A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13.

The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a critical need to discover more effective antivirals. While therapeutics for SARS-CoV-2 exist, its nonstructural protein 13 (Nsp13) remains a clinically untapped target. Nsp13 is a helicase responsible for unwinding double-stranded RNA during viral replication and is essential for propagation. Like other helicases, Nsp13 has two active sites: a nucleotide binding site that hydrolyzes nucleoside triphosphates (NTPs) and a nucleic acid binding channel that unwinds double-stranded RNA or DNA. Targeting viral helicases with small molecules, as well as the identification of ligand binding pockets, have been ongoing challenges, partly due to the flexible nature of these proteins. Here, we use a virtual screen to identify ligands of Nsp13 from a collection of clinically used drugs. We find that a known ion channel inhibitor, IOWH-032, inhibits the dual ATPase and helicase activities of SARS-CoV-2 Nsp13 at low micromolar concentrations. Kinetic and binding assays, along with computational and mutational analyses, indicate that IOWH-032 interacts with the RNA binding interface, leading to displacement of nucleic acid substrate, but not bound ATP. Evaluation of IOWH-032 with microbial helicases from other superfamilies reveals that it is selective for coronavirus Nsp13. Furthermore, it remains active against mutants representative of observed SARS-CoV-2 variants. Overall, this work provides a new inhibitor for Nsp13 and provides a rationale for a recent observation that IOWH-032 lowers SARS-CoV-2 viral loads in human cells, setting the stage for the discovery of other potent viral helicase modulators.

Chinese Herbal Formula, Modified Guilu Erxian Glue, Alleviates Apoptosis of Hematopoietic Stem Cells by Regulating SLAM-SAP Signal Pathway in Aplastic Anemia Mice Model.

ETHNOPHARMACOLOGICAL RELEVANCE: Guilu Erxian Glue (GEG) and Danggui Buxue Tang (DBT) are traditional Chinese herbal formulas. According to the theory of traditional Chinese medicine, the combination of those two formulas (Modified Guilu Erxian Glue, MGEG) has the effects of tonifying the kidney and producing blood, was usually used to treat bone marrow failure diseases, including aplastic anemia (AA). AIM OF THE STUDY: T lymphocytes play a crucial role in the disease pathogenesis and progression of AA. Our preliminary results confirmed that GEG can improve the damage of hematopoietic stem cells in mice, while DBT can reduce the proliferation and differentiation of T lymphocytes and inhibit the production of IFN-γ. We hypothesized that the combination of those two herbal formulas could inhibit immune attack and restore hematopoietic function through multiple mechanisms. In this study, we aim to study the curative effect of MGEG on regulating the expression of Signal lymphocyte activating molecule (SLAM), an activation-related molecule in T lymphocytes, thereby suppressing the immune function of T cells and decelerating the damage to hematopoietic stem cells. MATERIALS AND METHODS: High-performance liquid chromatography-electrospray ionization/mass spectrometry system was used to identify the components of the MGEG formulation. Induction of aplastic anemia mouse model by injecting allogeneic lymphocyte suspension into BABL/c mice after ionizing radiation. Cyclosporine A (CsA) was used as a positive control drug. Flow cytometry was used to detect the number and apoptosis rate of hematopoietic stem cells in the bone marrow. Enzyme-linked immunosorbent assay was performed to measure the levels of IFN-γ and TNF-α. Immunofluorescence staining was used to assess the expression of T-bet and SLAM-SAP. Western Blot was conducted to examine the expression of activation-related molecules in T lymphocytes and proteins related to the Fas signal pathway. Hematoxylin-eosin staining was performed to observe pathological changes in the bone marrow tissue. Wright-Giemsa staining was utilized to evaluate alterations in the cellular composition and basic structure of the bone marrow cells (BMCs). Transmission electron microscopy was employed to observe changes in the structure and morphology of hematopoietic stem cells. The hematology analyzer was used to detect peripheral blood parameters. RESULTS: Twenty-three different components were identified in MGEG. After MGEG treatment, the expression levels of Fyn and SLAM-SAP binding were increased in AA mice, while the expression levels of T-bet were decreased and the secretion of IFN-γ was reduced significantly. Additionally, MGEG also could downregulate the protein levels of Fas, caspase-3, and cleaved caspase-3 in AA mice. CONCLUSION: MGEG could attenuate the production of IFN-γ by promoting the SLAM-SAP signal pathway to regulate the generation and distribution of T-bet in T cells. Additionally, it suppresses apoptosis of HSCs through intervention in the Fas-dependent pathway, thereby mitigating immune-mediated damage to HSCs.

Accurate Prediction of NMR Chemical Shifts: Integrating DFT Calculations with Three-Dimensional Graph Neural Networks.

Computer prediction of NMR chemical shifts plays an increasingly important role in molecular structure assignment and elucidation for organic molecule studies. Density functional theory (DFT) and gauge-including atomic orbital (GIAO) have established a framework to predict NMR chemical shifts but often at a significant computational expense with a limited prediction accuracy. Recent advancements in deep learning methods, especially graph neural networks (GNNs), have shown promise in improving the accuracy of predicting experimental chemical shifts, either by using 2D molecular topological features or 3D conformational representation. This study presents a new 3D GNN model to predict 1H and 13C chemical shifts, CSTShift, that combines atomic features with DFT-calculated shielding tensor descriptors, capturing both isotropic and anisotropic shielding effects. Utilizing the NMRShiftDB2 data set and conducting DFT optimization and GIAO calculations at the B3LYP/6-31G(d) level, we prepared the NMRShiftDB2-DFT data set of high-quality 3D structures and shielding tensors with corresponding experimentally measured 1H and 13C chemical shifts. The developed CSTShift models achieve the state-of-the-art prediction performance on both the NMRShiftDB2-DFT test data set and external CHESHIRE data set. Further case studies on identifying correct structures from two groups of constitutional isomers show its capability for structure assignment and elucidation. The source code and data are accessible at https://yzhang.hpc.nyu.edu/IMA.

Dynamics underlie the drug recognition mechanism by the efflux transporter EmrE.

The multidrug efflux transporter EmrE from Escherichia coli requires anionic residues in the substrate binding pocket for coupling drug transport with the proton motive force. Here, we show how protonation of a single membrane embedded glutamate residue (Glu14) within the homodimer of EmrE modulates the structure and dynamics in an allosteric manner using NMR spectroscopy. The structure of EmrE in the Glu14 protonated state displays a partially occluded conformation that is inaccessible for drug binding by the presence of aromatic residues in the binding pocket. Deprotonation of a single Glu14 residue in one monomer induces an equilibrium shift toward the open state by altering its side chain position and that of a nearby tryptophan residue. This structural change promotes an open conformation that facilitates drug binding through a conformational selection mechanism and increases the binding affinity by approximately 2000-fold. The prevalence of proton-coupled exchange in efflux systems suggests a mechanism that may be shared in other antiporters where acid/base chemistry modulates access of drugs to the substrate binding pocket.

FoxO3 Regulates Mouse Bone Mesenchymal Stem Cell Fate and Bone-Fat Balance During Skeletal Aging.

Age-related osteoporosis is characterized by an imbalance between osteogenic and adipogenic differentiation in bone mesenchymal stem cells (BMSCs). Forkhead box O 3 (FoxO3) transcription factor is involved in lifespan and cell differentiation. In this study, we explore whether FoxO3 regulates age-related bone loss and marrow fat accumulation. The expression levels of FoxO3 in BMSCs during aging were detected in vivo and in vitro. To explore the role of FoxO3 in osteogenic and adipogenic differentiation, primary BMSCs were isolated from young and aged mice. FoxO3 expression was modulated by adenoviral vector transfection. The role of FoxO3 in bone-fat balance was evaluated by alizarin red S staining, oil red O staining, quantitative reverse transcription-polymerase chain reaction, Western blot, and histological analysis. Age-related bone loss and fat deposit are associated with downregulation of FoxO3. Overexpression of FoxO3 alleviated age-related bone loss and marrow fat accumulation in aged mice. Mechanistically, FoxO3 reduced adipogenesis and enhanced osteogenesis of BMSCs via downregulation of PPAR-γ and Notch signaling, respectively. In conclusion, FoxO3 is an essential factor controlling the fate of BMSCs and is a potential target for the prevention of age-related osteoporosis.

A Bionic Thermosensitive Sustainable Delivery System for Reversing the Progression of Osteoarthritis by Remodeling the Joint Homeostasis.

Although the pathogenesis of osteoarthritis (OA) is unclear, inflammatory cytokines are related to its occurrence. However, few studies focused on the therapeutic strategies of regulating joint homeostasis by simultaneously remodeling the anti-inflammatory and immunomodulatory microenvironments. Fibroblast growth factor 18 (FGF18) is the only disease-modifying OA drug (DMOAD) with a potent ability and high efficiency in maintaining the phenotype of chondrocytes within cell culture models. However, its potential role in the immune microenvironment remains unknown. Besides, information on an optimal carrier, whose interface and chondral-biomimetic microenvironment mimic the native articular tissue, is still lacking, which substantially limits the clinical efficacy of FGF18. Herein, to simulate the cartilage matrix, chondroitin sulfate (ChS)-based nanoparticles (NPs) are integrated into poly(D, L-lactide)-poly(ethylene glycol)-poly(D, L-lactide) (PLEL) hydrogels to develop a bionic thermosensitive sustainable delivery system. Electrostatically self-assembled ChS and ε-poly-l-lysine (EPL) NPs are prepared for the bioencapsulation of FGF18. This bionic delivery system suppressed the inflammatory response in interleukin-1ß (IL-1ß)-mediated chondrocytes, promoted macrophage M2 polarization, and inhibited M1 polarization, thereby ameliorating cartilage degeneration and synovitis in OA. Thus, the ChS-based hydrogel system offers a potential strategy to regulate the chondrocyte-macrophage crosstalk, thus re-establishing the anti-inflammatory and immunomodulatory microenvironment for OA therapy.

Integrated Molecular Modeling and Machine Learning for Drug Design.

Modern therapeutic development often involves several stages that are interconnected, and multiple iterations are usually required to bring a new drug to the market. Computational approaches have increasingly become an indispensable part of helping reduce the time and cost of the research and development of new drugs. In this Perspective, we summarize our recent efforts on integrating molecular modeling and machine learning to develop computational tools for modulator design, including a pocket-guided rational design approach based on AlphaSpace to target protein-protein interactions, delta machine learning scoring functions for protein-ligand docking as well as virtual screening, and state-of-the-art deep learning models to predict calculated and experimental molecular properties based on molecular mechanics optimized geometries. Meanwhile, we discuss remaining challenges and promising directions for further development and use a retrospective example of FDA approved kinase inhibitor Erlotinib to demonstrate the use of these newly developed computational tools.

Deciphering the Allosteric Activation Mechanism of SIRT6 Using Molecular Dynamics Simulations.

As a member of the histone deacetylase protein family, the NAD+-dependent SIRT6 plays an important role in maintaining genomic stability and regulating cell metabolism. Interestingly, SIRT6 has been found to have a preference for hydrolyzing long-chain fatty acyls relative to deacetylation, and it can be activated by fatty acids. However, the mechanisms by which SIRT6 recognizes different substrates and can be activated by small molecular activators are still not well understood. In this study, we carried out extensive molecular dynamic simulations to shed light on these mechanisms. Our results revealed that the binding of the myristoylated substrate stabilizes the catalytically favorable conformation of NAD+, while the binding of the acetyl-lysine substrate leads to a loose binding of NAD+ in SIRT6. Based on these observations, we proposed a reasonable allosteric binding mode for myristic acid, which can enhance the catalytic activity of SIRT6 by stabilizing the binding of NAD+ with His131 as well as the acetylated substrate. Furthermore, our molecular dynamics simulations demonstrated that synthetic SIRT6 activators, such as UBCS039, MDL-801, and 12q, block the flipping of ribose in NAD+ and therefore can stabilize substrate-NAD+-His131 interactions in a manner similar to fatty acids. In summary, our newly proposed activation mechanism of SIRT6 highlights the importance of protein-substrate interactions, which would facilitate the rational design of new SIRT6 activators.

Angiogenesis coupled with osteogenesis in a bone tissue engineering scaffold enhances bone repair in osteoporotic bone defects.

Increased life expectancy has resulted in an increase in osteoporosis incidence worldwide. The coupling of angiogenesis and osteogenesis is indispensable for bone repair. Although traditional Chinese medicine (TCM) exerts therapeutic effects on osteoporosis, TCM-related scaffolds, which focus on the coupling of angiogenesis and osteogenesis, have not yet been used for the treatment of osteoporotic bone defects.Panax notoginsengsaponin (PNS), the active ingredient ofPanax notoginseng, was added to a poly (L-lactic acid) (PLLA) matrix. Osteopractic total flavone (OTF), the active ingredient ofRhizoma Drynariae, was encapsulated in nano-hydroxyapatite/collagen (nHAC) and added to the PLLA matrix. Magnesium (Mg) particles were added to the PLLA matrix to overcome the bioinert character of PLLA and neutralize the acidic byproducts generated by PLLA. In this OTF-PNS/nHAC/Mg/PLLA scaffold, PNS was released faster than OTF. The control group had an empty bone tunnel; scaffolds containing OTF:PNS = 100:0, 50:50, and 0:100 were used as the treatment groups. Scaffold groups promoted new vessel and bone formation, increased the osteoid tissue, and suppressed the osteoclast activity around osteoporotic bone defects. Scaffold groups upregulated the expression levels of angiogenic and osteogenic proteins. Among these scaffolds, the OTF-PNS (50:50) scaffold exhibited a better capacity for osteogenesis than the OTF-PNS (100:0 and 0:100) scaffolds. Activation of the bone morphogenic protein (BMP)-2/BMP receptor (BMPR)-1A/runt-related transcription factor (RUNX)-2signaling pathway may be a possible mechanism for the promotion of osteogenesis. Our study demonstrated that the OTF-PNS/nHAC/Mg/PLLA scaffold could promote osteogenesis via the coupling of angiogenesis and osteogenesis in osteoporotic rats with bone defects, and activating theBMP-2/BMPR1A/RUNX2signaling pathway may be an osteogenesis-related mechanism. However, further experiments are necessary to facilitate its practical application in the treatment of osteoporotic bone defects.

Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease.

The SARS-CoV-2 main protease (Mpro) is critical for the production of functional viral proteins during infection and, like many viral proteases, can also target host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 can be recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes global protein synthesis and cellular redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain required for tRNA modification activity in cells. Evolutionary analysis shows that the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 may be resistant to cleavage. In primates, regions outside the cleavage site with rapid evolution could indicate adaptation to ancient viral pathogens. We determined the structure of a TRMT1 peptide in complex with Mpro, revealing a substrate binding conformation distinct from the majority of available Mpro-peptide complexes. Kinetic parameters for peptide cleavage showed that the TRMT1(526-536) sequence is cleaved with comparable efficiency to the Mpro-targeted nsp8/9 viral cleavage site. Mutagenesis studies and molecular dynamics simulations together indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis that follows substrate binding. Our results provide new information about the structural basis for Mpro substrate recognition and cleavage that could help inform future therapeutic design and raise the possibility that proteolysis of human TRMT1 during SARS-CoV-2 infection suppresses protein translation and oxidative stress response to impact viral pathogenesis.

Gatekeeper mutations activate FGF receptor tyrosine kinases by destabilizing the autoinhibited state.

Many types of human cancers are being treated with small molecule ATP-competitive inhibitors targeting the kinase domain of receptor tyrosine kinases. Despite initial successful remission, long-term treatment almost inevitably leads to the emergence of drug resistance mutations at the gatekeeper residue hindering the access of the inhibitor to a hydrophobic pocket at the back of the ATP-binding cleft. In addition to reducing drug efficacy, gatekeeper mutations elevate the intrinsic activity of the tyrosine kinase domain leading to more aggressive types of cancer. However, the mechanism of gain-of-function by gatekeeper mutations is poorly understood. Here, we characterized fibroblast growth factor receptor (FGFR) tyrosine kinases harboring two distinct gatekeeper mutations using kinase activity assays, NMR spectroscopy, bioinformatic analyses, and MD simulations. Our data show that gatekeeper mutations destabilize the autoinhibitory conformation of the DFG motif locally and of the kinase globally, suggesting they impart gain-of-function by facilitating the kinase's ability to populate the active state.

Chinese herbal formula, modified Xianfang Huoming Yin, alleviates the inflammatory proliferation of rat synoviocytes induced by IL-1ß through regulating the migration and differentiation of T lymphocytes.

ETHNOPHARMACOLOGICAL RELEVANCE: Xianfang Huoming Yin (XFH) is a traditional Chinese herbal formula, which has the effect of clearing heat and detoxifying toxins, dispersing swellings, activating blood circulation, and relieving pain. It is usually applied to treat various autoimmune diseases, including Rheumatoid arthritis (RA). AIM OF THE STUDY: The migration of T lymphocytes plays an indispensable role in the pathogenesis of RA. Our previous studies demonstrated that modified Xianfang Huoming Yin (XFHM) could modulate the differentiation of T, B, and NK cells, and contribute to the restoration of immunologic balance. It also could downregulate the production of pro-inflammatory cytokines by regulating the activation of NF-κ B and JAK/STAT signaling pathways in the collagen-induced arthritis mouse model. In this study, we want to investigate whether XFHM has therapeutic effects on the inflammatory proliferation of rat fibroblast-like synovial cells (FLSs) by interfering with the migration of T lymphocytes in vitro experiments. MATERIALS AND METHODS: High performance liquid chromatography-electrospray ionization/mass spectrometer system was used to identify the constituents of the XFHM formula. A co-culture system of rat fibroblast-like synovial cells (RSC-364 cells) and peripheral blood lymphocytes stimulated by interleukin-1 beta (IL-1ß) was used as the cell model. IL-1ß inhibitor (IL-1ßRA) was used as a positive control medicine, and two concentrations (100 µg/mL and 250 µg/mL) of freeze-dried XFHM powder were used as intervention measure. The lymphocyte migration levels were analyzed by the Real-time xCELLigence analysis system after 24 h and 48 h of treatment. The percentage of CD3+CD4+ T cells and CD3+CD8+ T cells, and the apoptosis rate of FLSs were detected by flow cytometry. The morphology of RSC-364 cells was observed by hematoxylin-eosin staining. The protein expression of key factors for T cell differentiation and NF-κ B signaling pathway-related proteins in RSC-364 cells were examined by western-blot analysis. The migration-related cytokines levels of P-selectin, VCAM-1, and ICAM-1 in the supernatant were measured by enzyme-linked immunosorbent assay. RESULTS: Twenty-one different components in XFHM were identified. The migration CI index of T cells was significantly decreased in treatment with XFHM. XFHM also could significantly downregulate the levels r of CD3+CD4+T cells and CD3+CD8+T cells that migrated to the FLSs layer. Further study found that XFHM suppresses the production of P-selectin, VCAM-1, and ICAM-1. Meanwhile, it downregulated the protein levels of T-bet, ROR γ t, IKKα/ß, TRAF2, and NF-κ B p50, upregulated the expression of GATA-3 and alleviated synovial cells inflammation proliferation, contributing to the FLSs apoptosis. CONCLUSION: XFHM could attenuate the inflammation of synovium by inhibiting T lymphocyte cell migration, regulating differentiation of T cells through modulating the activation of the NF-κ B signaling pathway.

Multitask Deep Ensemble Prediction of Molecular Energetics in Solution: From Quantum Mechanics to Experimental Properties.

The past few years have witnessed significant advances in developing machine learning methods for molecular energetics predictions, including calculated electronic energies with high-level quantum mechanical methods and experimental properties, such as solvation free energy and logP. Typically, task-specific machine learning models are developed for distinct prediction tasks. In this work, we present a multitask deep ensemble model, sPhysNet-MT-ens5, which can simultaneously and accurately predict electronic energies of molecules in gas, water, and octanol phases, as well as transfer free energies at both calculated and experimental levels. On the calculated data set Frag20-solv-678k, which is developed in this work and contains 678,916 molecular conformations, up to 20 heavy atoms, and their properties calculated at B3LYP/6-31G* level of theory with continuum solvent models, sPhysNet-MT-ens5 predicts density functional theory (DFT)-level electronic energies directly from force field-optimized geometry within chemical accuracy. On the experimental data sets, sPhysNet-MT-ens5 achieves state-of-the-art performances, which predict both experimental hydration free energy with a RMSE of 0.620 kcal/mol on the FreeSolv data set and experimental logP with a RMSE of 0.393 on the PHYSPROP data set. Furthermore, sPhysNet-MT-ens5 also provides a reasonable estimation of model uncertainty which shows correlations with prediction error. Finally, by analyzing the atomic contributions of its predictions, we find that the developed deep learning model is aware of the chemical environment of each atom by assigning reasonable atomic contributions consistent with our chemical knowledge.

CovBinderInPDB: A Structure-Based Covalent Binder Database.

Covalent inhibition has emerged as a promising orthogonal approach for drug discovery, despite the significant challenge in achieving target specificity. To facilitate the structure-based rational design of target-specific covalent modulators, we developed an integrated computational protocol to curate covalent binders from the RCSB Protein Data Bank (PDB). Starting from the macromolecular crystallographic information files (mmCIF) in the PDB archive, covalent bond records, which indicate the side chain modification of amino acid residue by a covalent binder, were collected and cleaned. Then, residue-binder adducts, which are products of chemical reactions between targeted residues and covalent binders, were recovered with the help of the Chemical Component Dictionary in PDB. Finally, several strategies were employed to curate the pre-reaction forms of covalent binders from the adducts. Our curated CovBinderInPDB database contains 7375 covalent modifications in which 2189 unique covalent binders target nine types of amino acid residues (Cys, Lys, Ser, Asp, Glu, His, Met, Thr, and Tyr) from 3555 complex structures of 1170 unique protein chains. This database would set a solid foundation for developing and benchmarking computational strategies for covalent modulator design and is freely accessible at https://yzhang.hpc.nyu.edu/CovBinderInPDB.

Contralateral bridge fixation of freehand minimally invasive pedicle screws combined with unilateral MIS-TLIF vs. open TLIF in the treatment of multi-segmental lumbar degenerative diseases: A five years retrospective study and finite element analysis.

Objective: To evaluate the efficacy, safety, feasibility and biomechanical stability of contralateral bridge fixation of freehand minimally invasive pedicle screws (Freehand MIPS) combined with unilateral minimally invasive surgery-transforaminal lumbar interbody fusion (MIS-TLIF) (smile-face surgery) and open TLIF for the treatment of multi-segmental lumbar degenerative diseases (LDDs). Methods: From January 2013 to January 2016, clinical data of multi-segmental (2- or 3-level) LDDs receiving smile-face surgery or open TLIF were retrospectively collected and analyzed. The back and leg pain VAS and ODI were used to assess clinical outcomes preoperatively and postoperatively. The MacNab criteria were used to evaluate the satisfaction of patient. The disc height (DH), lumbar lordosis (LL) and segmental lordosis angle (SLA) were measured before and after surgery. We used patient's CT data to establish the finite element model of smile-face surgery and open TLIF, and analyze biomechanical stability of two methods. Results: Smile-face surgery group showed shorter operation time, shorter incision, less blood loss, shorter hospital stay than open TLIF (P < 0.05). The back VAS in smile-face surgery group was significantly lower than that in open TLIF immediately and 3 months after surgery, and no significant difference was observed 1 year, 2 years and 5 years after surgery. There was no significant difference in the leg pain VAS and ODI between both groups after surgery. No significant difference was observed between two groups in the DH, LL and SLA. At 5-year follow-up, grade I or II fusion was achieved in 99.00% (100/101) segments of smile-face surgery group and 97.67% (84/86) segments of open TLIF group according to Bridwell system. The complication rate of open TLIF was higher than that of smile-face surgery (24.32% vs. 0%, P < 0.01). After verification, the established finite element model can accurately simulate the biological structure of lumbar spine and there was no significant difference in biomechanical stability between two methods. Conclusions: Smile-face surgery has some advantages over open TLIF including smaller aggression, less blood loss, and lower cost, indicating that it is a good choice of treatment for multi-segmental LDDs. Both methods can achieve good biomechanical stability.

Clinical Application of a Modified Local Transposition Flap (Parallelogram Flap) Surgery in Repairing Fingertip Defects.

OBJECTIVE: Parallelogram flap was performed for transverse finger amputation with the loss of distal pulp, nails, and bone. This study aimed to compare the clinical effects of parallelogram flap, antegrade homodigital island flaps, and reverse digital artery island flaps in fingertip reconstruction. PATIENTS AND METHODS: From January 2017 to January 2021, clinical patient data with parallelogram flaps (78 cases), antegrade homodigital island flaps (78 cases), and reverse digital artery island flaps (78 cases) to repair fingertip defects were collected and analyzed. Two hundred thirty-four cases (234 fingers) were included in our study. All operations were performed by one surgical team. The operation time, 2-point discrimination, total active movement, and the Michigan Hand Questionnaire (MHQ) of the injured fingers were recorded to evaluate the therapeutic effect. RESULTS: Parallelogram flaps (group A), antegrade homodigital island flaps (group B), and reverse digital artery island flaps (group C) had survived postoperatively. The operative duration of group A is the shortest (A < B < C, P < 0.05). At the last 6-month follow-up, there was no difference with the 2-point discrimination of the palmar part of the flaps in group A and group B but better than group C (P < 0.05). There was no difference with the total active movement of injured figures in 3 groups (P > 0.05). The MHQ summary scores in group A were much higher than those in group B and group C (P < 0.05). Evaluation of the MHQ subscale performance showed that the overall hand function, activities of daily living, work performance, and pain score had no differences (P > 0.05), but aesthetics and satisfaction score was the highest in group A (A > B > C, P < 0.05). CONCLUSIONS: The reconstruction of transverse finger amputation using parallelogram flaps can achieve a shorter operation time, a more satisfying appearance. Parallelogram flaps and antegrade homodigital island flaps can both achieve a better sensory recovery. Parallelogram flaps is a better choice for reconstruction of transverse finger amputation with the loss of distal pulp, nails, and bone.

Biomechanical research of medial femoral circumflex vascularized bone-grafting in the treatment of early-to-mid osteonecrosis of the femoral head: a finite element analysis.

PURPOSE: Hip preservation therapy of early ONFH (Osteonecrosis of the femoral head) has emerged as one of the hot areas of research. We have optimized the procedure of traditional MFCVBG (medial femoral circumflex vascularized bone grafting) by using specialized surgical tools and used the finite element analysis to guide the implantation position of the bone flap during surgery and validate the biological mechanical stability of the modified MFCVBG. METHODS: This study was based on the data of a male patient with left hip (ARCO stage IIB, JIC type C) hormonal ONFH. Harris score (HHS), anteroposterior and lateral hip radiographs, frog position hip radiographs and SPECT/CT of femoral head flow imaging were performed postoperatively to evaluate clinical efficacy. The patient's CT data were used to establish upper femur finite element model of the normal group, osteonecrosis group and postoperative group, respectively. The force on the femoral structure of each group was analyzed under four different loads in the gait cycle of 0.5 times the body weight (0.5 G, standing on two feet), 2.75 G (standing on one foot), 4 G (walking with the middle foot on the ground) and 7 G (walking with the toe off the ground) to validate the biological mechanical stability of the modified MFCVBG, predict femoral head collapse risk, simulate of the different healing conditions of postoperative bone flap, and analyze the postoperative effect of non-ideal surgical model. RESULTS: According to the follow-up results, the bone flap and the inner wall of decompression channel healed well, no osteonecrosis progression, no local collapse or micro-fracture occurred in the femoral head, and the articular surface was intact and the necrosis was well repaired. According to the result of the finite element analysis, compared with the osteonecrosis group, the overall stress and displacement peak of the upper femur and the cortical bone stress peak of the femoral head in the postoperative group and normal group were significantly reducing; modified MFCVBG can significantly improve the biomechanical stability of necrotic femoral head and reduce the risk of femoral head collapse; there was no obvious abnormal stress distribution in the greater trochanter and intertrochanter region after the flap was removed; the bone flap of the complete removal of necrotic focus + long bone flap group was directly placed at the bottom of the decompression passage, and the bone flap cortical bone can provide substantial mechanical support; in theory, patients can try to reduce the load with crutches or walking aids and carry out appropriate flat activities to effectively promote the early postoperative recovery. CONCLUSIONS: The modified MFCVBG resulted in good efficacy, safety and feasibility. The necrotic focus should be completely removed during the operation, and the long bone flap should be placed directly under the subchondral bone. For patients with better bone healing ability, a more positive attitude can be taken to promote early postoperative weight-bearing.

The Herbal Combination of Radix astragali, Radix angelicae sinensis, and Caulis lonicerae Regulates the Functions of Type 2 Innate Lymphocytes and Macrophages Contributing to the Resolution of Collagen-Induced Arthritis.

Type 2 innate lymphocytes (ILC2s), promoting inflammation resolution, was a potential target for rheumatoid arthritis (RA) treatment. Our previous studies confirmed that R. astragali and R. angelicae sinensis could intervene in immunologic balance of T lymphocytes. C. lonicerae also have anti-inflammatory therapeutic effects. In this study, the possible molecular mechanisms of the combination of these three herbs for the functions of ILC2s and macrophages contributing to the resolution of collagen-induced arthritis (CIA) were studied. Therefore, we used R. astragali, R. angelicae sinensis, and C. lonicerae as treatment. The synovial inflammation and articular cartilage destruction were alleviated after herbal treatment. The percentages of ILC2s and Tregs increased significantly. The differentiation of Th17 cells and the secretion of IL-17 and IFN-γ significantly decreased. In addition, treatment by the combination of these three herbs could increase the level of anti-inflammatory cytokine IL-4 secreted, active the STAT6 signaling pathway, and then contribute to the transformation of M1 macrophages to M2 phenotype. The combination of the three herbs could promote inflammation resolution of synovial tissue by regulating ILC2s immune response network. The synergistic effects of three drugs were superior to the combination of R. astragali and R. angelicae sinensis or C. lonicerae alone.

Protein-Ligand Docking in the Machine-Learning Era.

Molecular docking plays a significant role in early-stage drug discovery, from structure-based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive power is critically dependent on the protein-ligand scoring function. In this review, we give a broad overview of recent scoring function development, as well as the docking-based applications in drug discovery. We outline the strategies and resources available for structure-based VS and discuss the assessment and development of classical and machine learning protein-ligand scoring functions. In particular, we highlight the recent progress of machine learning scoring function ranging from descriptor-based models to deep learning approaches. We also discuss the general workflow and docking protocols of structure-based VS, such as structure preparation, binding site detection, docking strategies, and post-docking filter/re-scoring, as well as a case study on the large-scale docking-based VS test on the LIT-PCBA data set.

Parallelogram flap versus homodigital island flap in the treatment of fingertip defects with bone exposure: a prospective controlled study.

PURPOSE: A modified local transposition flap (we call it "parallelogram flap") surgery was performed for fingertip injuries. This study aimed to compare the clinical effects of parallelogram flap and homodigital island flaps in fingertip reconstruction. METHODS: The study collected patients who underwent parallelogram transposition flaps and homodigital island flaps to repair fingertip defects from 2019 to 2021. 150 cases (150 fingers) were included in our study. All operations were performed by one surgical team. Record the operation time, two-point discrimination (2PD), Total Active Movement (TAM) and the MHQ (Michigan Hand Questionnaire) of the injured fingers to evaluate the therapeutic effect. RESULTS: All parallelogram (Group A) and homodigital island flap (Group B) had survived postoperatively. The operative duration of Group A (31.2 ± 3.3 min) is shorter than Group B (97.8 ± 6.1 min) (P < 0.05). At the 6-month follow-up, there was no difference with the two-point discrimination (2PD) of the palmar part of the flaps and the Total Active Movement (TAM) of injured figures in Group A and Group B. The MHQ summary scores in Group A (94.29 ± 3.14) were much higher than in Group B (91.73 ± 3.41) (P < 0.05). Evaluation of the MHQ subscale performance showed that the overall hand function, activities of daily living, work performance and pain score had no differences(P > 0.05), but aesthetics (92.15 ± 7.16) and satisfaction (92.45 ± 5.61) score in Group A was higher than aesthetics (86.56 ± 5.60) and satisfaction (86.72 ± 8.21) score in Group B (P < 0.05 for both). CONCLUSIONS: The reconstruction using parallelogram flaps is a easier and more versatile treatment with better functions, less morbidity and better aesthetics. This method is a better choice for reconstruction of fingertip injury.