Target Protein Binding Research Articles

Designed endocytosis-inducing proteins degrade targets and amplify signals.

Endocytosis and lysosomal trafficking of cell surface receptors can be triggered by endogenous ligands. Therapeutic approaches such as lysosome-targeting chimaeras1,2 (LYTACs) and cytokine receptor-targeting chimeras3 (KineTACs) have used this to target specific proteins for degradation by fusing modified native ligands to target binding proteins. Although powerful, these approaches can be limited by competition with native ligands and requirements for chemical modification that limit genetic encodability and can complicate manufacturing, and, more generally, there may be no native ligands that stimulate endocytosis through a given receptor. Here we describe computational design approaches for endocytosis-triggering binding proteins (EndoTags) that overcome these challenges. We present EndoTags for insulin-like growth factor 2 receptor (IGF2R) and asialoglycoprotein receptor (ASGPR), sortilin and transferrin receptors, and show that fusing these tags to soluble or transmembrane target protein binders leads to lysosomal trafficking and target degradation. As these receptors have different tissue distributions, the different EndoTags could enable targeting of degradation to different tissues. EndoTag fusion to a PD-L1 antibody considerably increases efficacy in a mouse tumour model compared to antibody alone. The modularity and genetic encodability of EndoTags enables AND gate control for higher-specificitytargeted degradation, and the localized secretion of degraders from engineered cells. By promoting endocytosis, EndoTag fusion increases signalling through an engineered ligand-receptor system by nearly 100-fold. EndoTags have considerable therapeutic potential as targeted degradation inducers, signalling activators for endocytosis-dependent pathways, and cellular uptake inducers for targeted antibody-drug and antibody-RNA conjugates.

A novel Affi-Cova magnetic nanoparticles for one-step covalent immobilization of His-tagged enzyme directly from crude cell lysate

Owing to the rapid advancement of in vitro synthetic biology, functional carriers capable of covalently binding target proteins from crude lysates under mild conditions have garnered escalating attention. Herein, a magnetic nanoparticle with affinity/covalent bifunction (MNP@Affi-Cova) was developed for the direct covalent immobilization of the recombinant enzyme of His-tagged birA (r-birA) from crude cell lysates in a single step. This innovative approach is attributed to the presence of chelated Ni2+ ions and epoxy groups on the surface of the beads. The fabricated magnetic nanoparticles were characterized by SEM, FT-IR spectrum, and zeta potential. The application conditions and stability of the MNP@Affi-Cova beads were systematically evaluated. Notably, the MNP@Affi-Cova beads exhibited a covalent capture efficiency of 91.25 μg r-birA/mg beads from a cell lysate supernatant containing 2.62 mg/mL crude protein. The immobilized r-birA exhibited significantly enhanced pH and thermal stability compared to the free counterpart. Additionally, the reusability of the immobilized r-birA on MNP@Affi-Cova demonstrated the retention of 76.1 % of its initial activity over ten cycles. These results suggest that the MNP@Affi-Cova presents considerable potential as a support for the covalent immobilization of recombinant His-tagged enzymes directly from crude lysates, thereby circumventing the labor-intensive purification process typically required before enzyme immobilization.

Predicting monoclonal antibody binding sequences from a sparse sampling of all possible sequences

Previous work has shown that binding of target proteins to a sparse, unbiased sample of all possible peptide sequences is sufficient to train a machine learning model that can then predict, with statistically high accuracy, target binding to any possible peptide sequence of similar length. Here, highly sequence-specific molecular recognition is explored by measuring binding of 8 monoclonal antibodies (mAbs) with specific linear cognate epitopes to an array containing 121,715 near-random sequences about 10 residues in length. Network models trained on resulting sequence-binding values are used to predict the binding of each mAb to its cognate sequence and to an in silico generated one million random sequences. The model always ranks the binding of the cognate sequence in the top 100 sequences, and for 6 of the 8 mAbs, the cognate sequence ranks in the top ten. Practically, this approach has potential utility in selecting highly specific mAbs for therapeutics or diagnostics. More fundamentally, this demonstrates that very sparse random sampling of a large amino acid sequence spaces is sufficient to generate comprehensive models predictive of highly specific molecular recognition.

One-Pot Detection of Proteins Using a Two-Way Extension-Based Assay with Cas12a.

Protein biomarkers are an important class of biomarkers in disease diagnosis and are traditionally detected by enzyme-linked immunosorbent assay and mass spectrometry, which involve multiple steps and a complex workflow. In recent years, many CRISPR-Cas12a-based methods for protein detection have been developed; however, most of them have not overcome the workflow complications observed in traditional assays, limiting their applicability in point-of-care testing. In this work, we designed a single-step, one-pot, and proximity-based isothermal immunoassay integrating CRISPR Cas12a for homogeneous protein target detection with a simplified workflow and high sensitivity. Probes consisting of different binders (small molecule, aptamer, and antibody) conjugated with oligonucleotides undergo two-way extension upon binding to the protein targets, leading to downstream DNA amplification by a pair of nicking enzymes and polymerases to generate target sequences for Cas12a signal generation. We used the streptavidin-biotin model to demonstrate the design of our assay and proved that all three elements of protein detection (target protein binding, DNA amplification, and Cas12a signal generation) could coexist in one pot and proceed isothermally in a single buffer system at a low reaction volume of 10 μL. The plug-and-play applicability of our assay has been successfully demonstrated using four different protein targets, streptavidin, PDGF-BB, antidigoxigenin antibody, and IFNγ, with the limit of detection ranging from fM to pM.

Synthesis, characterization, and molecular docking studies of novel hippuric acid anhydrides as potential antiurolithic, analgesic and free radical scavenging agents

Hippuric acid is a biotransformation product in humans which is excreted through urine. Dietary intake of phenolic compounds increases its concentration in urine. Hippuric acid is experimentally proved to be a regulator of calcium oxalate super saturation in human urine and has a solvent effect on oxalate salts. Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used analgesics employed in associated renal colic of urolithiasis. The objective of the present study was to chemically link hippuric acid through anhydride linkage to various NSAIDs to synthesize potential mutual prodrugs for urolithiasis and associated renal colic. Hippuric acid was linked to eleven NSAIDs through anhydride linkage by first synthesizing hippuryl chloride using oxalyl chloride as chlorinating agent, followed by its reaction with sodium salts of NSAIDs. Structures of obtained compounds were elucidated using UV spectrophotometry, FTIR spectrometry, 1H NMR and C-13 NMR spectrometry. Synthesized compounds were evaluated for in vitro antioxidant, in vivo acute toxicity, in vivo antiurolithic, in vivo analgesic and in vitro hydrolysis studies. Molecular docking analysis on TNF-α and COX-2 was carried out to determine target protein binding. Synthesized compounds showed stability at acidic pH which indicate potential gastro protective effect of synthesized conjugates. Compounds P9 an P6 showed maximum in vivo antiurolithic activity while P9 and P8 showed maximum in vitro antioxidant activity. All the conjugates except P2 showed significant analgesic activity which show that conjugation of hippuric acid to NSAIDs did not result in loss of analgesic potential. Docking studies showed better affinity with TNF-α as compared to COX-2.

Gibbs Free Energy and Enthalpy–Entropy Compensation in Protein–Ligand Interactions

The thermodynamics of protein–ligand interactions seems to be associated with a narrow range of Gibbs free energy. As a consequence, a linear enthalpy–entropy relationship showing an apparent enthalpy–entropy compensation (EEC) is frequently associated with protein–ligand interactions. When looking for the most negative values of ∆H to gain affinity, the entropy compensation gives rise to a barely noticeable increase in affinity, therefore negatively affecting the design and discovery of new and more efficient drugs capable of binding protein targets with a higher affinity. Originally attributed to experimental errors, compensation between ∆H and T∆S values is an observable fact, although its molecular origin has remained obscure and controversial. The thermodynamic parameters of a protein–ligand interaction can be interpreted in terms of the changes in molecular weak interactions as well as in vibrational, rotational, and translational energy levels. However, a molecular explanation to an EEC rendering a linear enthalpy–entropy relationship is still lacking. Herein, we show the results of a data search of ∆G values of 3025 protein–ligand interactions and 2558 “in vivo” ligand concentrations from the Protein Data Bank database and the Metabolome Database (2020). These results suggest that the EEC may be plausibly explained as a consequence of the narrow range of ∆G associated with protein–ligand interactions. The Gaussian distribution of the ∆G values matches very well with that of ligands. These results suggest the hypothesis that the set of ∆G values for the protein–ligand interactions is the result of the evolution of proteins. The conformation versatility of present proteins and the exchange of thousands (even millions) of minute amounts of energy with the environment may have functioned as a homeostatic mechanism to make the ∆G of proteins adaptive to changes in the availability of ligands and therefore achieve the maximum regulatory capacity of the protein function. Finally, plausible strategies to avoid the EEC consequences are suggested.

Pharmacophore modelling based virtual screening and molecular dynamics identified the novel inhibitors and drug targets against Waddlia chondrophila

Waddlia chondrophila is a possible cause of fetal death in humans. This Chlamydia-related bacterium is an emergent pathogen that causes human miscarriages and ruminant abortions, which results in financial losses. Despite the years of efforts, the underlying mechanism behind the pathogenesis of W. chondrophila is little known which hindered the development of novel treatment options. In the framework of current study, computational approaches were used to identify novel inhibitors (phytocompounds) and drug targets against W. chondrophila. At first, RNA polymerase sigma factor SigA and 3-deoxy-d-manno-octulosonic acid transferase were identified through subtractive proteomics pipeline. Afterwards, extensive docking and simulation analyses were conducted to optimize potentially novel phytocompounds by assessing their binding affinity to target proteins. A 100ns molecular dynamics simulation well complimented the compound's binding affinity and indicated strong stability of predicted compounds at the docked site. The calculation of binding free energies with MMGBSA corroborated the significant binding affinity between phytocompounds and target protein binding sites. The proposed phytocompounds may be a viable treatment option for patients infected with W. chondrophila; however, further research is required to ensure their safety.

Hybrid Caffeic Acid-Based DHFR Inhibitors as Novel Antimicrobial and Anticancer Agents.

A novel series of 1,2,4-triazole analogues of caffeic acid was designed, synthesized, characterized, and assessed for their capacity to inhibit DHFR, as well as their anticancer and antimicrobial properties. A molecular docking analysis was conducted on DHFR, utilizing PDB IDs 1U72 and 2W9S, aiming to design anticancer and antimicrobial drugs, respectively. Among all the synthesized derivatives, compound CTh7 demonstrated the highest potency as a DHFR inhibitor, with an IC50 value of 0.15 μM. Additionally, it exhibited significant cytotoxic properties, with an IC50 value of 8.53 µM. The molecular docking analysis of the CTh7 compound revealed that it forms strong interactions with key residues of homo sapiens DHFR such as Glu30, Phe34, Tyr121, Ile16, Val115, and Phe31 within the target protein binding site and displayed excellent docking scores and binding energy (-9.9; -70.38 kcal/mol). Additionally, synthesized compounds were screened for antimicrobial properties, revealing significant antimicrobial potential against bacterial strains and moderate effects against fungal strains. Specifically, compound CTh3 exhibited notable antibacterial efficacy against Staphylococcus aureus (MIC = 5 µM). Similarly, compound CTh4 demonstrated significant antibacterial activity against both Escherichia coli and Pseudomonas aeruginosa, with MIC values of 5 µM for each. A docking analysis of the most active antimicrobial compound CTh3 revealed that it forms hydrogen bonds with Thr121 and Asn18, a π-cation bond with Phe92, and a salt bridge with the polar residue Asp27.

Delivery of endolysin across outer membrane of Gram-negative bacteria using translocation domain of botulinum neurotoxin

The emergence of multidrug-resistant pathogens has outpaced the development of new antibiotics, leading to renewed interest in endolysins. Endolysins have been investigated as novel biocontrol agents for Gram-positive bacteria. However, their efficacy against Gram-negative species is limited by the barrier presented by their outer membrane, which prevents endolysin access to the peptidoglycan substrate. Here, we used the translocation domain of botulinum neurotoxin to deliver endolysin across the outer membrane of Gram-negative bacteria. The translocation domain selectively interacts with and penetrates membranes composed of anionic lipids, which have been used in nature to deliver various proteins into animal cells. In addition to the botulinum neurotoxin translocation domain, we have fused bacteriophage-derived receptor binding protein to endolysins. This allows the attached protein to efficiently bind to a broad spectrum of Gram-negative bacteria. By attaching these target-binding and translocation machineries to endolysins, we aimed to develop an engineered endolysin with broad-spectrum targeting and enhanced antibacterial activity against Gram-negative species. To validate our strategy, we designed engineered endolysins using two well-known endolysins, T5 and LysPA26, and tested them against 23 strains from six species of Gram-negative bacteria, confirming that our machinery can act broadly. In particular, we observed a 2.32 log reduction in 30 min with only 0.5 µM against an Acinetobacter baumannii isolate. We also used the SpyTag/SpyCatcher system to easily attach target-binding proteins, thereby improving its target-binding ability. Overall, our newly developed endolysin engineering strategy may be a promising approach to control multidrug-resistant Gram-negative bacterial strains.

Not All Binding Sites Are Equal: Site Determination and Folding State Analysis of Gas-Phase Protein-Metallodrug Adducts.

Modern approaches in metallodrug research focus on compounds that bind protein targets rather than DNA. However, the identification of protein targets and binding sites is challenging. Using intact mass spectrometry and proteomics, we investigated the binding of the antimetastatic agent RAPTA-C to the model proteins ubiquitin, cytochrome c, lysozyme, and myoglobin. Binding to cytochrome c and lysozyme was negligible. However, ubiquitin bound up to three Ru moieties, two of which were localized at Met1 and His68 as [Ru(cym)], and [Ru(cym)] or [Ru(cym)(PTA)] adducts, respectively. Myoglobin bound up to four [Ru(cym)(PTA)] moieties and five sites were identified at His24, His36, His64, His81/82 and His113. Collision-induced unfolding (CIU) studies via ion-mobility mass spectrometry allowed measuring protein folding as a function of collisional activation. CIU of protein-RAPTA-C adducts showed binding of [Ru(cym)] to Met1 caused a significant compaction of ubiquitin, likely from N-terminal S-Ru-N chelation, while binding of [Ru(cym)(PTA)] to His residues of ubiquitin or myoglobin induced a smaller effect. Interestingly, the folded state of ubiquitin formed by His functionalization was more stable than Met1 metalation. The data suggests that selective metalation of amino acids at different positions on the protein impacts the conformation and potentially the biological activity of anticancer compounds.

Discovery and Characterization of a Novel Cereblon-Recruiting PRC1 Bridged PROTAC Degrader.

Bridged PROTAC is a novel protein complex degrader strategy that exploits the target protein's binding partner to degrade undruggable proteins by inducing proximity to an E3 ubiquitin ligase. In this study, we discovered for the first time that cereblon (CRBN) can be employed for the bridged PROTAC approach and report the first-in-class CRBN-recruiting and EED-binding polycomb repressive complex 1 (PRC1) degrader, compound 1 (MS181). We show that 1 induces preferential degradation of PRC1 components, BMI1 and RING1B, in an EED-, CRBN-, and ubiquitin-proteosome system (UPS)-dependent manner. Compound 1 also has superior antiproliferative activity in multiple metastatic cancer cell lines over EED-binding PRC2 degraders and can be efficacious in VHL-defective cancer cells. Altogether, compound 1 is a valuable chemical biology tool to study the role of PRC1 in cancer. Importantly, we show that CRBN can be utilized to develop bridged PROTACs, expanding the bridged PROTAC technology for degrading undruggable proteins.

Molecular Imprinting-Based SERS Detection Strategy for the Large-Size Protein Quantitation and Curbing Non-Specific Recognition.

Molecular imprinting-based surface-enhanced Raman scattering (MI-SERS) sensors have shown remarkable potential from an academic standpoint. However, their practical applications, especially in the detection of large-size protein (≥10 nm), face challenges due to the lack of versatile sensing strategies and nonspecific fouling of matrix species. Herein, we propose a Raman reporter inspector mechanism (RRIM) implemented on a protein-imprinted polydopamine (PDA) layer coated on the SERS active substrate. In the RRIM, after large-size protein recognition, the permeability of the PDA imprinted cavities undergoes changes that are scrutinized by Raman reporter molecules. Target proteins can specifically bind and fully occupy the imprinted cavities, whereas matrix species cannot. Then, Raman reporter molecules with suitable size are introduced to serve as both inspectors of the recognition status and inducers of the SERS signal, which can only penetrate through the vacant and nonspecifically filled cavities. Consequently, changes in the SERS signal exclusively originate from the specific binding of target proteins, while the nonspecific recognition of matrix species is curbed. The RRIM enables reproducible quantitation of the large-size cyanobacteria-specific protein model (≥10 nm), phycocyanin, at the level down to 2.6 × 10-3 μg L-1. Finally, the practical applicability of the RRIM is confirmed by accurately analyzing crude urban waterway samples over 21 min without any pretreatment.

Screening of Potential Phytochemicals for the Identified Candidate Virulence Proteins in Enterobacter huaxiensis

ABSTRACT: Enterobacter huaxiensis, a novel gram-negative bacterium of the family Enterobacteriaceae, was recovered from the blood of the patients at West China Hospital. The present study aims to predict potential lead molecules against the identified virulence-associated antibiotic-resistant protein for drug designing. Two virulence-associated antibiotic-resistance proteins belonging to the OqxAB efflux protein family of the RND superfamily were identified in the pathogen using bioinformatics tools/databases. Based on the structure prediction by homology modeling and validations, the RND transporter permease subunit, OqxB was selected as the potential target for lead identification. The binding pocket of the target protein was calculated using CASTp. A total of 204 phytochemicals were screened virtually to obtain compounds that had better binding affinity, drug-likeness and pharmacokinetic potential to be used as safe ligands against the target protein. Among these, Chrysoeriol, Isopimaric acid, Baicalein and Biochanin A were found to be within the permissible range of Lipinski rule of five for drug-likeness, possessing better ADMET properties, and lower target-protein binding energy (less than -8.0 kcal/mol). Ligand-protein docking showed stable non-covalent interactions between active site residues and ligands. Thus, these compounds may be considered potential inhibitors of the target protein that may inactivate the efflux pump and restore antibiotic sensitivity.

Chimeric Antigen Receptor (CAR)-T Cell Therapy for Non-Hodgkin's Lymphoma.

This review focuses on the use of chimeric antigen receptor (CAR)-T cell therapy to treat non-Hodgkin's lymphoma (NHL), a classification of heterogeneous malignant neoplasms of the lymphoid tissue. Despite various conventional and multidrug chemotherapies, the poor prognosis for NHL patients remains and has prompted the utilization of groundbreaking personalized therapies such as CAR-T cells. CAR-T cells are T cells engineered to express a CAR that enables T cells to specifically lyse tumor cells with extracellular expression of a tumor antigen of choice. A CAR is composed of an extracellular antibody fragment or target protein binding domain that is conjugated to activating intracellular signaling motifs common to T cells. In general, CAR-T cell therapies for NHL are designed to recognize cellular markers ubiquitously expressed on B cells such as CD19+, CD20+, and CD22+. Clinical trials using CAR-T cells such as ZUMA-7 and TRANSFORM demonstrated promising results compared to standard of care and ultimately led to FDA approval for the treatment of relapsed/refractory NHL. Despite the success of CAR-T therapy for NHL, challenges include adverse side effects as well as extrinsic and intrinsic mechanisms of tumor resistance that lead to suboptimal outcomes. Overall, CAR-T cell therapies have improved clinical outcomes in NHL patients and generated optimism around their future applications.

Oxyepiberberine from the Active Site of Coptidis Rhizoma Inhibits Lung Adenocarcinoma by Regulating SRC-related Pathways in vivo

Background Huanglian (HL), also known as Coptis chinensis Franch., was initially documented in “Sheng Nong’s Herbal Classic” as a high-quality product used to cure ailments such as fever, indigestion, bloating, nausea, dysentery, diarrhea, abdominal pain, and tuberculosis. Nowadays, it is extensively employed in clinical settings to alleviate pulmonary diseases, like tuberculosis, lobular lung disease, and pulmonary abscess, and is worth exploring further. Nevertheless, there is limited research on the precise advancements of anti-lung adenocarcinoma (LUAD). Objectives Using biological experiments and network pharmacology, the objective of this research was to investigate the most effective parts and chemical constituents of C. chinensis against LUAD and ascertain the probable targets and pathways. Materials and Methods First, an MTT experiment verified the impact of each part on A549 and BEAS-2B cells. High performance liquid chromatography (HPLC) was then used to identify the chemical components of the effective substance in C. chinensis against LUAD. Then, network pharmacology was used to screen potential pathways and binding target proteins. Finally, a subcutaneous tumor model was established in mice using LLC cells to observe the effects of the effective components of C. chinensis against LUAD in tumor-bearing mice. Results The MTT assay demonstrated the efficacy of oxyepiberberine (OPB) as an anti-LUAD compound with minimal toxicity and side effects. According to the results of network pharmacology and molecular docking, SRC appears to be the primary target of C. chinensis active substance against LUAD. In vivo experiments revealed that the OPB group exhibited lowered toxicity and side effects. Additionally, the density of tumor cells decreased and the nuclei were destroyed in OPB groups of tumor tissues. Finally, OPB could regulate apoptosis, migration, and protein expression significantly related to the SRC pathway in tumor cells. Conclusion Our research reveals the anti-LUAD properties of C. chinensis through a combination of experimentation and network analysis. These findings establish a theoretical foundation for C. chinensis as a clinical antitumor agent. Furthermore, our work provided an essential groundwork for further investigations into the medicinal properties of C. chinensis.

PAR-dCLIP: Enabling detection of RNA binding protein target transcripts bound at 5' termini through the incorporation of a decapping step.

RNA binding proteins (RBPs) are responsible for facilitating a wealth of post-transcriptional gene regulatory functions. The role of an RBP on regulated transcripts can be investigated through a pull-down of the RBP and high-throughput sequencing (HTS) of the associated transcripts. PhotoactivatableRibonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), is one such pull-down method that isolates, detects, and sequences the cDNA of RBP-associated transcripts. PAR-CLIP relies on a photoactivatable ribonucleoside analogue, 4-thiouridine, to facilitate covalent RNA-protein crosslinks at 365nm. These crosslinks permit stringent wash conditions and result in T to C mismatch incorporations during reverse transcription, a unique parameter for the computational analysis of high-confidence binding sites. However, until now, RBPs that bind at the 5'-termini of RNAs have been uniquely restricted from the full potential bandwidth of autoradiographic detection and HTS library preparation. The 5'-termini of RNAs are highly modified, including the most common Pol-II derived modification: the 7-methylguanosine (m7G) cap. In the conventional PAR-CLIP protocol, cap-binding proteins protect the m7G cap from the RNase treatment that generates the necessary substrate for autoradiographic detection and 5' adapter ligation-thus occluding entire populations of RNA from visualization and HTS. Here, we introduce decapping-PAR-CLIP or PAR-dCLIP. We incorporate a decapping step into the PAR-CLIP protocol to generate the necessary substrate to sequence m7G capped transcripts. While PAR-dCLIP was originally targeted towards known m7G-cap binding proteins, we argue that all RBP inquiries, and particularly those suspected to regulate translation, should incorporate this decapping step to ensure that all possible populations of bound transcripts are identified.

M2 macrophage exosome-derived lncRNA AK083884 protects mice from CVB3-induced viral myocarditis through regulating PKM2/HIF-1α axis mediated metabolic reprogramming of macrophages

Viral myocarditis (VM) is a clinically common inflammatory disease. Accumulating literature has indicated that M2 macrophages protect mice from Coxsackievirus B3 (CVB3)-induced VM. However, mechanisms that underlie M2 macrophages alleviating myocardial inflammation remain largely undefined. We found that M2 macrophage-derived exosomes (M2-Exo) can effectively attenuate VM. The long non-coding RNA (lncRNA) AK083884 in M2-Exo was found to be involved in the regulation of macrophage polarization by exosome lncRNA sequencing combined with in vitro functional assays. M2-Exo-derived AK083884 promotes macrophage M2 polarization and protects mice from CVB3-induced VM. Furthermore, we identified pyruvate kinase M2 (PKM2) as a protein target binding to AK083884 and found that PKM2 knockdown could promote macrophages to polarize to M2 phenotype. Intriguingly, functional assay revealed that downregulation of AK083884 promotes metabolic reprogramming in macrophages. In addition, co-immunoprecipitation was performed to reveal AK083884 could interact with PKM2 and inhibition of AK083884 can facilitate the binding of PKM2 and HIF-1α. Collectively, our findings uncovered an important role of M2-Exo-derived AK083884 in the regulation of macrophage polarization through metabolic reprogramming, identified a new participant in the development of VM and provided a potential clinically important therapeutic target.

Target-Based Design, Synthesis, and Biological Evaluation of Novel 1,2,4-Triazolone Derivatives as Potential nAChR Modulators.

Novel agrochemicals have been successfully developed using target-based drug design (TBDD). To discover a novel, efficient, and highly selective nicotinic insecticide candidate, we developed a unified pharmacological model using TBDD by studying the binding modes of 11 nicotinic acetylcholine receptor (nAChR) modulators with acetylcholine binding protein (AChBP) targets for the first time. This model was used to design and develop a series of 1,2,4-triazolone derivatives. Bioassays demonstrated excellent insecticidal activities against Aphis glycines of compounds 4k (LC50 = 4.95 mg/L) and 4q (LC50 = 3.17 mg/L), and low toxicities to Apis mellifera. Additionally, compound 4q was stably bound to Aplysia californica AChBP, which was consistent with the pharmacological model obtained via molecular docking and molecular dynamics simulations. Therefore, compound 4q could be a potential lead candidate targeting nAChR. The explicit pharmacological model of nAChR modulators with Ac-AChBP in this study may facilitate the future rational design of eco-friendly nicotinic insecticides.

A Comparative Study of Binding Interactions of Natural Flavonoids and Conventional Drug Donepezil for Multiple Alzheimer's Disease Targets Using In silico Approach

Background: Alzheimer's disease (AD) is one of the major causes of morbidity, affecting more than 36 million population worldwide. Current anti-AD treatments result in limited therapeutic outcomes owing to the complexity of the disease. Some natural promising herbal drugs and phytoconstituents utilized as an alternative treatment for AD have been reported by several researchers for their neuroprotective action. Objective: This study aimed at carrying out molecular docking studies of selected promising flavonoids such as curcumin, quercetin, bilobalide, ferulic acid, reseveratrol for their molecular interactions with multiple AD target proteins and further compare the data with the standard acetylcholine esterase inhibitor drug donepezil. Methods: The molecular docking interactions were studied between the selected actives and the AD target proteins acetylcholine esterase, butyrylcholine esterase, and tau protein using the AutoDock Vina software. The Swiss ADME approach performed prediction of the ADME properties. Binding interactions of the ligands at the target protein binding sites were examined using the Discovery Studio Visualizer 2021. Results: The binding energy for quercetin in the active site of the selected target enzymes acetylcholine esterase, butyrylcholine esterase, and tau protein was -9.5 , -7.8 , and -8.2 kcal/mol, respectively which was much greater than other flavonoids and comparable to the standard drug donepezil binding energy - 10.3, -7.5,-7.9 kcal/mol respectively. Conclusion: This work focuses on recognizing structural features and comparing selected flavonoids and standard acetylcholine esterase (AChEs) inhibitors for molecular docking with three primary targets of AD, namely AChEs, Butyrylcholine esterase, and tau protein. This in silico study concluded that quercetin had significant docking interactions and good pharmacokinetic features, making it a potential therapeutic candidate for the treatment of AD.

High-throughput virtual screening approach and dynamic simulation of natural compounds as target inhibitors of BACE1 in Alzheimer's disease

Background Beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) protein holds significance in the development of Alzheimer’s disease (AD). This protein is highly expressed in the central nervous system, playing a significant role in the conversion of amyloid precursor protein (APP) into amyloid-beta peptides. The primary objective of the current study was to perform in silico inhibition investigations on this protein, utilizing computational methodologies such as molecular docking and molecular dynamics, to identify novel inhibitors with potential against BACE1. Our focus was on targeting the active site of BACE1, aiming to discover optimal interactions between the ligands and key residues of the target protein. Methods The natural compounds inhibitors data was carefully reviewed from the literature review articles. Molecular docking was conducted using AutoDock Vina with an active site defined by CB-Dock2. We assessed drug-likeness and toxicity using Lipinski’s rule of fives via SwissADME and the ProTox-II web server. Interaction visualization was facilitated using Discovery Studio, while molecular dynamics simulations were performed for 100 nanoseconds with hinokiflavone and BACE1 using Schrodinger LLC Desmond software. Results The molecular docking results showed promising binding affinities and the best binding free energy values were selected, and after conducting Lipinski’s rule of five using SwissADME as well as predicting toxicity using ProTox-II, only one molecule, hinokiflavone was filtered and succeeded in all the analyses to be a potential candidate. Molecular docking results were supported by molecular dynamics simulation. These results demonstrate the stability of the compound in the target protein binding site. Conclusions Finally, these obtained outcomes represent a strong lead to developing promising new natural compound inhibitors against BACE1. For future works, it is essential to concentrate on further experimental validation to ensure the effectiveness of the proposed approach.