Active Site Of Protein Research Articles

Desing and In Silico Validation of Vitamin B5 and Its Derivatives As A Potential Target Against Cyclophilin A (CyPA)

The title molecule (N-(2,4-dihydroxy-3,3-dimethylbutyryl)b-alanine), DDBBA and its derivatives were selected for theoretical investigations viz geometry optimization, ADME profiling, binding affinity using quantum-mechanical calculations and modelling simulation tools. Geometry optimization by Gaussian 09 program revealed the stability and electrophilic nature of the investigated molecules. In order to depict the charge density distributions that may be related to biological activity, the contour maps of HOMO-LUMO as well as the associated chemical descriptors such as chemical potential (µ), electronegativity (χ), electrophilicity (ω), hardness (η) and softness (σ) were explored. Utilizing molecular docking, the antiviral, antibacterial, and anticancer activities was examined. The docked molecules showed strong propensity for binding to 2HQ6 cancer protein active sites. Vit B5-CH=CF2 and VitB5-CCl3 showed lowest binding energies (-5.861 and -5.478 kcal/mol) and low inhibition constant values (1.43 M). Studies on the (NBO) natural bond orbital, the Mulliken population, and the Fukui function were all analyzed. Further, the interactions between the derivatives and other molecules were studied using Hirshfeld surface analysis.

Pharmacophore-based virtual screening, molecular docking, and molecular dynamics investigation for the identification of novel, marine aromatase inhibitors.

Breast cancer remains a leading cause of mortality among women worldwide. Our current research focuses on identifying effective therapeutic agents by targeting the human aromatase enzyme. Aromatase inhibitors (AIs) have been effective in treating postmenopausal breast cancer but face challenges such as drug resistance and long-term side effects like cognitive decline and osteoporosis. Natural products, especially from marine organisms, are emerging as potential sources for new drug candidates due to their structural diversity and pharmacological properties. This study aims to discover marine natural products capable of inhibiting human aromatase by combining ligand-based and structure-based pharmacophore models for virtual screening against the Comprehensive Marine Natural Products Database. From the initial virtual screening of more than 31,000 compounds, 1,385 marine natural products were identified as possible candidates. Following initial molecular docking analysis, only four compounds managed to pass the criteria this research has introduced to confirm strong binding affinity to aromatase. All four compounds yielded acceptable binding affinities, with CMPND 27987 having the highest -10.1kcal/mol. All four hits were subjected to molecular dynamics, and CMPND 27987 was further confirmed to be the most stable at the protein's active site, with an MM-GBSA free binding energy of -27.75kcal/mol. Our in silico studies indicate that CMPND 27987 interacts effectively within the binding site of the human aromatase, maintaining high affinity and stability. Based on these findings, we propose that CMPND 27987 could hold significant potential for further lead optimization and drug development.

In Silico Efficacy of Oleic Acid, n-Hexanoic acid, and Epiglobulol Obtained from Conocarpus Lancifolius against Class D β-lactamases

Introduction: Antimicrobial resistance poses an escalating global challenge, compounded by the sluggish pace of new antibiotic discovery. Objectives: This study undertook an in silico analysis of phytochemicals derived from Conocarpus lancifolius, a local plant in the Jazan region of Saudi Arabia, to investigate potential antibacterial agents. Methods: The 3D crystallographic structure of OXA-48 was sourced from the RCSB protein databank (PDBID: 3HBR) and pre-processed. The Lib Dock algorithm facilitated the analysis of optimal binding orientations and potential interactions between compounds and the 3HBR. Results: The docking analysis outcome revealed Oleic acid as the most active compound and the binding mode exhibited that the -OH group of the terminal carboxylic acid moiety formed hydrogen bonds with Thr197 and Ala207, and the oxygen atom showed bonding with Lys116. Moreover, N-hexanoic acid also demonstrated promising binding interactions with the 3HBR, displaying hydrogen bond interactions with Lys208, Tyr211, and Ser70, along with hydrophobic alkyl interactions with Lys208 and Met115 at the protein's active sites. Unfavourable donor-donor and acceptor-acceptor bindings were also observed with Ser70 and Arg250 residues. Conclusions: The OXA-48 and NDM-1 predominate in countries of the Arabian Peninsula. Our findings suggest oleic acid as a promising candidate for combating OXA-48 β-lactamase, pending further assessment of its atomic structure via X-ray crystallography.

Two groups and three classes of the conserved structural organization of nucleophile and non-canonical ElbowFlankOxy networks in different superfamily proteins

The nucleophile elbow is a well-known structural motif, which exists in proteins with catalytic triads and contains a catalytic nucleophile and the first node of an oxyanion hole. Here, we show that structural similarities of proteins with the nucleophile elbow extend beyond simple nucleophile elbow motifs. The motifs are incorporated into larger conserved structural organizations, the ElbowFlankOxy networks, incorporating motifs and flanking residues and networks of conserved interactions. A detailed structural analysis shows two major types of ElbowFlankOxy networks, depending on the formation of the oxyanion hole. Additionally, the ElbowFlankOxy networks show three classes: Class 1-2-3, 3-1-2, and 2-3-1, defined by the order in which the catalytic nucleophile and key interacting residues are located in the amino acid sequence, giving rise to six ElbowFlankOxy network variations. This makes it possible to properly position homologous non-catalytic, non-standard, and unusual catalytic triad active sites of proteins with the nucleophile elbow within the fold classification.

Aluminum Fluorides as Noncovalent Lewis Acids in Proteins: The Case of Phosphoryl Transfer Enzymes.

The Protein Data Bank (PDB) was scrutinized for the presence of noncovalent O ⋅ ⋅ ⋅ Al Triel Bonding (TrB) interactions, involving protein residues (e. g. GLU and GLN), adenosine/guanine diphosphate moieties (ADP and GDP), water molecules and two aluminum fluorides (AlF3 and AlF4 -). The results were statistically analyzed, revealing a vast number of O ⋅ ⋅ ⋅ Al contacts in the active sites of phosphoryl transfer enzymes, with a marked directionality towards the Al σ-/π-hole. The physical nature of the TrBs studied herein was analyzed using Molecular Electrostatic Potential (MEP) maps, the Quantum Theory of Atoms in Molecules (QTAIM), the Non Covalent Interaction plot (NCIplot) visual index and Natural Bonding Orbital (NBO) studies. As far as our knowledge extends, it is the first time that O ⋅ ⋅ ⋅ Al TrBs are analyzed within a biological context, participating in protein trapping mechanisms related to phosphoryl transfer enzymes. Moreover, since they are involved in the stabilization of aluminum fluorides inside the protein's active site, we believe the results reported herein will be valuable for those scientists working in supramolecular chemistry, catalysis and rational drug design.

Novel bi-allelic DNAH3 variants cause oligoasthenoteratozoospermia.

Oligoasthenoteratozoospermia (OAT) is a widespread cause of male infertility. One of the usual clinical manifestations of OAT is multiple morphological abnormalities of the sperm flagella (MMAF), which are frequently associated with mutations and defects in the dynein family. However, the relationship between the newly identified Dynein Axonemal Heavy Chain 3 (DNAH3) mutation and oligonasthenospermia in humans has not yet been established. Whole exome sequencing, pathogenicity analysis, and species conservation analysis of mutation sites were conducted on two patients from different unrelated families with DNAH3 mutations. We identified representative mutation sites and predicted the protein structure following these mutations. The sperm characteristics of the two patients with DNAH3 mutations were verified using Papanicolaou staining, scanning electron microscopy, and transmission electron microscopy. Additionally, mRNA and protein levels were assessed through RT-qPCR and Western blotting. The biallelic mutations in the first progenitor included a heterozygous deletion and insertion, c.6535_6536 delinsAC (to infect mutation (p.Asp2179Thr), and stop codon premutation, c.3249G > A (p.Trp1083Ter). In Family II, the patient (P2) harbored a DNAH3 heterozygous missense mutation, c. 10439G> A(p.Arg3480Gln), along with a stop codon premutation, (c.10260G > A; p.Trp3420Ter). Patients with premature termination of transcription or translation due to DNAH3 mutations exhibit OAT phenotypes, including fibrous sheath dysplasia and multiple tail malformations. We identified the representative sites after mutation, predicted the protein structure, and assessed changes in the protein levels of DNAH3 and related genes following mutations. Notably,a significant reduction in DNAH3 protein expression was validated in these patients. We may explore in the future how DNAH3 affects sperm motility and quality through regulatory mechanisms involving protein structural changes. Novel biallelic mutations in DNAH3, especially those resulting in a premature stop codon, may alter protein expression, structure, and active site, leading to spermatogenic failure and potentially inducing OAT. The discovery of new mutations in DNAH3 may be the key to the diagnosis and treatment of OAT.

Unveiling the potential role of virus-encoded polyphosphate kinases in enhancing phosphorus removal in activated sludge systems

While microbial phosphate removal in activated sludge (AS) systems has been extensively studied, the role of viruses in this process remains largely unexplored. In this study, we identified 149 viral auxiliary metabolic genes associated with phosphorus cycling from 2,510 viral contigs (VCs) derived from AS systems. Notably, polyphosphate kinase 1 (ppk1) and polyphosphate kinase 2 (ppk2) genes, which are primarily responsible for phosphate removal, were found in five unclassified VCs. These genes exhibited conserved protein structures and active catalytic sites, indicating a pivotal role of viruses in enhancing phosphorus removal. Phylogenetic analysis demonstrated a close relationship between viral ppk genes and their bacterial counterparts, suggesting the occurrence of horizontal gene transfer. Furthermore, experimental assays validated that viral ppk genes enhanced host phosphate removal capabilities. VCs carrying ppk genes were observed across diverse ecological and geographical contexts, suggesting their potential to bolster host functions in varied environmental and nutrient settings, spanning natural and engineered systems. These findings uncover a previously underappreciated mechanism by which viruses enhance phosphate removal in wastewater treatment plants. Overall, our study highlights the potential for leveraging virus-encoded genes to improve the efficiency of biological phosphorus removal processes, offering new insights into the microbial ecology of AS systems and the role of viruses in biogeochemical cycling.

Synthesis and Spectral Studies of New Azomethine Metal Complexes With Biological Activity and Docking Studies Utilizing 3‐Methylpyridin‐2‐Amine as a Complexing Agent

ABSTRACTThe novel Schiff base, (Z)‐2‐(1‐((3‐methylpyridin‐2‐yl)imino)ethyl)phenol (HL), was synthesized by reacting 1‐(2‐hydroxyphenyl)ethanone with 3‐methylpyridin‐2‐amine. Metal complexes [M (L)n (H2O)2] (M = Co and Cu, n = 2) were synthesized and characterized utilizing various analytical techniques including UV–visible spectroscopy, FTIR, elemental analysis, molar conductance, 1H NMR, thermal analysis, and magnetic moment measurement. The findings indicated that the Co+2 and Cu+2 complexes exhibited octahedral geometries. In vitro biological activity testing was conducted to evaluate the antimicrobial potential of the complexes against Bacillus subtilis (B. subtilis) and Escherichia coli (E. coli) bacteria strains. Similarly, molecular docking was conducted to elucidate the interactions between the active sites of protein–metal complexes and dihydrofolate reductase as well as ferrochelatase.

Exploring the therapeutic mechanisms of millet in obesity through molecular docking, pharmacokinetics, and dynamic simulation.

Obesity, a prevalent global health concern, is characterized by excessive fat accumulation, which confers significant nutritional and health risks, including a shortened lifespan and diminished wellbeing. Central to the regulation of energy balance and food intake is the fat mass and obesity-associated (FTO) protein, which modulates the interplay between caloric consumption and energy expenditure. Given its pivotal role in obesity regulation, the identification of effective inhibitors targeting the FTO protein is imperative for developing therapeutic interventions. Currently available anti-obesity drugs are often plagued by undesirable side effects. In contrast, natural plant-derived bioactive compounds are gaining prominence in the pharmaceutical industry due to their efficacy and lower incidence of adverse effects. Little Millet, a traditional cereal known for its rich nutritional profile and high satiety index, was investigated in this study using molecular docking and dynamics simulation approach for its potential as an anti-obesity agent. Our research demonstrates that four bioactive compounds from Little Millet exhibit superior binding energies ranging from 7.22 to 8.83 kcal/mol, compared to the standard anti-obesity drug, orlistat, which has a binding energy of 5.96 kcal/mol. These compounds fulfilled all drug-like criteria, including the Lipinski, Ghose, Veber, Egan, and Muegge rules, and exhibited favorable profiles in terms of distribution, metabolism, and prolonged half-life without toxicity. Conversely, orlistat was associated with hepatotoxicity, a reduced half-life, and multiple violations of drug-likeness parameters, undermining its efficacy. Molecular dynamics simulations and Gibbs free energy assessments revealed that the four identified compounds maintain stable interactions with key residues in the FTO protein's active site. We propose further validation through extensive In vitro, In vivo, and clinical studies to ascertain the therapeutic potential of these compounds in combating obesity.

Design, synthesis, and evaluation of triazoline schiff bases as potential antibacterial agents against methicillin-resistant Staphylococcus aureus (MRSA): A comprehensive computational and experimental study

In this study, a series of novel triazoline Schiff bases are designed and synthesized on a triazole-based AADHR_1 hypothesis pharmacophore model tailored to meet structural requirements for antibacterial activity. FT-IR, 1H NMR, and 13C NMR spectroscopy techniques confirmed molecular structures. Assessment of ADMET properties utilizing the pkCSM online tool unveiled encouraging pharmacokinetic profiles. Detailed Density Functional Theory (DFT) calculations showed significant electronic properties, delineating certain compounds as potent electron donors or acceptors. Docking studies unveil that, the compound 1-((1-(p-tolyl)piperidin-4-yl)methyl)-1H-1,2,3-triazole-4-carboxylic acid (2b) binded into the active site of the Penicillin-binding protein (PBP2a) of Methicillin-resistant Staphylococcus aureus (MRSA) with the docking score of -8.0 kcal/mol. Molecular dynamics simulations further corroborated the stability of the protein-ligand complex, emphasizing the compound 2b is enduring interaction at the MRSA protein's active site. Antibacterial assays against MRSA showed selective compounds exhibiting minimum inhibitory concentrations (MICs) of 20 µg/mL and Zone of inhibition up to 14 mm, highlighting their potential as effective antimicrobial agents against antibiotic-resistant bacteria. These findings collectively suggest the promising therapeutic prospects of the synthesized triazoline Schiff bases in combatting MRSA infections.

Machine-Learning Prediction of Protein Function from the Portrait of Its Intramolecular Electric Field.

We introduce a machine learning framework designed to predict enzyme functionality directly from the heterogeneous electric fields inherent to protein active sites. We apply this method to a curated data set of heme-iron oxidoreductases, spanning three enzyme classes: monooxygenases, peroxidases, and catalases. Conventional analysis, focused on simplistic, point electric fields along the Fe-O bond, is shown to be inadequate for accurate activity prediction. Our model demonstrates that the enzyme's heterogeneous 3-D electric field, alone, can accurately predict its function, without relying on additional protein-specific information. Through feature selection, we uncover key electric field components that not only validate previous studies but also underscore the crucial role of multiple components beyond the traditionally emphasized electric field along the Fe-O bond in heme enzymes. Furthermore, by integrating protein dynamics, principal component analysis, clustering, and QM/MM calculations, we reveal that while dynamic complexities in protein structures can obscure predictions, the model still retains its accuracy. This research significantly advances our understanding of how protein scaffolds possess signature electric fields tailored to their functions at the active site. Moreover, it presents a novel electrostatics-based tool to harness these signature electric fields for predicting enzyme function.

Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits.

The origin of the enzyme's powerful role in accelerating chemical reactions is one of the most critical and still widely discussed questions. It is already accepted that enzymes impose an electrostatic field onto their substrates by adopting complex three-dimensional structures; therefore, the preorganization of electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanisms and rate constant enhancement. In this work, we focus on three catalytically active β-subunits of 20S proteasomes with low sequence identity (∼30%) whose active sites, although situated in an electrostatically miscellaneous environment, catalyze the same chemical reaction with similar catalytic efficiency. Our in silico experiments reproduce the experimentally observed equivalent reactivity of the three sites and show that obliteration of the electrostatic potential in all active sites would deprive the enzymes of their catalytic power by slowing down the chemical process by a factor of 1035. To regain enzymatic efficiency, besides catalytic Thr1 and Lys33 residues, the presence of aspartic acid in position 17 and an aqueous solvent is required, proving that the electrostatic potential generated by the remaining residues is insignificant for catalysis. Moreover, it was found that the gradual decay of atomic charges on Asp17 strongly correlates with the enzyme's catalytic rate deterioration as well as with a change in the charge distributions due to introduced mutations. The computational procedure used and described here may help identify key residues for catalysis in other biomolecular systems and consequently may contribute to the process of designing enzyme-like synthetic catalysts.

The Potential of Clove (Syzygium aromaticum) Essential Oil as Sunscreen and Anti-Aging Agents: An In Vitro and In Silico Study

The earth thermal conditions increase exposure to sunlight, triggering skin damage. The skin has defense mechanisms but needs additional protection to prevent photoaging. Using sunscreen is an effort to reduce the harmful effects of sun exposure. Natural ingredients with antioxidant activity can be developed into sunscreen and antiaging products, including cloves. This study aims to assess the antioxidant, sun protection, and anti-aging properties of essential oils derived from clove leaves and buds. The antioxidant activity was assessed by the DPPH system and then formulated into 5 and 10 % clove leaves cream, as well as 5 and 10 % clove bud cream. The SPF values were assessed using a spectrophotometer and the Mansur formula. The antiaging potential was assessed using the in silico method with MMP-1 protein employing the Auto Dock Vina software, followed by analysis and visualization using BIOVIA Discovery Studio. The essential oils from clove leaves and buds have DPPH IC50 values of 23.09 and 30.31 ppm. The SPF values of clove leaves essential oil, 5 % leaves cream, and 10 % leaves cream are 38.61, 14.32, and 22.15. Meanwhile, the SPF values of clove bud essential oil, 5 % bud cream, and 10 % bud cream are 38.19, 9.32, and 18.16. The in silico test revealed that caryophyllene, eugenol, humulene, and phenol, 2-methoxy-4-(2-propenyl), acetate) have strong interactions because they can interact with the active site of proteins using hydrogen, hydrophobic, and van der Waals bonds. The essential oils from clove leaves and buds exhibit very strong antioxidant activity and offer ultra-protection as a sunscreen. The cream formulations still exhibit sunscreen activity, albeit at a lower level compared to pure essential oil. Caryophyllene, eugenol, humulene, and phenol, 2-methoxy-4-(2-propenyl)-, acetate), have potential as antiaging agents, as indicated by their binding affinity and chemical bond interactions observed in the in silico test. HIGHLIGHTS Clove buds and leaves exhibit antioxidant properties. Essential oil from clove buds and leaves demonstrates a substantial Sun Protection Factor (SPF). The compounds contained in clove essential oil exhibit promise as prospective agents in anti-aging applications. GRAPHICAL ABSTRACT

Assessment of the in vitro anti-diabetic activity with molecular dynamic simulations of limonoids isolated from Adalia lemon peels

Limonoids are important constituents of citrus that have a significant impact on promoting human health. Therefore, the primary focus of this research was to assess the overall limonoid content and isolate limonoids from Adalia lemon (Citrus limon L.) peels for their potential use as antioxidants and anti-diabetic agents. The levels of limonoid aglycones in the C. limon peel extract were quantified through a colorimetric assay, revealing a concentration of 16.53 ± 0.93 mg/L limonin equivalent. Furthermore, the total concentration of limonoid glucosides was determined to be 54.38 ± 1.02 mg/L. The study successfully identified five isolated limonoids, namely limonin, deacetylnomilin, nomilin, obacunone 17-O-β-D-glucopyranoside, and limonin 17-O-β-D-glucopyranoside, along with their respective yields. The efficacy of the limonoids-rich extract and the five isolated compounds was evaluated at three different concentrations (50, 100, and 200 µg/mL). It was found that both obacunone 17-O-β-D-glucopyranoside and limonin 17-O-β-D-glucopyranoside possessed the highest antioxidant, free radical scavenging, and anti-diabetic activities, followed by deacetylnomilin, and then the limonoids-rich extract. The molecular dynamic simulations were conducted to predict the behavior of the isolated compounds upon binding to the protein's active site, as well as their interaction and stability. The results revealed that limonin 17-O-β-D-glucopyranoside bound to the protein complex system exhibited a relatively more stable conformation than the Apo system. The analysis of Solvent Accessible Surface Area (SASA), in conjunction with the data obtained from Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF), and Radius of Gyration (ROG) computations, provided further evidence that the limonin 17-O-β-D-glucopyranoside complex system remained stable within the catalytic domain binding site of the human pancreatic alpha-amylase (HPA)-receptor. The research findings suggest that the limonoids found in Adalia lemon peels have the potential to be used as effective natural substances in creating innovative therapeutic treatments for conditions related to oxidative stress and disorders in carbohydrate metabolism.

Characterization and Cytotoxic Assessment of Bis(2-hydroxy-3-carboxyphenyl)methane and Its Nickel(II) Complex.

A condensation reaction of salicylic acid with formaldehyde in the presence of sulfuric acid led to the synthesization of the bis(2-hydroxy-3-carboxyphenyl)methane (BHCM) ligand, which was subsequently allowed to bind with nickel (II) ions. In light of the information obtained from the elemental analyses (C, H, and M), spectral (IR, MS, 1H-NMR, and UV-Vis) and thermal and magnetic measurements, the most likely structures of the ligand and complex have been identified. It has been suggested that the BHCM coordinates in a tetradentate manner with two Ni(II) ions to produce an octahedral binuclear complex. The SEM and TEM morphology of the compounds showed spherical shapes. An X-ray diffraction analysis indicated a considerable difference in the diffraction patterns between BHCM (crystalline) and Ni-BHCM (amorphous), and the Scherrer equation was used to calculate the crystallite size. Some optical characteristics were estimated from UV-Vis spectra. The ligand and its nickel(II) complex underlie the range of semiconductors. It was verified that for human lung (A-549) cancer, the BHCM compound displayed a significant barrier to the proliferation test in noncancerous cells (human lung fibroblasts, WI-38), which was also undertaken. To demonstrate the binding affinities of the chosen compounds (BHCM and Ni-BHCM) in the receptor protein's active site [PDB ID: 5CAO], a molecular docking (MD) study was carried out.

20S-Ginsenoside Rh2, the major bioactive saponin in Panax notoginseng flowers, ameliorates cough by inhibition of NaV1.7 and TRPV1 channel currents and downregulation of TRPV1 expression

Ethnopharmacological relevancePanax notoginseng flowers, which are the buds of the traditional Chinese medicinal herb Sanqi, are widely used in China for their cough-ameliorating properties, with demonstrated therapeutic effects in the treatment of both acute and chronic coughs. However, both the antitussive mechanism and active compound basis of P. notoginseng flowers remain poorly understood. Aim of the studyWe investigated the antitussive effects of P. notoginseng flowers, identified the bioactive constituents responsible for alleviating cough symptoms, and elucidated the underlying pharmacological mechanisms. Materials and methodsWe analyzed the major chemical constituents of aqueous extracts of P. notoginseng flowers using liquid chromatography–mass spectrometry and quantitatively analyzed the key component, 20S-ginsenoside Rh2, using high-performance liquid chromatography. Using a cough reflex model in healthy mice and an ovalbumin-induced, highly sensitive guinea pig cough model, we verified the suppressive effects of P. notoginseng flowers and their saponin constituents on coughing. Furthermore, we explored the mechanisms of action of the key ion channels, NaV1.7 and TRPV1, using whole-cell patch-clamp techniques and molecular docking. Finally, the therapeutic mechanisms of P. notoginseng flowers on pathological cough were revealed using hematoxylin and eosin staining, immunohistochemistry, and western blotting. ResultsThe active components of P. notoginseng flowers were primarily protopanaxadiol-type saponins, among which 20S-ginsenoside Rh2 had the highest content (51.46 mg/g). In the mouse model, P. notoginseng flowers exhibited antitussive effects comparable to those of pentoxyverine citrate. Although its main saponin component, 20S-ginsenoside Rh2, showed slightly weaker effects, it still demonstrated concentration-dependent inhibition of channel activity. The whole-cell patch-clamp technique and virtual molecular docking showed that Rh2 might exert its effects by directly binding to the NaV1.7 and TRPV1 channels. In the guinea pig model, P. notoginseng flowers and their saponin components not only reduced cough frequency and prolonged the latency period before cough onset, but also significantly inhibited tracheal and pulmonary inflammation and the overexpression of TRPV1. Conclusions20S-Ginsenoside Rh2, the major bioactive saponin in P. notoginseng flowers, exhibits potent antitussive effects. The potential mechanism of action of 20S-Ginsenoside Rh2 in the treatment of cough may involve inhibiting NaV1.7 and TRPV1 channel currents through direct binding to core protein active sites and downregulating TRPV1 expression.

Addressing epistasis in the design of protein function

Mutations in protein active sites can dramatically improve function. The active site, however, is densely packed and extremely sensitive to mutations. Therefore, some mutations may only be tolerated in combination with others in a phenomenon known as epistasis. Epistasis reduces the likelihood of obtaining improved functional variants and dramatically slows natural and lab evolutionary processes. Research has shed light on the molecular origins of epistasis and its role in shaping evolutionary trajectories and outcomes. In addition, sequence- and AI-based strategies that infer epistatic relationships from mutational patterns in natural or experimental evolution data have been used to design functional protein variants. In recent years, combinations of such approaches and atomistic design calculations have successfully predicted highly functional combinatorial mutations in active sites. These were used to design thousands of functional active-site variants, demonstrating that, while our understanding of epistasis remains incomplete, some of the determinants that are critical for accurate design are now sufficiently understood. We conclude that the space of active-site variants that has been explored by evolution may be expanded dramatically to enhance natural activities or discover new ones. Furthermore, design opens the way to systematically exploring sequence and structure space and mutational impacts on function, deepening our understanding and control over protein activity.

Synthesis and in-silico Studies of 4-phenyl thiazol-2-amine Derivatives as Putative Anti-breast Cancer Agents.

Breast cancer (BC) is the second-leading cause of cancer-related fatalities in women after lung cancer worldwide. The development of BC is significantly influenced by estrogen receptors (ERs). The problem with current cancer treatments is selectivity, target specificity, cytotoxicity, and developing resistance. Thiazole scaffolds are gaining popularity in drug discovery due to their broad range of biological activity. It has the extraordinary capacity to control a variety of cellular pathways, and its potential for selective anticancer activity can be explored. Synthesis and in-silico</i> studies of 4-Phenyl thiazol-2-amine derivatives as anti-breast cancer agents and molecular docking was used to assess the compounds' capacity to bind ER-α protein target. In this study, 4-Phenylthiazol-2-amine derivatives (3a-j) have been synthesized, and using Schrodinger software, molecular docking and ADME studies of the compounds were conducted. Most of the synthesized compounds have shown dock scores ranging from -6.658 to - 8.911 kcal/mol, which is better than the standard drug tamoxifen (-6.821 kcal/mol). According to molecular docking, all compounds fit in the protein's active site and have the same hydrophobic pocket as the standard drug tamoxifen. Further, all of the compounds' ADME properties are below acceptable limits. Compound 3e showed the best docking score of -8.911. All compounds' ADME properties are within acceptable limits, and their p/o coefficients fall within a range, suggesting they will all have sufficient absorption at the site of action. These compounds can be evaluated invitro</i> and in-vivo</i> in the future.

Marine fungal diversity unlocks potent antivirals against monkeypox through methyltransferase inhibition revealed by molecular dynamics and free energy landscape

The escalating threat posed by the Monkeypox virus (MPXV) to global health necessitates the urgent discovery of effective antiviral agents, as there are currently no specific drugs available for its treatment, and existing inhibitors are hindered by toxicity and poor pharmacokinetic profiles. This study aimed to identify potent MPXV inhibitors by screening a diverse library of small molecule compounds derived from marine fungi, focusing on the viral protein VP39, a key methyltransferase involved in viral replication. An extensive virtual screening process identified four promising compounds—CMNPD15724, CMNPD28811, CMNPD30883, and CMNPD18569—alongside a control molecule. Rigorous evaluations, including re-docking, molecular dynamics (MD) simulations, and hydrogen bond analysis, were conducted to assess their inhibitory potential against MPXV VP39. CMNPD15724 and CMNPD30883, in particular, demonstrated a superior binding affinity and stable interactions within the target protein's active site throughout the MD simulations, suggesting a capacity to overcome the limitations associated with sinefungin. The stability of these VP39-compound complexes, corroborated by MD simulations, provided crucial insights into the dynamic behavior of these interactions. Furthermore, Principal Component Analysis (PCA) based free energy landscape assessments offered a detailed understanding of the dynamic conformational changes and energetic profiles underlying these compounds' functional disruption of VP39. These findings establish CMNPD15724, CMNPD28811, CMNPD30883, and CMNPD18569 as promising MPXV inhibitors and highlight marine fungi as a valuable source of novel antiviral agents. These compounds represent potential candidates for further experimental validation, advancing the development of safer and more effective therapeutic options to combat this emerging viral infection.

Discovery of New Heteroaryldihydropyrimidine Compounds as HBV Capsid Protein Inhibitors Based on QSAR, Molecular Docking and Molecular Dynamics Simulations**

AbstractHepatitis B virus (HBV) infection is a major global public health problem and a serious threat to human health. The assembly of the HBV outer shell protein is an important step in the HBV life cycle. Influencing the assembly of core proteins to block viral DNA replication has become a popular target for anti‐HBV drug development. In this study, 47 heteroarylpyrimidine (HAP) compounds were investigated by QSAR, and Topomer CoMFA and HQSAR models with strong predictive ability were developed. Eight new compounds with high activity were successfully designed by searching R groups in Topomer Search. The results of molecular docking and ADMET performance prediction showed that all these compounds have good docking scores and potential medicinal values. To further understand the possible conformations and interactions of the compounds at the protein active site, we performed molecular dynamics simulations of the four compounds with high docking scores and confirmed that these complexes have stable binding conformations by free energy mapping. The free energy calculations verified the stable binding results. These results provide an important reference and theoretical basis for the design and development of effective heteroaryldihydropyrimidine analogs as potential HBV capsid inhibitors.