth and migration, and for inducing G1-phase cell cycle arrest and apoptosis. Collectively, these findings demonstrate the utility of a computational framework for independent validation of drugs being tested in CRPC clinical trials, and for nominating drugs with enhanced biological activity in models of enzalutamide-resistant CRPC. The efficiency of this method relative to traditional drug development approaches indicates a high potential for accelerating drug development for CRPC.

MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2.

MOTIVATION: Today, the prediction of structures of large protein complexes solely from their sequence information requires prior knowledge of the stoichiometry of the complex. To address this challenge, we have enhanced the Monte Carlo Tree Search algorithms in MoLPC to enable the assembly of protein complexes while simultaneously predicting their stoichiometry. RESULTS: In MoLPC2, we have improved the predictions by allowing sampling alternative AlphaFold predictions. Using MoLPC2, we accurately predicted the structures of 50 out of 175 nonredundant protein complexes (TM-score ≥ 0.8) without knowing the stoichiometry. MoLPC2 provides new opportunities for predicting protein complex structures without stoichiometry information. AVAILABILITY AND IMPLEMENTATION: MoLPC2 is freely available at https://github.com/hychim/molpc2. A notebook is also available from the repository for easy use.

Elucidation of the key role of Pt···Pt interactions in the directional self-assembly of platinum(II) complexes.

Here, we report the use of an amphiphilic Pt(II) complex, K[Pt{(O3SCH2CH2CH2)2bzimpy}Cl] (PtB), as a model to elucidate the key role of Pt···Pt interactions in directing self-assembly by combining temperature-dependent ultraviolet-visible (UV-Vis) spectroscopy, stopped-flow kinetic experiments, quantum mechanics (QM) calculations, and molecular dynamics (MD) simulations. Interestingly, we found that the self-assembly mechanism of PtB in aqueous solution follows a nucleation-free isodesmic model, as revealed by the temperature-dependent UV-Vis experiments. In contrast, a cooperative growth is found for the self-assembly of PtB in acetone­water (7:1, vol/vol) solution, which is further verified by the stopped-flow experiments, which clearly indicates the existence of a nucleation phase in the acetone­water (7:1, vol/vol) solution. To reveal the underlying reasons and driving forces for these self-assembly processes, we performed QM calculations and show that the Pt···Pt interactions arising from the interaction between the pz and dz2 orbitals play a crucial role in determining the formation of ordered self-assembled structures. In subsequent oligomer MD simulations, we demonstrate that this directional Pt···Pt interaction can indeed facilitate the formation of linear structures packed in a helix-like fashion. Our results suggest that the self-assembly of PtB in acetone­water (7:1, vol/vol) solution is predominantly driven by the directional noncovalent Pt···Pt interaction, leading to the cooperative growth and the formation of fibrous nanostructures. On the contrary, the self-assembly in aqueous solution forms spherical nanostructures of PtB, which is primarily due to the predominant contribution from the less directional hydrophobic interactions over the directional Pt···Pt and π−π interactions that result in an isodesmic growth.

Synthesis, Characterization, and Resistive Memory Behaviors of Highly Strained Cyclometalated Platinum(II) Nanohoops.

Strained carbon nanohoops exhibit attractive photophysical properties due to their unique π-conjugated structure. However, incorporation of such nanohoops into the pincer ligand of metal complexes has rarely been explored. Herein, a new family of highly strained cyclometalated platinum(II) nanohoops has been synthesized and characterized. Strain-promoted C-H bond activation has been observed during the metal coordination process, and Hückel-Möbius topology and random-columnar packing in the solid state are found. Transient absorption spectroscopy revealed the size-dependent excited state properties of the nanohoops. Moreover, the nanohoops have been successfully employed as active materials in the fabrication of solution-processable resistive memory devices, including the use of the smallest platinum(II) nanohoop for the fabrication of a binary memory, with low switching threshold voltages of ca. 1.5 V, high ON/OFF current ratios, and good stability. These results demonstrate that strain incorporation into the structure can be an effective strategy to fundamentally fine-tune the reactivity, optoelectronic, and resistive memory properties.

Toward the Design and Construction of Supramolecular Functional Molecular Materials Based on Metal-Metal Interactions.

Supramolecular functional materials represent an emerging class of materials that have been governed by the supramolecular chemistry of self-assembled molecules. Such high-order molecular hierarchies have been stabilized by various kinds of noncovalent intermolecular forces including hydrogen bonding, electrostatic, donor-acceptor, π-π stacking interactions, and dispersion forces. Recently, metal-metal interactions have also emerged as an unconventional type of noncovalent interaction that is unique in the metal complex system for the construction of self-assembled metal-based materials. These metal-metal interactions have further imparted the self-assembled materials with rich spectroscopic functionalities. However, the systematic control of these hierarchical architectures through metal-metal interactions remains challenging. In this Perspective, we aim to stimulate research direction in the field with the utilization of such intriguing and unique directional noncovalent metal-metal interactions as one of the driving forces, highlighting the roles and significance of metal-metal interactions and ultimately facilitating a controlled and rational design and synthesis of metallosupramolecular functional materials with rich spectroscopic properties and huge potential for various applications.

Molecular Alignment of Alkynylplatinum(II) 2,6-Bis(benzimidazol-2-yl)pyridine Double Complex Salts and the Formation of Well-Ordered Nanostructures Directed by Pt···Pt and Donor-Acceptor Interactions.

A new class of alkynylplatinum(II) bzimpy (bzimpy = bis(benzimidazol-2-yl)pyridine) double complex salts (DCSs) containing dialkoxynaphthalene or pyromellitic diimide moieties on the alkynyl ligand has been reported to display distinct morphological properties compared to their precursor alkynylplatinum(II) complexes, with the capability of being aligned by the directional Pt···Pt and/or π-π stacking interactions. The incorporation of donor and acceptor units on the alkynyl ligands has been found to significantly perturb the alignment of the oppositely charged complex ions in the DCSs to stack in a twisted head-to-head manner, attributed to the additional driving forces of electrostatic and donor-acceptor interactions. The modulation of the Pt···Pt distances and the extent of aggregate formation have been demonstrated by altering the charge matching between the platinum(II) bzimpy moieties and the donor or acceptor moieties on the alkynyl ligand.

A platinum(II) molecular hinge with motions visualized by phosphorescence changes.

With the rapidly growing exploration of artificial molecular machines and their applications, there is a strong demand to develop molecular machines that can have their motional states and configuration/conformation changes detectable by more sensitive and innovative methods. A visual artificial molecular hinge with phosphorescence behavior changes is designed and synthesized using square-planar cyclometalated platinum(II) complex and rigid aromatic alkynyl groups as the building blocks to construct the wings/flaps and axis, respectively. The molecular motions of this single molecular hinge and its reversible processes can be powered by both solvent and temperature changes. The rotary motion can be conveniently observed by the visual phosphorescence changes from deep-red to green emission in real time.

Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer.

A hallmark of prostate cancer progression is dysregulation of lipid metabolism via overexpression of fatty acid synthase (FASN), a key enzyme in de novo fatty acid synthesis. Metastatic castration-resistant prostate cancer (mCRPC) develops resistance to inhibitors of androgen receptor (AR) signaling through a variety of mechanisms, including the emergence of the constitutively active AR variant V7 (AR-V7). Here, we developed an FASN inhibitor (IPI-9119) and demonstrated that selective FASN inhibition antagonizes CRPC growth through metabolic reprogramming and results in reduced protein expression and transcriptional activity of both full-length AR (AR-FL) and AR-V7. Activation of the reticulum endoplasmic stress response resulting in reduced protein synthesis was involved in IPI-9119-mediated inhibition of the AR pathway. In vivo, IPI-9119 reduced growth of AR-V7-driven CRPC xenografts and human mCRPC-derived organoids and enhanced the efficacy of enzalutamide in CRPC cells. In human mCRPC, both FASN and AR-FL were detected in 87% of metastases. AR-V7 was found in 39% of bone metastases and consistently coexpressed with FASN. In patients treated with enzalutamide and/or abiraterone FASN/AR-V7 double-positive metastases were found in 77% of cases. These findings provide a compelling rationale for the use of FASN inhibitors in mCRPCs, including those overexpressing AR-V7.

Supramolecular Assembly of Organoplatinum(II) Complexes for Subcellular Distribution and Cell Viability Monitoring with Differentiated Imaging.

The ability to precisely control the subcellular distribution of luminous materials presents unprecedented advantages for understanding cell biology and disease therapy. We introduce a luminescence tool for subcellular distribution imaging and differentiation of live and dead cells, utilizing cationic organoplatinum(II) complexes that exhibit well-defined monomeric to aggregate nanostructures along with concentration-dependent switchable luminescence from green to red due to assembly via PtII ⋅⋅⋅PtII and π-π stacking interactions. One of the complexes was chosen to demonstrate the unique lysosome-to-nucleus subcellular re-distribution and imaging capability in live and dead cells, respectively, which represents the first example to discriminate the subcellular localization of platinum(II) complexes through differential luminescence response. These new findings facilitate the fundamental understanding of self-assembly behaviors of platinum(II) complexes for potential subcellular detection assays.

Solvent-Dependent Supramolecular Host-Guest Assemblies of Platinum(II) Tweezers and a Guest System: From Discrete Molecules to High-Ordered Oligomers.

A series of platinum(II) calix[4]arene-based molecular tweezers was synthesized. The studies of the host-guest association with a charge-neutral cyclometalated platinum(II) complex showed a drastic color change and the turning on of near-infrared emission resulting from Pt⋅⋅⋅Pt and π-π interactions. Control of the host-guest assembly process by varying the solvent composition can lead to a change from discrete host and guest molecules to high-ordered host-guest oligomers with the formation of sheet-like nanostructures, demonstrating a rare example of three-state supramolecular host-guest system with high solubility in solvents of diverse polarity. The change in host-guest assembly behaviors could be probed by drastic color changes from yellow to orange to green. The present study provides insights into the systematic design of solvent-responsive molecular materials using molecular tweezers-directed host-guest assembly, with potential applications in colorimetric sensing of changes in the micro-environment.

Phosphorescent Cyclometalated Platinum(II) Enantiomers with Circularly Polarized Luminescence Properties and Their Assembly Behaviors.

Platinum(II) complexes as supramolecular luminescent materials have received considerable attention due to their unique planar structures and fascinating photophysical properties. However, the molecular design of platinum(II) complexes with impressive circularly polarized luminescence properties still remains challenging and rarely explored. Herein, we reported a series of cyclometalated platinum(II) complexes with benzaldehyde and its derived imine-containing alkynyl ligands to investigate their phosphorescent, chiroptical, and self-assembly behaviors. An isodesmic growth mechanism is found for their temperature-dependent self-assembly process. The chiral sense of the enantiomers can be transferred from the chiral alkynyl ligands to the cyclometalated platinum(II) dipyridylbenzene N^C^N chromophore and further amplified through supramolecular assembly via intermolecular noncovalent interactions. Notably, distinctive phosphorescent properties and nanostructured morphologies have been found for enantiomers 4R and 4S. Their intriguing self-assembled nanostructures and phosphorescence behaviors are supported by crystal structure determination, 1H NMR, emission, and UV-vis absorption spectroscopy, scanning electron microscopy, and X-ray powder diffraction studies.

Realization of Distinct Mechano- and Piezochromic Behaviors via Alkoxy Chain Length-Modulated Phosphorescent Properties and Multidimensional Self-Assembly Structures of Dinuclear Platinum(II) Complexes.

In this work, through the introduction of different lengths of alkoxy chains to the dinuclear cyclometalated platinum(II) complexes, the apparent color, solubility, luminescence properties, and self-assembly behaviors have been remarkably modulated. In the solid state, the luminescence properties have been found to arise from emission origins that switch between the 3MMLCT excited state in the red solids and the 3IL excited state in the yellow state, depending on the alkoxy chain lengths. The luminescence of the yellow solids is found to show obvious bathochromic shifts under mechanical grinding and decreased intensity under controllable hydrostatic pressure. However, the emission of the red solids exhibits both a bathochromic shift and reduced intensity due to the isotropic compression-induced shortening of the Pt···Pt and π-π distances. By combining the data obtained from X-ray diffraction (XRD), infrared (IR), and X-ray single crystal structure, a better understanding of the relationship between molecular aggregation and photophysical properties has been realized, suggesting that the length of the alkoxy chains plays an important role in governing the supramolecular assemblies.

Bisphosphonate therapy after liver transplant improves bone mineral density and reduces fracture rates: an updated systematic review and meta-analysis.

To investigate the efficacy of bisphosphonates and compare oral and IV formulations on bone mineral density (BMD) and fracture incidence in post-orthotopic liver transplant (OLT) patients. Electronic databases were searched, and six RCTs and three cohort studies were included out of 711 articles. Main outcomes included post-OLT BMD changes, fracture incidence, and treatment adverse reactions. Pairwise meta-analysis was conducted for binary and continuous outcomes, while pooled fracture incidence utilized single-arm meta-analysis. Post-OLT fracture incidence was reported in nine studies (n = 591). Total fracture incidence was 6.6% (CI: 3.4-12.4%) in bisphosphonate group and 19.1% (CI: 14.3-25.1%) in calcium and vitamin D group. Total fractures were significantly lower in patients on bisphosphonate, compared to calcium and vitamin D (n = 591; OR = 0.037; CI: 0.18-0.77; P = 0.008). Overall fractures were significantly lower in the oral group (n = 263; OR = 0.26; CI: 0.08-0.85; P = 0.02) but not in the IV group (n = 328; OR = 0.45; CI: 0.16-1.26; P = 0.129). Both oral and IV bisphosphonates are effective in reducing fracture incidence post-OLT compared to calcium and vitamin D. Oral formulations may also have an advantage over IV in reducing bone loss and fracture incidence post-OLT.

Stimuli-Responsive Two-Dimensional Supramolecular Polymers Based on Trinuclear Platinum(II) Scaffolds: Reversible Modulation of Photoluminescence, Cavity Size, and Water Permeability.

Here we report the first two-dimensional (2D) supramolecular polymer, which has varying structure and function arising from the perturbation of noncovalent metal···metal interactions in response to acid-base stimuli. This 2D assembly possesses a positively charged, honeycomb-like nanostructure consisting of trinuclear alkynylplatinum(II) terpyridine complexes appended with acid-sensitive dimethylamino groups. Upon addition of acids and bases, reversible switching mediated by protonation and deprotonation of dimethylamino and dimethylammonium moieties intrinsically alters the positive charge density of the constituent cationic units, which causes interior cavities to adaptively adjust their size, accompanied by drastic photoluminescence changes. When water molecules pass through the membranes obtained from 2D supramolecular polymers, the permeating flux can also be tuned by the pH values of the buffer media. This work paves the way toward supramolecularly engineered 2D smart materials with stimuli-responsive properties.

Multiple-Color Platinum Complex with Super-Large Stokes Shift for Super-Resolution Imaging of Autolysosome Escape.

It is of great significance to track the platinum drugs in real time with super-resolution to elucidate their mechanism of action, such as their behavior and distribution in live cells. Such information is required for further drug development. However, it is always challenging to design platinum complexes suitable for such research. Herein, we design a luminescent building block (L) for metal complexes and a dinuclear platinum complex (Pt2 L) for super-resolution imaging. Because of its super-large Stokes shift and excellent photophysical properties, Pt2 L is capable of serving as an ideal candidate for super-resolution imaging with extremely low luminescence background and high photobleaching resistance. Moreover, upon light stimulation, a matter flux of Pt2 L escaping from autolysosomes to nucleus was observed, which represents a new transportation path. Utilizing the photoactivated escape properties, we can regulate the nuclear accessibility of Pt2 L form autolysosomes with photo-selectivity, which provides a new way to improve the targeting of platinum drugs.

Rational Design of Multi-Stimuli-Responsive Scaffolds: Synthesis of Luminescent Oligo(ethynylpyridine)-Containing Alkynylplatinum(II) Polypyridine Foldamers Stabilized by Pt···Pt Interactions.

A series of oligo(ethynylpyridine)-containing alkynylplatinum(II) terpyridine/bzimpy (bzimpy = 2,6-bis(N-alkylbenzimidazol-2'-yl)pyridine) metallofoldamers has been designed and synthesized to investigate the potential applications of metallofoldamers imparted by the rich spectroscopic responses of Pt···Pt interactions. Apart from the control of the folding/unfolding processes by solvent compositions and temperatures, this class of metallofoldamers has also been found to exhibit reversible folding/unfolding behaviors mediated by the addition of acids/bases due to the incorporation of the acid-sensitive oligo(ethynylpyridine) derivatives. More importantly, the intramolecular Pt···Pt interaction has been found to play a crucial role in governing the folded state conformation. The conformation of this class of metallofoldamers has been investigated by 2D ROESY NMR, electronic absorption, and emission spectroscopy, which provide further insights into the rational molecular design and multidimensional control of metallofoldamers upon the application of various external stimuli, leading to the preparation of multi-stimuli-responsive materials for potential applications in material sciences.

Controlling Self-Assembly Mechanisms through Rational Molecular Design in Oligo( p-phenyleneethynylene)-Containing Alkynylplatinum(II) 2,6-Bis( N-alkylbenzimidazol-2'-yl)pyridine Amphiphiles.

The systematic control over association mechanisms of self-assembled materials has been demonstrated through the rational design and synthesis of a series of amphiphilic dinuclear alkynylplatinum(II) bzimpy (bzimpy = 2,6-bis( N-alkylbenzimidazol-2'-yl)pyridine) complexes containing the shape-persistent oligo( p-phenyleneethynylene)s. Multistage morphological transformations from plates to fibers and to spherical nanostructures under different solvent compositions have been demonstrated. The subtle balances between multiple noncovalent interactions including Pt···Pt, hydrophobic, hydrophilic, and π-π stacking interactions are found to have profound impact on the supramolecular assembly of the system, in which a change in the association mechanism from isodesmic to cooperative and back to isodesmic growth has been observed upon increasing hydrophilicity of the complexes.

Synthesis of Luminescent Platinum(II) 2,6-Bis(N-dodecylbenzimidazol-2'-yl)pyridine Foldamers and Their Supramolecular Assembly and Metallogel Formation.

Dinuclear alkynylplatinum(II) metallofoldamers with an oligomeric m-phenyleneethynylene backbone have been designed with the incorporation of a sterically undemanding, π-conjugated, and hydrophobic 2,6-bis(N-dodecylbenzimidazol-2'-yl)pyridine pincer ligand. The complex with the optimal chain length has been found to exhibit gelation behavior via stabilization by noncovalent Pt···Pt and π-π stacking interactions in the hierarchical architecture constructed from the single-turn helix. The chain lengths of the complexes have been found to be a critical determinant for their gelation behavior, conformations, and morphologies. Such a gelation process has been found to undergo a cooperative assembly mechanism according to the nucleation-elongation model. Their self-assembly via the Pt···Pt and π-π stacking interactions has been studied by 1H NMR, 2D ROESY NMR (ROESY = rotating-frame Overhauser spectroscopy), electronic absorption, and emission spectroscopy, and density functional theory calculations have provided further insights into the folded state geometry of this class of metallofoldamers.

PERK Activation Promotes Medulloblastoma Tumorigenesis by Attenuating Premalignant Granule Cell Precursor Apoptosis.

Evidence suggests that activation of pancreatic endoplasmic reticulum kinase (PERK) signaling in response to endoplasmic reticulum stress negatively or positively influences cell transformation by regulating apoptosis. Patched1 heterozygous deficient (Ptch1(+/-)) mice reproduce human Gorlin's syndrome and are regarded as the best animal model to study tumorigenesis of the sonic hedgehog subgroup of medulloblastomas. It is believed that medulloblastomas in Ptch1(+/-) mice results from the transformation of granule cell precursors (GCPs) in the developing cerebellum. Here, we determined the role of PERK signaling on medulloblastoma tumorigenesis by assessing its effects on premalignant GCPs and tumor cells. We found that PERK signaling was activated in both premalignant GCPs in young Ptch1(+/-) mice and medulloblastoma cells in adult mice. We demonstrated that PERK haploinsufficiency reduced the incidence of medulloblastomas in Ptch1(+/-) mice. Interestingly, PERK haploinsufficiency enhanced apoptosis of premalignant GCPs in young Ptch1(+/-) mice but had no significant effect on medulloblastoma cells in adult mice. Moreover, we showed that the PERK pathway was activated in medulloblastomas in humans. These results suggest that PERK signaling promotes medulloblastoma tumorigenesis by attenuating apoptosis of premalignant GCPs during the course of malignant transformation.

Synthesis and Photochromic Studies of Dithienylethene-Containing Cyclometalated Alkynylplatinum(II) 1,3-Bis(N-alkylbenzimidazol-2'-yl)benzene Complexes.

Several photochromic cyclometalated alkynylplatinum(II) complexes with tridentate 1,3-bis(N-alkylbenzimidazol-2'-yl)benzene (bzimb) ligands have been synthesized by the reaction of the corresponding chloroplatinum(II) bzimb precursor complexes with the photochromic ligand TMS-C≡C-Th-DTE in the presence of sodium hydroxide. They have been characterized by (1)H NMR spectroscopy and positive-ion FAB or ESI mass spectrometry and confirmed by elemental analysis. One of the complexes has also been characterized by X-ray crystallography. Their photophysical, photochromic, and electrochemical properties have been studied. Upon photoexcitation, the yellow solutions in benzene display green phosphorescence originating from the triplet intraligand ((3)IL) excited state. All the cyclometalated alkynylplatinum(II) bzimb complexes exhibit reversible photochromism with solution colors changing between yellow and purple upon photoirradiation. The thermal bleaching kinetics of complex 2 has been studied in toluene at various temperatures with the activation barrier for the thermal cycloreversion reaction determined.