High Conformational Flexibility Research Articles

Molecular Dynamics of Steroidal Rotors Probed by Theoretical, Spectroscopic and Dielectric Methods.

Our study focuses on molecular rotors with fast-moving rotators and their potential applications in the development of new amphidynamic crystals. Steroidal molecular rotors with a dipolar fluorine-substituted phenyl group as the rotator were synthesized and characterized. Three different rotors were investigated with varying numbers of fluorine atoms. A comprehensive analysis was performed using vibrational spectroscopy (Raman, FT-IR), electronic circular dichroism (ECD), and dielectric response to understand the behavior of the investigated model rotors. The results were supported by theoretical calculations using Density Functional Theory (DFT) methods. The angle-dependent polarized Raman spectra confirmed the crystallinity of the samples. Nearly frequency and temperature-independent permittivity suggest low-frequency librational motion of stators. An in-depth analysis of ECD spectra revealed high conformational flexibility in solution, resulting in low ECD effects, while in the solid-state with restricted rotation, significant ECD effects were observed. These findings shed light on the conformational behavior and potential applications of the studied steroidal molecular rotors.

Self-Assembly of Insulin-Derived Chimeric Peptides into Two-Component Amyloid Fibrils: The Role of Coulombic Interactions.

Canonical amyloid fibrils are composed of covalently identical polypeptide chains. Here, we employ kinetic assays, atomic force microscopy, infrared spectroscopy, circular dichroism, and molecular dynamics simulations to study fibrillization patterns of two chimeric peptides, ACC1-13E8 and ACC1-13K8, in which a potent amyloidogenic stretch derived from the N-terminal segment of the insulin A-chain (ACC1-13) is coupled to octaglutamate or octalysine segments, respectively. While large electric charges prevent aggregation of either peptide at neutral pH, stoichiometric mixing of ACC1-13E8 and ACC1-13K8 triggers rapid self-assembly of two-component fibrils driven by favorable Coulombic interactions. The low-symmetry nonpolar ACC1-13 pilot sequence is crucial in enforcing the fibrillar structure consisting of parallel β-sheets as the self-assembly of free poly-E and poly-K chains under similar conditions results in amorphous antiparallel β-sheets. Interestingly, ACC1-13E8 forms highly ordered fibrils also when paired with nonpolypeptide polycationic amines such as branched polyethylenimine, instead of ACC1-13K8. Such synthetic polycations are more effective in triggering the fibrillization of ACC1-13E8 than poly-K (or poly-E in the case of ACC1-13K8). The high conformational flexibility of these polyamines makes up for the apparent mismatch in periodicity of charged groups. The results are discussed in the context of mechanisms of heterogeneous disease-related amyloidogenesis.

Twisted or Planar? Side‐Chain Tailoring of Fluorene‐Based Hole‐Transport Materials for Efficient and Stable Perovskite Solar Cells

The functionalization of small‐molecule hole‐transport materials (HTMs) heavily relies on the rational design of molecular geometry, which can optimize both intrinsic HTM properties and interfacial properties for realizing high‐performance and stable lead halide perovskite solar cells (LHPSCs). Herein, two fluorene‐based donor–π linker–donor HTMs are seen, FL01 and FL02, whose side chains are tailored with planar phenyl‐carbazole groups and twisted triphenylamine groups, respectively. Benefiting from the high conformational flexibility of twisted side chains, the strong and oriented interaction via PbO bonding is well coordinated at the perovskite and FL02 interface, which favors the interfacial charge transfer as well as the protection of perovskite layer by effectively blocking or mitigating the diffusion of hygroscopic dopants toward the perovskite surface. Consequently, the performance of FL02 HTM‐based n–i–p LHPSCs is significantly enhanced by achieving a power conversion efficiency of 17.8%, which is twice higher than that (8.6%) of FL01 HTM‐based ones and comparable with the case (18.8%) of conventional spiro‐OMeTAD HTM‐based devices. More importantly, the FL02‐based devices exhibit impressively high operation and storage stabilities with T80 and TS80 lifetimes of >98 h and ≈270 days, respectively, which are among the longest lifespans for the type of hygroscopically doped LHPSCs.

Cross-linking disulfide bonds govern solution structures of diabodies.

In the last years, antibodies have emerged as a promising new class of therapeutics, due to their combination of high specificity with long serum half-life and low risk of side-effects. Diabodies are a popular novel antibody format, consisting of two Fv domains connected with short linkers. Like IgG antibodies, they simultaneously bind two target proteins. However, they offer altered properties, given their smaller size and higher rigidity. In this study, we conducted the-to our knowledge-first molecular dynamics (MD) simulations of diabodies and find a surprisingly high conformational flexibility in the relative orientation of the two Fv domains. We observe rigidifying effects through the introduction of disulfide bonds in the Fv -Fv interface and characterize the effect of different disulfide bond locations on the conformation. Additionally, we compare VH -VL orientations and paratope dynamics between diabodies and an antigen binding fragment (Fab) of the same sequence. We find mostly consistent structures and dynamics, indicating similar antigen binding properties. The most significant differences can be found within the CDR-H2 loop dynamics. Of all CDR loops, the CDR-H2 is located closest to the artificial Fv -Fv interface. All examined diabodies show similar VH -VL orientations, Fv -Fv packing and CDR loop conformations. However, the variant with a P14C-K64C disulfide bond differs most from the Fab in our measures, including the CDR-H3 loop conformational ensemble. This suggests altered antigen binding properties and underlines the need for careful validation of the disulfide bond locations in diabodies.

Local Rigidity by Flexibility: Unusual Design for Organic THz‐Device Materials

AbstractTerahertz (THz) waves interact with molecular phonon vibrations of organic matter. When designing organic THz‐device materials, conformational flexible groups (CFGs) are in most cases avoided. CFGs create many low‐energy conformers with high conformational entropy, which results in large and many phonon vibration modes that lead to undesired self‐absorption of THz waves. Here, nonpolar CFGs only having weak intermolecular interaction capability are unusually introduced into organic THz‐device materials, utilized for efficient THz wave generation. Newly designed THz‐source crystals possess nonpolar methylene (CH2)n units having high conformational flexibility. Compared to previously reported benchmark crystals without methylene CFGs, introducing methylene CFGs significantly reduces void volume in newly designed crystals. This leads to the suppression of molecular phonon vibrations below 2.0 THz (i.e., introducing flexibility results in local rigidity). At infrared pump wavelengths, new CFG‐contained crystals generate a strong THz electric field that is one order of magnitude stronger than that generated in inorganic ZnTe crystals. CFG‐contained crystals exhibit a flatter spectral shape of the generated THz wave than benchmark crystals without methylene CFGs. Therefore, the introduction of CFGs is a very intriguing design strategy for organic THz‐device materials to reduce the limitations caused by phonon vibrations.

Distinguishing Oligosaccharide Isomers Using Far-Infrared Ion Spectroscopy: Identification of Biomarkers for Inborn Errors of Metabolism.

Distinguishing isomeric saccharides poses a major challenge for analytical workflows based on (liquid chromatography) mass spectrometry (LC-MS). In recent years, many studies have proposed infrared ion spectroscopy as a possible solution as the orthogonal, spectroscopic characterization of mass-selected ions can often distinguish isomeric species that remain unresolved using conventional MS. However, the high conformational flexibility and extensive hydrogen bonding in saccharides cause their room-temperature fingerprint infrared spectra to have broad features that often lack diagnostic value. Here, we show that room-temperature infrared spectra of ion-complexed saccharides recorded in the previously unexplored far-infrared wavelength range (300-1000 cm-1) provide well-resolved and highly diagnostic features. We show that this enables distinction of isomeric saccharides that differ either by their composition of monosaccharide units and/or the orientation of their glycosidic linkages. We demonstrate the utility of this approach from single monosaccharides up to isomeric tetrasaccharides differing only by the configuration of a single glycosidic linkage. Furthermore, through hyphenation with hydrophilic interaction liquid chromatography, we identify oligosaccharide biomarkers in patient body fluid samples, demonstrating a generalized and highly sensitive MS-based method for the identification of saccharides found in complex sample matrices.

A dual stable MOF constructed through ligand exchange for enzyme immobilization with improved performance in biodiesel production

The poor stability of metal-organic frameworks (MOFs) limits their practical applications in many fields. Zeolitic imidazolate frameworks (ZIF-8) has been widely studied as an enzyme immobilization carrier. In this paper, the stability of ZIF-8-immobilized lipase in methanolysis for biodiesel production was studied. Fatty acids as conventional substances involved in lipase-mediated natural acylation were found to destroy the structure of ZIF-8 through ligand exchange mechanism. A new MOF was successfully constructed by using phthalic acid (pKa much smaller than 2-methylimidazole) as the exchange ligand. This novel MOF (abbreviated as LeZIF-8-PAX, X represents reaction hours) had dual stability in water and even in pure oleic acid. Lipase immobilized on LeZIF-8-PA0.5 showed higher specific activity. FTIR analysis showed that enzyme molecule immobilized on Le-ZIF-8-PA0.5 had higher conformational flexibility than that with ZIF-8 as the carrier. When applied to methanolysis for biodiesel production, ET 2.0/LeZIF-8-PA0.5 maintained intact morphology while ET 2.0/ZIF-8 almost lost its original morphology, with enzyme activity of 81.5% and 60.2% retained respectively after 5 batch reactions. This work is anticipated to provide new ideas for constructing stable MOFs and promoting the application of MOFs-immobilized enzymes in many chemical and pharmaceutical industrial processes.

Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.

Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence-structure-function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.

α-Aminophosphonate inhibitors of metallo-β-lactamases NDM-1 and VIM-2.

The upswing of antibiotic resistance is an escalating threat to human health. Resistance mediated by bacterial metallo-β-lactamases is of particular concern as these enzymes degrade β-lactams, our most frequently prescribed class of antibiotics. Inhibition of metallo-β-lactamases could allow the continued use of existing β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems, whose applicability is becoming ever more limited. The design, synthesis, and NDM-1, VIM-2, and GIM-1 inhibitory activities (IC50 4.1-506 μM) of a series of novel non-cytotoxic α-aminophosphonate-based inhibitor candidates are presented herein. We disclose the solution NMR spectroscopic and computational investigation of their NDM-1 and VIM-2 binding sites and binding modes. Whereas the binding modes of the inhibitors are similar, VIM-2 showed a somewhat higher conformational flexibility, and complexed a larger number of inhibitor candidates in more varying binding modes than NDM-1. Phosphonate-type inhibitors may be potential candidates for development into therapeutics to combat metallo-β-lactamase resistant bacteria.

Aggrecan and Hyaluronan: The Infamous Cartilage Polyelectrolytes - Then and Now.

Cartilages are unique in the family of connective tissues in that they contain a high concentration of the glycosaminoglycans, chondroitin sulfate and keratan sulfate attached to the core protein of the proteoglycan, aggrecan. Multiple aggrecan molecules are organized in the extracellular matrix via a domain-specific molecular interaction with hyaluronan and a link protein, and these high molecular weight aggregates are immobilized within the collagen and glycoprotein network. The high negative charge density of glycosaminoglycans provides hydrophilicity, high osmotic swelling pressure and conformational flexibility, which together function to absorb fluctuations in biomechanical stresses on cartilageduring movement of an articular joint. We have summarized information on the history and current knowledge obtained by biochemical and genetic approaches, on cell-mediated regulation of aggrecan metabolism and its role in skeletal development, growth as well as duringthe development of joint disease. In addition, we describe the pathways for hyaluronan metabolism, with particular focus on the role as a "metabolic rheostat" during chondrocyte responses in cartilage remodeling in growth and disease.Future advances in effective therapeutic targeting of cartilage loss during osteoarthriticdiseases of the joint as an organ as well as in cartilage tissue engineering would benefit from 'big data' approaches and bioinformatics, to uncover novel feed-forward and feed-back mechanisms for regulating transcription and translation of genes and their integration into cell-specific pathways.

C7 Epimerization of Benzylidene-Protected β-d-Idopyranosides Brings Structural Insights into Idose Conformational Flexibility.

Idose is unique among other aldohexoses because of its high conformational flexibility in solution. We herein show that benzylidene acetal-protected 3-O-acyl-β-d-idopyranosides undergo Lewis acid-catalyzed C7 epimerization with concomitant 4C1 to 1C4 ring inversion. The reaction conditions and structural parameters for this transformation to occur have been thoroughly investigated through an extensive glycosylation study combined with NMR analyses, X-ray diffraction, and quantum molecular modeling. In addition to reporting a direct, β-stereoselective idosylation approach, our work brings fundamental structural insights into the conformational flexibility of idose.

To probe the activation mechanism of the Delta opioid receptor by an agonist ADL5859 started from inactive conformation using molecular dynamic simulations

The δ-opioid receptor (DOR) is a critical pharmaceutical target for pain management. Although the high-resolution crystal structures of the DOR with both agonist and antagonist have recently been solved, the activation mechanism remains to be elusive. In this study, a DOR agonist ADL5859 was docked to the inactive DOR and multiple microsecond molecular dynamic (MD) simulations were conducted to probe the activation mechanism. While the receptor with the crystal ligand (i.e. antagonist naltrindole) maintained the inactive conformation in all three independent simulations, the receptor with ADL5859 was adopting toward the active conformation in three out of six independent simulations. Major conformational differences were located on transmembrane (TM) 5 and 6, as well as intracellular loop 3. Compared to naltrindole, ADL5859 exhibited high conformational flexibility and strong interaction with the transmission switch. The putative key residues (W274, D95, V267, L139, V263, M142, T260, R146, R258 and others) involving in the activation pathway were identified through the conventional molecular switch analysis and a pairwise distance analysis, which provides a short list for experimental mutagenesis study. These insights will facilitate further development of therapeutic agents targeting the DOR. Communicated by Ramaswamy H. Sarma

Human Serum Amyloid a Impaired Structural Stability of High-Density Lipoproteins (HDL) and Apolipoprotein (Apo) A-I and Exacerbated Glycation Susceptibility of ApoA-I and HDL.

Human serum amyloid A (SAA) is an exchangeable apolipoprotein (apo) in high-density lipoprotein (HDL) that influences HDL quality and functionality, particularly in the acute phase of inflammation. On the other hand, the structural and functional correlations of HDL containing SAA and apoA-I have not been reported. The current study was designed to compare the change in HDL quality with increasing SAA content in the lipid-free and lipid-bound states in reconstituted HDL (rHDL). The expressed recombinant human SAA1 (13 kDa) was purified to at least 98% and characterized in the lipid-free and lipid-bound states with apoA-I. The dimyristoyl phosphatidylcholine (DMPC) binding ability of apoA-I was impaired severely by the addition of SAA, while SAA alone could not bind with DMPC. The recombinant human SAA1 was incorporated into the rHDL (molar ratio 95:5:1, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC): cholesterol: apoA-I) with various apoA-I:SAA molar ratios from 1:0 to 1:0.5, 1:1 and 1:2. With increasing SAA1 content, the rHDL particle size was reduced from 98 Å to 93 Å, and the α-helicity of apoA-I:SAA was decreased from 73% to 40% for (1:0) and (1:2), respectively. The wavelength maximum fluorescence (WMF) of tryptophan in rHDL was red-shifted from 339 nm to 345 nm for (1:0) and (1:2) of apoA-I:SAA, respectively, indicating that the addition of SAA to rHDL destabilized the secondary structure of apoA-I. Upon denaturation by urea treatment from 0 M to 8 M, SAA showed only a 3 nm red-shift in WMF, while apoA-I showed a 16 nm red-shift in WMF, indicating that SAA is resistant to denaturation and apoA-I had higher conformational flexibility than SAA. The glycation reaction of apoA-I in the presence of fructose was accelerated up to 1.8-fold by adding SAA in a dose-dependent manner than that of apoA-I alone. In conclusion, the incorporation of SAA in rHDL impaired the structural stability of apoA-I and exacerbated glycation of HDL and apoA-I.

Connecting Molecular and Supramolecular Shapeshifting by the Ostwald's Nucleation Stages of a Star Giant Molecule.

The shapeshifting behavior for synthetic matters was found at either the molecular or supramolecular level, but the connection between shapeshifting at the two hierarchical levels remains missing. In this study, an 8-arm star giant molecule, NPOSS, was synthesized to connect the molecular and supramolecular shapeshifting. Controlling the conditions of bulk self-assembly allowed us to bring NPOSS into three different Ostwald's stages of nucleation. The high conformational flexibility of NPOSS facilitates molecular shapeshifting and allows NPOSS to take the discotic, rod-like and star-like geometries in different Ostwald's stages. Simultaneous changes in the supramolecular scaffolds were observed as the discotic, rod-like and star-like NPOSS molecules self-assembled into the supramolecular scaffolds of 1D columns, 2D lamellae, and 3D networks, respectively. These changes in the hierarchical structures also affect the CO2 affinity of NPOSS. Therefore, the connection between the molecular/supramolecular shapeshifting and the structure-driven property changes of NPOSS were established by taking advantage of the high conformational freedom of the 8-arm star giant molecule and its diverse self-assembly pathways leading to the different Ostwald's stages.

Topological methods for analysis and design of coordination polymers

A comprehensive review of the methods for topological analysis of crystalline compounds as applied to the structures of coordination polymers is presented for the first time. The basic concepts of reticular chemistry, a new branch of science, which combines methods of synthetic chemistry with methods for topological design of polymer compounds, are considered. Reticular chemistry methods are illustrated with examples of the analysis and design of coordination polymers. The most complete classification of coordination polymers, which are similar in terms of various compositional and topological parameters, is given. This review describes and integrates information on the topological analysis tools, such as computer software and electronic databases. A special attention is paid to the application of topological methods in the machine analysis and the prediction of structures and properties of coordination polymers, in particular to the establishment of chemical composition–structure–property relationships and the development of knowledge bases and artificial intelligence systems. A procedure for the search for the general crystal-chemical features using automatic heuristic analysis of large sets of structural data is discussed. It is shown how this analysis can be used to determine the limits of applicability of reticular chemistry and the possibility of its extension to coordination polymers containing structurally, chemically and topologically complex building units with high conformational flexibility. Approaches of reticular chemistry are considered in detail in relation to the design of proton-conductive coordination polymers, which have received considerable attention in the past decade. The specific features of the topological structures of this class of compounds are described in a systematic way. The relationships between the chemical composition, structure and conductive properties of these compounds and the applicability of targeted design are discussed.<br> The bibliography includes 303 references.

Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements

Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In yeast, dysregulation of Lon protease (PIM1) attenuates lifespan and leads to gross mitochondrial morphological perturbations. Although structures of the bacterial and human Lon protease reveal a hexameric assembly, yeast PIM1 was speculated to form a heptameric assembly and is uniquely characterized by a ∼50-residue insertion between the ATPase and protease domains. To further understand the yeast-specific properties of PIM1, we determined a high-resolution cryo-electron microscopy structure of PIM1 in a substrate-translocating state. Here, we reveal that PIM1 forms a hexamer, conserved with that of bacterial and human Lon proteases, wherein the ATPase domains form a canonical closed spiral that enables pore loop residues to translocate substrates to the protease chamber. In the substrate-translocating state, PIM1 protease domains form a planar protease chamber in an active conformation and are uniquely characterized by a ∼15-residue C-terminal extension. These additional C-terminal residues form an α-helix located along the base of the protease domain. Finally, we did not observe density for the yeast-specific insertion between the ATPase and protease domains, likely due to high conformational flexibility. Biochemical studies to investigate the insertion using constructs that truncated or replaced the insertion with a glycine-serine linker suggest that the yeast-specific insertion is dispensable for PIM1’s enzymatic function. Altogether, our structural and biochemical studies highlight unique components of PIM1 machinery and demonstrate evolutionary conservation of Lon protease function.

HDL and Cholesterol Ester Transfer Protein (CETP).

Cholesterol ester transfer protein (CETP) is important clinically and is one of the major targets in cardiovascular disease studies. With high conformational flexibility, its tunnel structure allows unforced movement of high-density lipoproteins (HDLs), VLDLs, and LDLs. Research in reverse cholesterol transports (RCT) reveals that the regulation of CETP activity can change the concentration of cholesteryl esters (CE) in HDLs, VLDLs, and LDLs. These molecular insights demonstrate the mechanisms of CETP activities and manifest the correlation between CETP and HDL. However, animal and cell experiments focused on CETP give controversial results. Inhibiting CETP is found to be beneficial to anti-atherosclerosis in terms of increasing plasma HDL-C, while it is also claimed that CETP weakens atherosclerosis formation by promoting RCT. Currently, the CETP-related drugs are still immature. Research on CETP inhibitors is targeted at improving efficacy and minimizing adverse reactions. As for CETP agonists, research has proved that they also can be used to resist atherosclerosis.

Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior.

Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Å2 in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.

Targeted Redesign of Suramin Analogs for Novel Antimicrobial Lead Development.

The emergence of new viral infections and drug-resistant bacteria urgently necessitates expedient therapeutic development. Repurposing and redesign of existing drugs against different targets are one potential way in which to accelerate this process. Suramin was initially developed as a successful antiparasitic drug but has also shown promising antiviral and antibacterial activities. However, due to its high conformational flexibility and negative charge, suramin is considered quite promiscuous toward positively charged sites within nucleic acid binding proteins. Although some suramin analogs have been developed against specific targets, only limited structure-activity relationship studies were performed, and virtual screening has yet to be used to identify more specific inhibitor(s) based on its scaffold. Using available structures, we investigated suramin's target diversity, confirming that suramin preferentially binds to protein pockets that are both positively charged and enriched in aromatic or leucine residues. Further, suramin's high conformational flexibility allows adaptation to structurally diverse binding surfaces. From this platform, we developed a framework for structure- and docking-guided elaboration of suramin analog scaffolds using virtual screening of suramin and heparin analogs against a panel of diverse therapeutically relevant viral and bacterial protein targets. Use of this new framework to design potentially specific suramin analogs is exemplified using the SARS-CoV-2 RNA-dependent RNA polymerase and nucleocapsid protein, identifying leads that might inhibit a wide range of coronaviruses. The approach presented here establishes a computational framework for designing suramin analogs against different bacterial and viral targets and repurposing existing drugs for more specific inhibitory activity.

Molecular “Hozo”: Thermally Stable Yet Conformationally Flexible Self-Assemblies Driven by Tight Molecular Meshing

Abstract Various noncovalent molecular interactions have been employed as driving forces to construct well-defined discrete self-assemblies. Among them, coordination and hydrogen bonds are widely used due to their high directionality and appropriate bond strength. However, the utilization of nondirectional, week molecular interactions for this purpose still presents a key challenge in supramolecular self-assembly. To tackle this critical issue, we presented a novel design concept, molecular “Hozo”, that the components with large, indented complementary hydrophobic surfaces tightly mesh with each other driven by the hydrophobic effect in water. Based on this concept, we developed a series of water-soluble cube-shaped molecular assemblies, i.e., nanocubes, composed of six molecules of identical gear-shaped amphiphiles (GSAs) with the aid of van der Waals (vdW) and cation-π interactions as well as the hydrophobic effect. The nanocubes exhibit unique properties derived from molecular meshing of the building blocks, such as high thermal stability yet as high conformational flexibility as biological molecules and emission whose intensity is affected by the structural change of the nanocube.