Binding Free Energy Research Articles

Cheminformatics-aided discovery of potential allosteric site modulators of ubiquitin-specific protease 7

Ubiquitin-specific peptidase 7 (USP7) is a deubiquitinating enzyme that mediates the stability and activity of numerous proteins. At basal expression levels, USP7 stabilizes p53 protein, even in the presence of excess MDM2. However, its overexpression leads to the deubiquitination of MDM2 at a rate faster than p53, leading to p53 degradation and pro-tumorigenic roles. Consequently, it is an attractive target for anticancer drug discovery via the modulation of its allosteric site from which the protein is activated. In this study, molecular modeling techniques and cheminformatics approaches were employed to unravel the potential of eighty compounds to serve as its allosteric site modulators. The compounds were initially subjected to virtual screening. Subsequently, the binding free energies of the top four compounds with the highest binding affinities were calculated, and their drug-likeness, and pharmacokinetic and toxicity profiles were evaluated. Ultimately, the complexes of the protein and hit compounds were subjected to a 100 nanoseconds (ns) molecular dynamics simulation. The results of the study revealed eight compounds from the compound library with docking scores ranging from − 7.491 to -11.43 kcal/mol, compared to P217564, which exhibited a docking score of -5.671 kcal/mol. The top four compounds with the highest affinities possessed drug-like properties, and good pharmacokinetic and toxicity profiles, and their predicted inhibitory potentials showed they will be effective at minimal concentration. Also, molecular dynamics simulation confirmed the stability of the protein-ligand complexes. Conclusively, the compounds identified in this study are worthy of further evaluation for the development of allosteric site modulators of USP7.

Design, synthesis and antioxidant studies of thiopyrimidine-based Passerini reaction: sulfur linked derivatives

Researchers have shown that sulfur-based heterocyclic frameworks form the backbone of a wide variety of synthetic analogues with a wide variety of medicinal actions. In this study, Passerini 3-component condensation reaction (P-3-CCR) approach has been used for the design strategy for imparting sulfur-based starting material, synthesis and antioxidant potential of sulfur containing pyrimidine (α-acyloxy amide) derivatives. The thorough assessment of antioxidant activities with a reference drug allows a proficient assessment of the structure–activity relationships (SARs) of the diversely synthesized molecules of the series. Compounds 4f with 3,4-(OMe)2 [17.35 ± 0.14 µM] and 4h with 4-NO2 [19.21 ± 0.14 µM] functionalities were identified as lead scaffolds with minimum IC50 values. A molecular docking investigation was also performed to compute the binding free energy of 4h and 4f to 1F9G. The results revealed a strong binding affinity (-7.1 kcal/mol) of both compounds as compared to that of ascorbic acid (-6.2 kcal/mol). A design strategy though molecular docking followed by MCRs approach to identify new α-acyloxy amides provided an outstanding approximation and shedded light on the sites of binding for their better use in medicinal field.

In silico screening of dyes for enhanced silk coloring using the feeding approach

Reducing redundant dyes in the production of colored silk is essential for environmental sustainability. This study aims to innovate silk dyeing processes by employing molecular docking techniques to screen a library of dyes with specific physical properties. For the first time, we identified Acid Blue 25 (Chemical Identifier, CID 22916) and Metanil Yellow (CID 11490) as cost-effective blue and yellow dyes, respectively, that enable the production of intrinsically colored silk by feeding dye-modified mulberry leaves to silkworms. Both dyes demonstrated high selective binding to silk fibroin and retained excellent color performance after degumming. Secondary structural analysis revealed that Acid Blue 25 enhanced mechanical properties by increasing β-sheet content, whereas Metanil Yellow did not. Furthermore, fluorescence spectroscopy indicated that Acid Blue 25 and Metanil Yellow effectively quenched the intrinsic fluorescence of silk fibroin primarily through static quenching, with Acid Blue 25 exhibiting a higher binding constant and more negative binding free energy. Classic molecular dynamic (cMD) simulations revealed that the extensive interaction network of Acid Blue 25, compared to Metanil Yellow, creates a thermodynamically favorable environment for dye-complex binding and stability. Overall, the combined application of virtual screening and the feeding method supports a highly cost-effective and environmentally friendly silk dyeing strategy, with the potential for scaling up in industrial applications.

Improving the catalytic performance of carbonyl reductase based on the functional loops engineering.

Vibegron functions as a potent and selective β3-adrenergic receptor agonist, with its chiral precursor (2S,3R)-aminohydroxy ester (1b) being crucial to its synthesis. In this study, loop engineering was applied to the carbonyl reductase (EaSDR6) from Exiguobacterium algae to achieve an asymmetric reduction of the (rac)-aminoketone ester 1a. The variant M5 (A138L/A190V/S193A/Y201F/N204A) was obtained and demonstrated an 868-fold increase in catalytic efficiency (kcat/Km = 260.3 s-1 mM-1) and a desirable stereoselectivity (>99% enantiomeric excess, e.e.; >99% diastereomeric excess, d.e.) for the target product 1b in contrast to the wild-type EaSDR6 (WT). Structural alignment with WT indicated that loops 137-154 and 182-210 potentially play vital roles in facilitating catalysis and substrate binding. Moreover, molecular dynamics (MD) simulations of WT-1a and M5-1a complex illustrated that M5-1a exhibits a more effective nucleophilic attack distance and more readily adopts a pre-reaction state. The interaction analysis unveiled that M5 enhanced hydrophobic interactions with substrate 1a on cavities A and B while diminishing unfavorable hydrophilic interactions on cavity C. Computational analysis of binding free energies indicated that M5 displayed heightened affinity towards substrate 1a compared to the WT, aligning with its decreased Km value. Under organic-aqueous biphasic conditions, the M5 mutant showed >99% conversion within 12 h with 300 g/L substrate 1a (highest substrate loading as reported). This study enhanced the catalytic performance of carbonyl reductase through functional loops engineering and established a robust framework for the large-scale biosynthesis of the vibegron intermediate.

Repurposing of Oxicam Derivatives to Inhibit NDM-1: Molecular Docking and Molecular Dynamic Simulation Studies

The New Delhi Metallo-β-lactamase-1 (NDM-1) causes hydrolysis of broad spectrum β-lactam antibiotics, such as carbapenems, resulting in the development of antimicrobial resistance. Still, there are not any approved NDM-1 inhibitors, globally. Therefore, repositioning approved medicines as NDM-1 inhibitors to combine with carbapenems may be a crucial strategy to combat resistant pathogens. This study repurposes. Oxicam derivatives as inhibitors of bacterial NDM-1. The two-dimensional structures were obtained from the PubChem database. Twenty derivatives of oxicam were assessed computationally to realize their NDM-1 inhibition capability. To identify potential inhibitors of the NDM-1 target protein, a molecular docking protocol was used. In addition, drug-likeness and pharmacokinetic properties were predicted for the designed molecules. Three compounds with the most negative ΔGbinding results were chosen for additional study using molecular dynamic (MD) simulations. The compounds M010, M013, and M016 possessed a significantly more negative binding free energy than the positive control and other designed molecules, had stable MD simulations (Root-mean-square deviation < 0.5 Å), passed Lipinski's rule of five, and possessed favourable physicochemical and pharmacokinetic properties. The findings can inform In vitro studies of the promising compounds.

Development of novel CDK9 and CYP3A4 inhibitors for cancer therapy through field and computational approaches.

Cyclin-dependent kinase 9 (CDK9) and cytochrome P450 3A4 (CYP3A4) have emerged as promising targets in the development of anticancer drugs, presenting a consistent challenge in the quest for potent inhibitors. CDK9 inhibitors can selectively target fast-growing cancer cells by disrupting transcription elongation, which in turn hinders the production of proteins essential for cell cycle progression and survivaŚ. Understanding how CYP3A4 metabolizes specific chemotherapy drugs allows for personalized treatment plans, optimizing drug dosages according to a patient's metabolic profile. Since many cancer patients undergo combination therapies, and CYP3A4 is vital in drug metabolism, its inhibition or induction by one drug can alter the plasma levels of others, potentially leading to treatment failure or increased toxicity. Therefore, managing CYP3A4 activity is critical for effective cancer treatment. Employing a range of computational methodologies, this study systematically investigated the binding mechanisms of pyrimidine derivatives against CDK9 and CYP3A4. The field-based model demonstrated high R 2 values (0.99), with Q2 (0.66), demonstrating its ability to predict in silico inhibitory activity against the target of this study. The screening process followed in this work led to the discovery of powerful new inhibitor compounds. Of the 15 new compounds designed, three have a high affinity with the target (ranging from -8 to -9kcal/molkcal/mol) and were singled out through docking filtration for more detailed investigation. As well as, a reference compound with a substantial pIC50 value of 8.4, serving as the foundation for the development of the new compounds, was included for comparative analysis. To elucidate the essential features of CDK9 and CYP3A4 inhibitor design, a comparative analysis was conducted between 3D-QSAR-generated contours and molecular docking conformations of ligands. Molecular dynamics simulations were carried out for a duration of 100 ns on selected docked complexes, specifically those involving novel compounds with CDK9 and CYP3A4 enzymes. Additionally, the binding free energy for these complexes was assessed using the MM/PBSA method, which evaluates the free energy landscape of protein-ligand interactions. The results of MM/PBSA highlighted the strength of the new compounds in enhancing interactions with the target protein, which favors the results of molecular docking and MD simulation. These insights contribute to a deeper understanding of the mechanisms underlying CDK9 and CYP3A4 inhibition, offering potential avenues for the development of innovative and effective CDK9 inhibitors.

The Generation of ROS by Exposure to Trihalomethanes Promotes the IκBα/NF-κB/p65 Complex Dissociation in Human Lung Fibroblast.

Background: Disinfection by-products used to obtain drinking water, including halomethanes (HMs) such as CH2Cl2, CHCl3, and BrCHCl2, induce cytotoxicity and hyperproliferation in human lung fibroblasts (MRC-5). Enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) modulate these damages through their biotransformation processes, potentially generating toxic metabolites. However, the role of the oxidative stress response in cellular hyperproliferation, modulated by nuclear factor-kappa B (NF-κB), remains unclear. Methods: In this study, MRC-5 cells were treated with these compounds to evaluate reactive oxygen species (ROS) production, lipid peroxidation, phospho-NF-κB/p65 (Ser536) levels, and the activities of SOD, CAT, and GPx. Additionally, the interactions between HMs and ROS with the IκBα/NF-κB/p65 complex were analyzed using molecular docking. Results: Correlation analysis among biomarkers revealed positive relationships between pro-oxidant damage and antioxidant responses, particularly in cells treated with CH2Cl2 and BrCHCl2. Conversely, negative relationships were observed between ROS levels and NF-κB/p65 levels in cells treated with CH2Cl2 and CHCl3. The estimated relative free energy of binding using thermodynamic integration with the p65 subunit of NF-κB was -3.3 kcal/mol for BrCHCl2, -3.5 kcal/mol for both CHCl3 and O2•, and -3.6 kcal/mol for H2O2. Conclusions: Chloride and bromide atoms were found in close contact with IPT domain residues, particularly in the RHD region involved in DNA binding. Ser281 is located within this domain, facilitating the phosphorylation of this protein. Similarly, both ROS interacted with the IPT domain in the RHD region, with H2O2 forming a side-chain oxygen interaction with Leu280 adjacent to the phosphorylation site of p65. However, the negative correlation between ROS and phospho-NF-κB/p65 suggests that steric hindrance by ROS on the C-terminal domain of NF-κB/p65 may play a role in the antioxidant response.

Mitoxantrone release from Fmoc-protected amino acids coated magnetic carbon nanotubes: Computational and experimental study for cancer treatment

Nanoparticles have a high potential for use as drug carrier systems in cancer treatment to reduce severe side effects, as in the treatment of many other diseases. Due to their unique properties, carbon-based nanoparticles such as carbon nanotubes (CNTs) are among the most frequently used nanoparticles in drug carrier systems. In this study, magnetic single-walled CNTs (mCNTs) were synthesized, characterized, coated and their ability to carry the anticancer drug mitoxantrone (MTO) was investigated using computational and experimental methods. First, the mCNT coating capabilities of Fmoc-protected amino acids, Fmoc-Cys(trt)-OH and Fmoc-Trp-OH were demonstrated by Raman spectroscopy, thermogravimetric analysis, and X-ray photoelectron spectroscopy. Then, full-atom molecular dynamics simulations of MTO-CNT complexes in explicit water were used to understand Fmoc-amino acid and MTO loading experiments at the molecular level. Binding free energies calculated by the Molecular Mechanics/Poisson-Boltzmann Surface Area method suggested MTO-CNT complex stability even at elevated temperatures up to 350 K that can be achieved due to external magnetic stimuli. Drug loading at pH 9 and releases at physiological (pH 7.4) and lysosomal pH (pH 5.5) were carried out for uncoated and coated mCNTs. The drug release and characterization results showed that coated mCNTs have pH-responsive drug release, enhanced dispersibility, and superparamagnetic properties so they promise to be beneficial for MTO delivery in cancer treatment. Cell viability results demonstrated that the mCNT-Fmoc-Cys samples had higher cell viability compared to the mCNT and mCNT-Fmoc-Trp groups.

Estimation of Bond Free Energy with Gmx_Mmpbsa in Ndm-1 Complexes

We report the values obtained for the binding free energies (ΔGbind) of the complexes: NDM-1-M25 (43.80 kcal/mol), NDM-1-M26 (12.71 kcal/mol), NDM-1-M35 (19.92 kcal/mol), NDM-1-M37 (2.46 kcal/mol) and the reference system NDM-1-Meropenem (-10.09 kcal/mol). These results are based on previous absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties, docking, and molecular dynamics calculations performed on a small library of potential NDM-1 enzyme inhibitors reported in the literature. Subsequently, the selected systems were evaluated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method using the gmx_MMPBSA software. The MMPBSA method has been widely adopted to estimate protein-ligand binding affinities due to its efficiency and high correlation with experimental data. The obtained results suggest that, unlike the reference complex, the studied ligands probably do not bind to the receptor under the simulation conditions, which is in significant agreement with experimental data.

Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations.

Carbohydrates are key biological mediators of molecular recognition and signaling processes. In this case study, we explore the ability of absolute binding free energy (ABFE) calculations to predict the affinities of a set of five related carbohydrate ligands for the lectin protein, concanavalin A, ranging from 27-atom monosaccharides to a 120-atom complex-type N-linked glycan core pentasaccharide. ABFE calculations quantitatively rank and estimate the affinity of the ligands in relation to microcalorimetry, with a mean signed error in the binding free energy of -0.63 ± 0.04 kcal/mol. Consequently, the diminished binding efficiencies of the larger carbohydrate ligands are closely reproduced: the ligand efficiency values from isothermal titration calorimetry for the glycan core pentasaccharide and its constituent trisaccharide and monosaccharide compounds are respectively -0.14, -0.22, and -0.41 kcal/mol per heavy atom. ABFE calculations predict these ligand efficiencies to be -0.14 ± 0.02, -0.24 ± 0.03, and -0.46 ± 0.06 kcal/mol per heavy atom, respectively. Consequently, the ABFE method correctly identifies the high affinity of the key anchoring mannose residue and the negligible contribution to binding of both β-GlcNAc arms of the pentasaccharide. While challenges remain in sampling the conformation and interactions of these polar, flexible, and weakly bound ligands, we nevertheless find that the ABFE method performs well for this lectin system. The approach shows promise as a quantitative tool for predicting and deconvoluting carbohydrate-protein interactions, with potential application to design of therapeutics, vaccines, and diagnostics.

Multitargeted docking approach reveals droxidopa against DNA replication and repair-related protein of cervical cancer

Cervical cancer begins in the cells lining the cervix and is caused by persistent infection with certain types of human papillomavirus (HPV). Initially, it has no symptoms, and later it causes pelvic pain, abnormal vaginal bleeding, and pain during intercourse. It is the fourth-ranked cancer among women, and many women die from cervical cancer every year, particularly in low-income countries and the majority could be prevented with early detection and treatment. In this study, we have taken Cervical Cancer DNA Replication and Repair-Related Protein with the PDBID- 3H15, 5VBN, and 6NT9 and performed the multitargeted molecular docking with the FDA-approved drug library using HTVS, SP and XP docking. Then, the poses were filtered with MM\\GBSA for proper computations of free energy, identified a multitargeted inhibitor Droxidopa with docking and MM\\GBSA scores ranging from − 5.559 to − 6.835 Kcal/mol and − 26.04 to − 37.33 Kcal/mol, respectively. We also performed interaction fingerprints revealing 2VAL, 2LYS, 1ALA, 1ARG, 1ASN, 1CYS, 1GLN, 1GLU, 1ILE, 1MET, 1PHE, 1PRO, 1SER, and 1THR were most interacted residues and computed the ADMET properties with QikProp and DFT with Jaguar, which supported the study and compounds’ suitability. Moreover, we performed the 100ns MD simulation in water, showing the controlled deviation and fluctuations of the residues with many interactions, and MM\\GBSA was performed with the same trajectories, showing a better understanding of each frame’s total complex and binding-free energy. The whole study favours droxidopa as an inhibitor of cervical cancer DNA Replication and Repair-Related Proteins—however, experimental studies are needed before use.

Computational modeling to understand the interaction of TMPyP4 with a G-quadruplex

The potential of small molecules to bind to G-quadruplex-forming sequences in oncogene promoter regions, thereby regulating their structural equilibrium, has been explored as a promising strategy for cancer chemotherapy. The model drug 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)porphine (TMPyP4) has been shown to have an affinity toward G-quadruplex DNA. However, the precise sites and modes of TMPyP4 binding to G-quadruplex DNA remain a subject of debate. In this study, we focus on identifying potential binding sites on a mutant c-MYC sequence known to fold into a single 1:2:1 loop isomer quadruplex. Our findings provide insights into the 4:1 stoichiometry reported for TMPyP4 binding to this G-quadruplex. Binding enthalpy and free energy calculations show that intercalation of a TMPyP4 molecule between the quadruplexes is thermodynamically favorable. Our calculations suggest that two of the binding sites are located at the top and bottom of the quadruplex, respectively, while the remaining two are likely intercalations.

Family Malvaceae: a potential source of secondary metabolites with chemopreventive and anticancer activities supported with in silico pharmacokinetic and pharmacodynamic profiles.

Cancer is the second most widespread cause of mortality following cardiovascular disorders, and it imposes a heavy global burden. Nowadays, herbal nutraceutical products with a plethora of bioactive metabolites represent a foundation stone for the development of promising chemopreventive and anticancer agents. Certain members of the family Malvaceae have traditionally been employed to relieve tumors. The literature concerning the chemopreventive and anticancer effects of the plant species along with the isolated cytotoxic phytometabolites was reviewed. Based on the findings, comprehensive computational modelling studies were performed to explore the pharmacokinetic and pharmacodynamic profiles of the reported cytotoxic metabolites to present basis for future plant-based anticancer drug discovery. All the available information about the anticancer research in family Malvaceae and its cytotoxic phytometabolites were retrieved from official sources. Extensive search was carried out using the keywords Malvaceae, cancer, cytotoxicity, mechanism and signalling pathway. Pharmacokinetic study was performed on the cytotoxic metabolites using SWISS ADME model. Acute oral toxicity expressed as median lethal dose (LD50) was predicted using Pro Tox 3.0 web tool. The compounds were docked using AutoDock Vina platform against epidermal growth factor receptor (EGFR kinase enzyme) obtained from the Protein Data Bank. Molecular dynamic simulations and MMGBSA calculations were performed using GROMACS 2024.2 and gmx_MMPBSA tool v1.5.2. One hundred forty-five articles were eligible in the study. Several tested compounds showed safe pharmacokinetic properties. Also, the molecular docking study showed that the bioactive metabolites possessed agreeable binding affinities to EGFR kinase enzyme. Tiliroside (25), boehmenan (30), boehmenan H (31), and isoquercetin (22) elicited the highest binding affinity toward the enzyme with a score of -10.4, -10.4, -10.2 and -10.1Kcal/mol compared to the reference drug erlotinib having a binding score equal to -9Kcal/mol. Additionally, compounds 25 and 31 elicited binding free energies equal to -42.17 and -42.68Kcal/mol, respectively, comparable to erlotinib. Overall, the current study presents helpful insights into the pharmacokinetic and pharmacodynamic properties of the reported cytotoxic metabolites belonging to family Malvaceae members. The molecular docking and dynamic simulations results intensify the roles of secondary metabolites from medicinal plants in fighting cancer.

Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1) lncRNA Conformational Dynamics in Complex with RNA-Binding Protein with Serine-Rich Domain 1 (RNPS1) in the Pan-cancer Splicing and Gene Expression.

Alternative splicing events increase the transcriptomic and proteomic complexity in cancers. Overexpression of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a highly conserved lncRNA, is widely known to promote cancer development, one mechanism for which may be through the regulation of alternative splicing and, thereby, gene expression. Its regulatory interactions with proteins have been a subject of much interest, yet little research has been carried out on the mechanisms adopted. It has been observed that MALAT1 binds to RNA-binding protein with serine-rich domain 1 (RNPS1), being colocalized in the nuclear speckles, and together, these two binding partners may regulate alternative splicing. Upregulated RNPS1 is predicted to play a key role in the pan-cancer development. Experimental tertiary structure of full-length MALAT1 is currently lacking despite the availability of the 3D structure of 3' expression and nuclear retention element. We hypothesize that the computationally modeled tertiary structures of the specific binding motifs in the M-region, E-region, and full-length structures of MALAT1 may adopt a modular structure and bind to the RNPS1 loop region of RS/P domain involved in exon skipping, interacting in a manner fully consistent with the biochemical experiments. Extensive observations using the powerful molecular dynamics (MD) simulations of MALAT1 regions bound to RNPS1 suggested that all three regions form interactive, yet stable complexes. The ranking of the MM-GBSA- and MM-PBSA-derived binding free energies between these complexes corroborated well in the MD simulations and experiments. Energy decomposition analyses suggested that arginines in the RNPS1 protein are among the major contributors toward the binding free energies as calculated by MM-GBSA present in the Amber package; while among the nucleotides, the major contributors were nucleotides with G and A nucleobases, with more contributory effect in comparison to arginines, across the bound M-region, E-region, and full-length MALAT1. This suggests that specific purines play a greater role in the complex formation, in a loop-specific manner, and the more proactive approach in complexation tilts toward MALAT1. To the best of our knowledge, our studies are the first studies taking a unique approach, utilizing the binding motifs to deduce a tertiary structure of MALAT1, toward our understanding of the lncRNA-protein interactions, stability, and binding on a structural basis. The therapeutic implications of targeting this complex formation to regulate splicing and hence, oncogenesis, is further envisaged.

Structure-based computer-aided drug design to identify potential lead molecules for Asparaginyl Endopeptidase inhibitors.

The enzyme Asparaginyl Endopeptidase (AEP) is associated with proteinopathy-related pathologies such as Alzheimer's disease (AD) and Frontal Temporal Dementia (FTD). The onset of pathologies by AEP is due to cleaved fragments forming protein aggregates resulting in neurodegeneration. Unfortunately, there are no clinically approved small molecule inhibitors for AEP, and therefore, it serves as an unmet medical need for the design and development of potential novel small molecules. In developing potential inhibitors for proteolytic activity, a structured approach utilizing structure-based computer-aided drug design (SB-CADD) parameters was employed. This involved virtual high throughput screening (vHTS) across various CNS-focused databases enriched with diverse functionality. We identified the top sixty ligands based on the glide XP-docking score out of 10 million ligands. The free binding energy was then calculated using MM-GBSA for all top selected molecules which resulted in discovering that AEPI-1 to AEPI-6 (Asparaginyl Endopeptidase inhibitors) displayed high affinity towards the catalytic triad. Further investigation determined that all top six hits form stable complexes during 50 ns molecular dynamic simulations. We also observed that AEPI-2 demonstrated the highest stability within the binding pockets. Post-MD analyses such as DCCM, PCA, PDF, and ADMET properties were also evaluated. By bridging all the observations, we observed these six molecules occupy the active site of the β-helix (β1, β3, and β4) of the S1 pocket and additional binding sites in α1 and β5, suggesting its suitability as a potential candidate for drug discovery against Asparaginyl Endopeptidase.

Phytochemicals of Swertia chirayita Roxb. ex Fleming against malarial dihydroorotate dehydrogenase: an in silico study

The global economic burden of malaria is rising and lack of effective drugs against it have imposed an insurmountable challenge in designing it that is both affordable and resistanceless. The plants with ethnobotanical values are relatively safer and its use is a viable option as therapeutics for various demographic locations. In this regard, the chemical components of a plant, Swertia chirayita Roxb. ex Fleming (traditionally used as an antimalarial agent) were explored by multiple computational tools against dihydroorotate dehydrogenase (DHODH) protein of Plasmodium falciparum (PDB ID: 6GJG), a causative agent of the disease. The docking scores were calculated to be − 10.220, − 10.131, − 10.071, − 10.024, and − 9.905 kcal/mol for the top five molecules (decussatin, swerchirin, 1-hydroxy-3,5,8-trimethoxyxanthen-9-one, swertinin, and chiratol), respectively with the native ligand possessing a higher value of − 9.873 kcal/mol. The adducts were geometrically and thermodynamically stable as revealed by several parameters extracted from 200 ns molecular dynamics simulations (MDS) and verified by a single run of 600 ns. The smooth RMSD profiles from a cumulative MDS of 2.0 μs, pointed towards a sturdy nature of the receptor geometry with limited translational or rotational motion of the ligands. The involvement of LEU11, CYS14, LEU15, CYS23, PHE27, ILE102, ARG104, TYR337, LEU340, and VAL341 amino acid residues with mainly hydrophobic interactions at the orthosteric site were observed for most of the adducts. The binding free energy changes (up to − 30.18 ± 4.38 kcal/mol) hinted at the feasibility and sustained thermodynamical spontaneity of the forward reaction of the complex formation. The hit molecules could possibly disrupt or inhibit the normal functioning of the DHODH receptor leading to the likely prevention and cure of the disease and are recommended for experimental trials.

Engineering affinity of humanized ScFv targeting CD147 antibody: A combined approach of mCSM-AB2 and molecular dynamics simulations

This study aims to assess the effectiveness of mCSM-AB2, a graph-based signature machine learning method, for affinity engineering of the humanized single-chain Fv anti-CD147 (HuScFvM6-1B9). In parallel, molecular dynamics (MD) simulations were used to gain valuable insights into the dynamics and affinity of the HuScFvM6-1B9-CD147 complex. The result analysis involved integrating free energy changes calculated from the mCSM-AB2 with binding free energy predictions from MD simulations. The simulated structures of the modified HuScFvM6-1B9-CD147 domain 1 complex from MD simulations were used to highlight critical residues participating in the binding surface. Interestingly, alterations in the pattern of amino acids of HuScFvM6-1B9 at the complementarity determining regions interacting with the 31EDLGS35 epitope were observed, particularly in mutants that lost binding activity. The predicted mutants of HuScFvM6-1B9 were subsequently engineered and expressed in E. coli for subsequent binding property validation. Compared to WT HuScFvM6-1B9, the mutant HuScFvM6-1B9L1:N32Y exhibited a 1.66-fold increase in binding affinity, with a KD of 1.75 × 10−8 M. While mCSM-AB2 demonstrates insignificant improvement in predicting binding affinity enhancements, it excels at predicting negative effects, aligning well with experimental validation. In addition to binding free energies, total entropy was considered to explain the discrepancy between mCSM-AB2 predictions and experimental results. This study provides guidelines and identifies the limitations of mCSM-AB2 and MD simulations in antibody engineering.

Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics.

Accurately describing protein-ligand binding and unbinding kinetics remains challenging. Computational calculations are difficult and costly, while experimental measurements often lack molecular detail and can be unobtainable. Here, we extend our multiscale milestoning method, Simulation-Enabled Estimation of Kinetics Rates (SEEKR), with metadynamics molecular dynamics simulations to yield accurate small molecule drug residence times. Using the pharmaceutically relevant threonine-tyrosine kinase (TTK) and eight long-residence-time (tens of seconds to hours) inhibitors, we demonstrate accurate prediction of absolute and rank-ordered ligand residence times and free energies of binding.

Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitorsof PRRSV-Nsp4.

Porcine reproductive and respiratory syndrome (PRRS) is one of the most serious infectious immunosuppressive diseases in the world. The nonstructural protein Nsp4 can be used as an ideal target for anti-PRRSV replication inhibitors. However, little is known about potential inhibitors that target Nsp4 to affect PRRSV replication. The purpose of this study was to screen potential natural inhibitors that affect PRRSV replication by inhibiting Nsp4. Five compounds with strong binding affinity to Nsp4 were selected by structure-based molecular docking method. The complexes of naringin dihydrochalcone (NDC), agathisflavone (AGT), and amentoflavone (AMF) with Nsp4 were stable throughout the molecular dynamics simulation. According to MM/PBSA analysis, the free energies of binding of NDC, AGT, and AMF to Nsp4 were less than-30 Kcal/mol. In conclusion, these three compounds are worthy of further investigation as novel inhibitors of PRRSV. This study provides a theoretical basis for the development of anti-PRRSV natural drugs.

Computational exploration of novel ketoprofen derivatives: Molecular dynamics simulations and MM-PBSA calculations for COX-2 inhibition as promising anti-inflammatory drugs

Computer-aided drug design is widely employed to identify novel compounds for therapeutic applications. Ketoprofen (KTP), a commonly used and marketed nonsteroidal anti-inflammatory drug (NSAID), is effective in treating pain, fever, inflammation, and some cancers. In this research, we explored the behavior of six analogues designed by structurally modifying the KTP molecule. Specifically, KTP-A and KTP-B contain a –CN group at the ortho position, KTP-C and KTP-D have a –CN group at the meta position, and KTP-E and KTP-F feature a –CF3 group at the meta position. To assess these analogues, we conducted molecular dynamics simulations (MD) to study their inhibitory effects on human cyclooxygenase 2 (COX-2), providing detailed insights into the structure and dynamics of the protein both with and without ligands. MD simulation, enhanced by technological advances, has proven to be a powerful tool for new drug discovery. We further quantified the binding affinity of these drug molecules toward COX-2 using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy calculations. The dynamic properties were evaluated through analyses of root mean square deviations (RMSD), root mean square fluctuations (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), covariance matrix, principal component analysis (PCA), and Gibbs free energy landscapes (FEL). Ultimately, this study confirms that the six KTP derivatives are promising candidates for the treatment of inflammation, with KTP-B standing out as particularly effective.