Chemoenzymatic synthesis, computational investigation, and antitumor activity of monocyclic lankacidin derivatives.

We investigated the importance of the δ-lactone ring (C1-C5) in lankacidin C using chemoenzymatic synthesis and computational prediction and assessing biological activity, including antitumor activity. Pyrroloquinoline quinone-dependent dehydrogenase (Orf23) in Streptomyces rochei was used in the chemoenzymatic synthesis of lankacyclinone C, a novel lankacidin C congener lacking the δ-lactone moiety. Orf23 could convert the monocyclic lankacidinol derivatives, lankacyclinol and 2-epi-lankacyclinol, to the C-24 keto compounds, lankacyclinone C and 2-epi-lankacyclinone C, respectively, elucidating the relaxed substrate specificity of Orf23. Computational prediction using molecular dynamics simulations and the molecular mechanics/generalized Born-surface area protocol indicated that binding energy values of all the monocyclic derivatives are very close to those of lankacidin C, which may reflect a comparable affinity to tubulin. Monocyclic lankacidin derivatives showed moderate antitumor activity when compared with bicyclic lankacidins, suggesting that the δ-lactone moiety is less important for antitumor activity in lankacidin-group antibiotics.

3D reconstruction of weakly scattering objects from 2D intensity-only measurements using the Wolf transform.

A new approach to optical diffraction tomography (ODT) based on intensity measurements is presented. By applying the Wolf transform directly to intensity measurements, we observed unexpected behavior in the 3D reconstruction of the sample. Such a reconstruction does not explicitly represent a quantitative measure of the refractive index of the sample; however, it contains interesting qualitative information. This 3D reconstruction exhibits edge enhancement and contrast enhancement for nanostructures compared with the conventional 3D refractive index reconstruction and thus could be used to localize nanoparticles such as lipids inside a biological sample.

Fluorescence-Based and Fluorescent Label-Free Characterization of Polymer Nanoparticle Decorated T Cells.

Cells are attractive carriers for the transport and delivery of nanoparticulate cargo. The use of cell-based carriers allows one to enhance control over the biodistribution of drug-loaded polymers and polymer nanoparticles. One key element in the development of cell-based delivery systems is the loading of the cell-based carrier with the nanoparticle cargo, which can be achieved either by internalization of the payload or by immobilization on the cell surface. The surface modification of cells with nanoparticles or the internalization of nanoparticles by cells is usually monitored with fluorescence-based techniques, such as flow cytometry and confocal microscopy. In spite of the widespread use of these techniques, the use of fluorescent labels also poses some risks and has several drawbacks. Fluorescent dyes may bleach, or leach from, the nanoparticles or alter the physicochemical properties of nanoparticles and their interactions with and uptake by cells. Using poly(d,l-lactic acid) nanoparticles that are loaded with Coumarin 6, BODIPY 493/503, or DiO dyes as a model system, this paper demonstrates that the use of physically entrapped fluorescent labels can lead to false negative or erroneous results. The use of nanoparticles that contain covalently tethered fluorescent dyes instead was found to provide a robust approach to monitor cell surface conjugation reactions and to quantitatively analyze nanoparticle-decorated cells. Finally, it is shown that optical diffraction tomography is an attractive, alternative technique for the characterization of nanoparticle-decorated cells, which obviates the need for fluorescent labels.

Accurate and efficient leap-frog beam propagation method for modeling micro and nanophotonic structures.

In this paper, a novel and efficient approach for solving the beam propagation method (BPM) governing equation is proposed. The approach is based on the reformulation of the beam propagation equation to solve real system matrices only at each propagation step. The reformulated equation utilizes a leap-frog (LF) technique to couple the real and imaginary components of the field in an iterative scheme. The method yields higher processing speed by at least 30% more than that of the conventional BPM method. To validate the proposed LF-BPM method, different photonic systems, including directional couplers and multimode interferometers, are simulated. Results have been experimentally verified by comparing them with results measured for fabricated micro-photonic structures. A stability analysis was performed to study the effect of the design parameters on the performance of the proposed scheme. The proposed LF-BPM approach is considered a promising technique for efficient modeling of optical structures.

Modeling the Colchicum autumnale Tubulin and a Comparison of Its Interaction with Colchicine to Human Tubulin.

Tubulin is the target for many small-molecule natural compounds, which alter microtubules dynamics, and lead to cell cycle arrest and apoptosis. One of these compounds is colchicine, a plant alkaloid produced by Colchicum autumnale. While C. autumnale produces a potent cytotoxin, colchicine, and expresses its target protein, it is immune to colchicine's cytotoxic action and the mechanism of this resistance is hitherto unknown. In the present paper, the molecular mechanisms responsible for colchicine resistance in C. autumnale are investigated and compared to human tubulin. To this end, homology models for C. autumnale α-ß tubulin heterodimer are created and molecular dynamics (MD) simulations together with molecular mechanics Poisson-Boltzmann calculations (MM/PBSA) are performed to determine colchicine's binding affinity for tubulin. Using our molecular approach, it is shown that the colchicine-binding site in C. autumnale tubulin contains a small number of amino acid substitutions compared to human tubulin. However, these substitutions induce significant reduction in the binding affinity for tubulin, and subsequently fewer conformational changes in its structure result. It is suggested that such small conformational changes are insufficient to profoundly disrupt microtubule dynamics, which explains the high resistance to colchicine by C. autumnale.

Explaining the Microtubule Energy Balance: Contributions Due to Dipole Moments, Charges, van der Waals and Solvation Energy.

Microtubules are the main components of mitotic spindles, and are the pillars of the cellular cytoskeleton. They perform most of their cellular functions by virtue of their unique dynamic instability processes which alternate between polymerization and depolymerization phases. This in turn is driven by a precise balance between attraction and repulsion forces between the constituents of microtubules (MTs)-tubulin dimers. Therefore, it is critically important to know what contributions result in a balance of the interaction energy among tubulin dimers that make up microtubules and what interactions may tip this balance toward or away from a stable polymerized state of tubulin. In this paper, we calculate the dipole-dipole interaction energy between tubulin dimers in a microtubule as part of the various contributions to the energy balance. We also compare the remaining contributions to the interaction energies between tubulin dimers and establish a balance between stabilizing and destabilizing components, including the van der Waals, electrostatic, and solvent-accessible surface area energies. The energy balance shows that the GTP-capped tip of the seam at the plus end of microtubules is stabilized only by - 9 kcal/mol, which can be completely reversed by the hydrolysis of a single GTP molecule, which releases + 14 kcal/mol and destabilizes the seam by an excess of + 5 kcal/mol. This triggers the breakdown of microtubules and initiates a disassembly phase which is aptly called a catastrophe.

Detailed Per-residue Energetic Analysis Explains the Driving Force for Microtubule Disassembly.

Microtubules are long filamentous hollow cylinders whose surfaces form lattice structures of αß-tubulin heterodimers. They perform multiple physiological roles in eukaryotic cells and are targets for therapeutic interventions. In our study, we carried out all-atom molecular dynamics simulations for arbitrarily long microtubules that have either GDP or GTP molecules in the E-site of ß-tubulin. A detailed energy balance of the MM/GBSA inter-dimer interaction energy per residue contributing to the overall lateral and longitudinal structural stability was performed. The obtained results identified the key residues and tubulin domains according to their energetic contributions. They also identified the molecular forces that drive microtubule disassembly. At the tip of the plus end of the microtubule, the uneven distribution of longitudinal interaction energies within a protofilament generates a torque that bends tubulin outwardly with respect to the cylinder's axis causing disassembly. In the presence of GTP, this torque is opposed by lateral interactions that prevent outward curling, thus stabilizing the whole microtubule. Once GTP hydrolysis reaches the tip of the microtubule (lateral cap), lateral interactions become much weaker, allowing tubulin dimers to bend outwards, causing disassembly. The role of magnesium in the process of outward curling has also been demonstrated. This study also showed that the microtubule seam is the most energetically labile inter-dimer interface and could serve as a trigger point for disassembly. Based on a detailed balance of the energetic contributions per amino acid residue in the microtubule, numerous other analyses could be performed to give additional insights into the properties of microtubule dynamic instability.

Chemical synthesis, pharmacological evaluation and in silico analysis of new 2,3,3a,4,5,6-hexahydrocyclopenta[c]pyrazole derivatives as potential anti-mitotic agents.

We have synthesized new, biologically active mono- and di-substituted 2,3,3a,4,5,6-hexahydrocyclopenta[c]pyrazole derivatives bearing electron withdrawing groups and electron donating groups. These derivative structures were characterized by their spectral and analytical data. The newly synthesized hexahydropyrazole analogues were evaluated for their in vitro anticancer activity against breast and lung cancer cell lines using a cytotoxicity bioassay. To understand their mechanism of action, tubulin binding assays were performed which pointed to their binding to microtubules in a mode similar to but not identical to colchicine, as evidenced by their KD value evaluation. Computational docking studies also suggested binding near the colchicine binding site on tubulin. These results were further confirmed by colchicine-binding assays on the most active compounds, which indicated that they bound to tubulin near but not at the colchicine site. The moderate cytotoxic effects of these compounds may be due to the presence of electron donating groups on the para-position of the phenyl ring, along with the hexahydropyrazole core nucleus. The observed anti-cancer activity based on inhibition of microtubule formation may be helpful in designing more potent compounds with a hexahydropyrazole moiety.

Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules.

Microtubules are key structural elements that, among numerous biological functions, maintain the cytoskeleton of the cell and have a major role in cell division, which makes them important cancer chemotherapy targets. Understanding the energy balance that brings tubulin dimers, the building blocks of microtubules, together to form a microtubule is especially important for revealing the mechanism of their dynamic instability. Several studies have been conducted to estimate various contributions to the free energy of microtubule formation. However, the hydrogen-bond contribution was not studied before as a separate component. In this work, we use concepts such as the quantum theory of atoms in molecules to estimate the per-residue strength of hydrogen bonds contributing to the overall stability that brings subunits together in pair of tubulin heterodimers, across both the longitudinal and lateral interfaces. Our study shows that hydrogen bonding plays a major role in the stability of tubulin systems. Several residues that are crucial to the binding of vinca alkaloids are shown to be strongly involved in longitudinal microtubule stabilization. This indicates a direct relation between the binding of these agents and the effect on the interfacial hydrogen-bonding network, and explains the mechanism of their action. Lateral contacts showed much higher stability than longitudinal ones (-462 ± 70 vs. -392 ± 59 kJ/mol), which suggests a dramatic lateral stabilization effect of the GTP cap in the ß-subunit. The role of the M-loop in lateral stability in absence of taxol was shown to be minor. The B-lattice lateral hydrogen bonds are shown to be comparable in strength to the A-lattice ones (-462 ± 70 vs. -472 ± 46 kJ/mol). These findings establish the importance of hydrogen bonds to the stability of tubulin systems.

Thin Skin in Rhinoplasty: Considerations for Camouflaging Dorsal Nasal Irregularities.

Thin skin presents a challenge for achieving optimal aesthetic outcomes and minimizing complications. The review analyzes various materials and techniques employed to achieve this goal. A comprehensive electronic search was conducted across various medical databases, retrieved 965 studies, from which 15 studies were eligible for inclusion in this review with a total number of 679 patients with thin nasal skin. Techniques that promote graft integration, minimize resorption, and provide a smooth dorsal contour are crucial for thin-skinned patients. Diced cartilage with PRP, fascia lata grafts, and laser-assisted rhinoplasty appear to be particularly effective based on the available evidence. Platelet-rich fibrin (PRF) appears to play a role in some techniques by enhancing healing and tissue regeneration. Natural materials, like fascia lata and ligamentous grafts, offer potential benefits but require further exploration. Fat grafting techniques show promise but necessitate more research. This review provides a comprehensive overview of various techniques for addressing dorsal irregularities in rhinoplasty for patients with thin skin. Surgeons can utilize this information to select the most appropriate approach for achieving optimal aesthetic outcomes while minimizing complications.

In silico molecular docking, dynamics simulation and repurposing of some VEGFR-2 inhibitors based on the SARS-CoV-2-main-protease inhibitor N3.

The global and rapid spread of the novel human coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has brought immediate urgency to the discovery of favorable targets for COVID-19 treatment. Here, we consider drug reuse as an attractive methodology for drug discovery by reusing existing drugs to treat diseases other than their initial indications. Here, we review current information concerning the global health issue of COVID-19 including VEGFR-2 inhibitors. Besides, we describe computational approaches to be used in drug repurposing and highlight examples of in silico studies of drug development efforts against SARS-CoV-2. The present study suggests the potential anti-SARS-CoV-2 activities of 35 reported VEGFR-2 inhibitors containing the amide and urea linkers. Nineteen members revealed the best in silico results and hence, were subjected to further molecular dynamics (MD) simulation for their inhibitory activities against SARS-CoV-2 Mpro across 100 ns. Furthermore, MD simulations followed by calculations of the free energy of binding were also carried out for the most promising ligand-pocket complexes from docking studies to clarify some information on their dynamic and thermodynamic properties and approve the docking results. These results we obtained probably provided an excellent lead candidate for the development of therapeutic drugs against COVID-19.Communicated by Ramaswamy H. Sarma.

Impact forces in backward falls: Subject-specific video-based rigid body simulation of backward falls.

A critical missing component in the study of real-world falls is the ability to accurately determine impact forces resulting from the fall. Subject-specific rigid body dynamic (RBD) models calibrated to video captured falls can quantify impact forces and provide additional insights into injury risk factors. RBD models were developed based on five backward falls captured on surveillance video in long-term care facilities in British Columbia, Canada. Model joint stiffness and initial velocities were calibrated to match the kinematics of the fall and contact forces were calculated. The effect of joint stiffnesses (neck, lumbar spine, hip, and knee joint) on head contact forces were determined by modifying the calibrated stiffness values ±25%. Fall duration, fall trajectories, and maximum velocities showed a close match between fall events and simulations. The maximum value of pelvic velocity difference between Kinovea (an open-source software 2D digitization software) and Madymo multibody modeling was found to be 6% ± 21.58%. Our results demonstrate that neck and hip stiffness values have a non-significant yet large effect on head contact force (t(3) = 1, p = 0.387 and t(3) = 2, p = 0.138), while lower effects were observed for knee stiffness, and the effect of lumbar spine stiffness was negligible. The subject-specific fall simulations constructed from real world video captured falls allow for direct quantification of force outcomes of falls and may have applications in improving the assessment of fall-induced injury risks and injury prevention methods.

Prevalence and associated factors of pediatric hypertension in Jazan region, south of the Kingdom of Saudi Arabia. A pilot cross-sectional study.

Hypertension (HTN) is a primary global health concern. Moreover, according to the 2010 Global Burden of Disease, hypertension accounted for roughly a quarter of cardiovascular disease fatalities and 1.9 percent of all deaths in Saudi Arabia in 2010. Also, hypertension is a significant risk factor for cardiovascular disease, morbidity, and mortality. However, assessing blood pressure (BP) and preventing hypertension among children and adolescents has become a global priority. This study aims to determine the prevalence of hypertension among children in the Jazan region of Saudi Arabia. Also, to determine the common risk factors associated with pediatric hypertension. We conducted this cross-sectional study among boys and girls aged 6-14 years visiting Al-Rashid Mall, one of the two main malls in Jazan city, the capital of Jazan region, Saudi Arabia, between November 2021 and January 2022. We included children willing to participate in the study after obtaining their parents' consent and children's assent. We used a standardized questionnaire to interview the parents to collect the children's data. We also measured the children's resting BP. Then we classified the measurements according to the updated International Pediatric Hypertension Association (IPHA) chart. We also measured the height and weight of the children and calculated their BMI. We used SPSS version 25 for the data entry and analysis. Our results showed that the prevalence of hypertension and prehypertension was insignificantly higher in females (11.84% and 12.65%) compared to males (11.52% and 11.52%), respectively. Our participants' main associated factors with prehypertension and hypertension were overweight, obesity, and family income. Pediatric hypertension and prehypertension were highly prevalent in Jazan region. Therefore, being overweight and obese should be considered risk factors for pediatric hypertension. Our study emphasizes the need for early intervention to prevent pediatric HTN, particularly among overweight and obese children.

Bioinspired computational design of lankacidin derivatives for improvement in antitumor activity.

Background: The 17-membered polyketide, lankacidin C, exhibits considerable antitumor activity as a microtubule stabilizer by binding to the paclitaxel binding site. Method: Esterification of the C-7/C-13 hydroxyl in lankacidin C was performed with acetyl, cinnamoyl and hydrocinnamoyl groups and their antitumor activity was assessed to improve the cytotoxicity of lankacidins through bioinspired computational design. Results: Compared with the cytotoxicity of parent lankacidin C against the HeLa cell line, 13-O-cinnamoyl-lankacidin C demonstrated sevenfold higher cytotoxicity. Furthermore, 7,13-di-O-cinnamoyl-lankacidin C exhibited considerable antitumor activity against three tested cell lines. Conclusion: C13-esterification by a cinnamoyl group dramatically improved antitumor activity, in agreement with computational predictions. This finding provides a potential substrate for next-generation lankacidin derivatives with significant antitumor activity.

The FDA-Approved Drug Cobicistat Synergizes with Remdesivir To Inhibit SARS-CoV-2 Replication In Vitro and Decreases Viral Titers and Disease Progression in Syrian Hamsters.

Combinations of direct-acting antivirals are needed to minimize drug resistance mutations and stably suppress replication of RNA viruses. Currently, there are limited therapeutic options against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and testing of a number of drug regimens has led to conflicting results. Here, we show that cobicistat, which is an FDA-approved drug booster that blocks the activity of the drug-metabolizing proteins cytochrome P450-3As (CYP3As) and P-glycoprotein (P-gp), inhibits SARS-CoV-2 replication. Two independent cell-to-cell membrane fusion assays showed that the antiviral effect of cobicistat is exerted through inhibition of spike protein-mediated membrane fusion. In line with this, incubation with low-micromolar concentrations of cobicistat decreased viral replication in three different cell lines including cells of lung and gut origin. When cobicistat was used in combination with remdesivir, a synergistic effect on the inhibition of viral replication was observed in cell lines and in a primary human colon organoid. This was consistent with the effects of cobicistat on two of its known targets, CYP3A4 and P-gp, the silencing of which boosted the in vitro antiviral activity of remdesivir in a cobicistat-like manner. When administered in vivo to Syrian hamsters at a high dose, cobicistat decreased viral load and mitigated clinical progression. These data highlight cobicistat as a therapeutic candidate for treating SARS-CoV-2 infection and as a potential building block of combination therapies for COVID-19. IMPORTANCE The lack of effective antiviral treatments against SARS-CoV-2 is a significant limitation in the fight against the COVID-19 pandemic. Single-drug regimens have so far yielded limited results, indicating that combinations of antivirals might be required, as previously seen for other RNA viruses. Our work introduces the drug booster cobicistat, which is approved by the FDA and typically used to potentiate the effect of anti-HIV protease inhibitors, as a candidate inhibitor of SARS-CoV-2 replication. Beyond its direct activity as an antiviral, we show that cobicistat can enhance the effect of remdesivir, which was one of the first drugs proposed for treatment of SARS-CoV-2. Overall, the dual action of cobicistat as a direct antiviral and a drug booster can provide a new approach to design combination therapies and rescue the activity of compounds that are only partially effective in monotherapy.

High speed, complex wavefront shaping using the digital micro-mirror device.

Digital micro-mirror devices (DMDs) have been deployed in many optical applications. As compared to spatial light modulators (SLMs), they are characterized by their much faster refresh rates (full-frame refresh rates up to 32 kHz for binary patterns) compared to 120 Hz for most liquid crystal SLMs. DMDs however can only display binary, unipolar patterns and utilize temporal modulation to represent with excellent accuracy multiple gray-levels in display applications. We used the built-in time domain dynamic range representation of the DMD to project 8-bit complex-fields. With this method, we demonstrated 8-bit complex field modulation with a frame time of 38.4 ms (around 0.15 s for the entire complex-field). We performed phase conjugation by compensating the distortions incurred due to propagation through free-space and a scattering medium. For faster modulation speed, an electro-optic modulator was used in synchronization with the DMD in an amplitude modulation mode to create grayscale patterns with frame rate ~ 833 Hz with display time of only 1.2 ms instead of 38.4 ms for time multiplexing gaining a speed up by a factor of 32.

Molecular dynamics simulation dataset of a microtubule ring in electric field.

We present molecular dynamics (MD) trajectories of a single ring of B-lattice microtubule ring consisting of 13 tubulin heterodimers. The data contain trajectories of this molecular system ran under various conditions (two temperature values, three ionic strength values, three values of electric field (including no field), and four electric field orientations). Our data enable us to analyze the effects of the electric field on microtubule under a variety of conditions. This data set was a basis of our in silico discovery, which demonstrates that the electric field can open microtubule lattice [1].

Electro-opening of a microtubule lattice in silico.

Modulation of the structure and function of biomaterials is essential for advancing bio-nanotechnology and biomedicine. Microtubules (MTs) are self-assembled protein polymers that are essential for fundamental cellular processes and key model compounds for the design of active bio-nanomaterials. In this in silico study, a 0.5 µs-long all-atom molecular dynamics simulation of a complete MT with approximately 1.2 million atoms in the system indicated that a nanosecond-scale intense electric field can induce the longitudinal opening of the cylindrical shell of the MT lattice, modifying the structure of the MT. This effect is field-strength- and temperature-dependent and occurs on the cathode side. A model was formulated to explain the opening on the cathode side, which resulted from an electric-field-induced imbalance between electric torque on tubulin dipoles and cohesive forces between tubulin heterodimers. Our results open new avenues for electromagnetic modulation of biological and artificial materials through action on noncovalent molecular interactions.

Pure testicular choriocarcinoma Cannonball metastases as a presenting imaging feature: A case report and a review of literature.

Pure testicular choriocarcinoma is an extremely rare subtype of nonseminomatous germ cell tumor, accounting for less than 1% of all germ cell tumors and only 0.19% of all testicular tumors. It is a highly aggressive malignant tumor with early multiorgan metastasis and poor prognosis. We present a case of 23-year-old male presented to the hospital with mild hemoptysis which was thought as a sequela of his past COVID-19 pneumonia infection, however; chest radiograph showed multiple rounded cannonball opacities seen throughout both lungs raising the suspicion of metastatic deposits to the lungs. During physical examination, left testicular painless swelling was noted leading to an ultrasound of the scrotum which revealed a left intratesticular infiltrative, heterogeneous mass. Tumor markers, including beta-human chorionic gonadotropin, lactate dehydrogenase and alpha fetoprotein were extremely high. Computed tomography scan of the brain, chest, abdomen, and pelvis showed hemorrhagic metastatic deposits to the brain, chest, and left para-aortic lymph nodes. The patient underwent radical orchiectomy and histopathology reports confirmed the diagnosis of pure testicular choriocarcinoma.

High-fidelity optical diffraction tomography of multiple scattering samples.

We propose an iterative reconstruction scheme for optical diffraction tomography that exploits the split-step non-paraxial (SSNP) method as the forward model in a learning tomography scheme. Compared with the beam propagation method (BPM) previously used in learning tomography (LT-BPM), the improved accuracy of SSNP maximizes the information retrieved from measurements, relying less on prior assumptions about the sample. A rigorous evaluation of learning tomography based on SSNP (LT-SSNP) using both synthetic and experimental measurements confirms its superior performance compared with that of the LT-BPM. Benefiting from the accuracy of SSNP, LT-SSNP can clearly resolve structures that are highly distorted in the LT-BPM. A serious limitation for quantifying the reconstruction accuracy for biological samples is that the ground truth is unknown. To overcome this limitation, we describe a novel method that allows us to compare the performances of different reconstruction schemes by using the discrete dipole approximation to generate synthetic measurements. Finally, we explore the capacity of learning approaches to enable data compression by reducing the number of scanning angles, which is of particular interest in minimizing the measurement time.