Binding Free Energy Analysis Research Articles

Ligand and Structure-Based In Silico Determination of the Most Promising SARS-CoV-2 nsp16-nsp10 2'-o-Methyltransferase Complex Inhibitors among 3009 FDA Approved Drugs.

As a continuation of our earlier work against SARS-CoV-2, seven FDA-approved drugs were designated as the best SARS-CoV-2 nsp16-nsp10 2′-o-methyltransferase (2′OMTase) inhibitors through 3009 compounds. The in silico inhibitory potential of the examined compounds against SARS-CoV-2 nsp16-nsp10 2′-o-methyltransferase (PDB ID: (6W4H) was conducted through a multi-step screening approach. At the beginning, molecular fingerprints experiment with SAM (S-Adenosylmethionine), the co-crystallized ligand of the targeted enzyme, unveiled the resemblance of 147 drugs. Then, a structural similarity experiment recommended 26 compounds. Therefore, the 26 compounds were docked against 2′OMTase to reveal the potential inhibitory effect of seven promising compounds (Protirelin, (1187), Calcium folinate (1913), Raltegravir (1995), Regadenoson (2176), Ertapenem (2396), Methylergometrine (2532), and Thiamine pyrophosphate hydrochloride (2612)). Out of the docked ligands, Ertapenem (2396) showed an ideal binding mode like that of the co-crystallized ligand (SAM). It occupied all sub-pockets of the active site and bound the crucial amino acids. Accordingly, some MD simulation experiments (RMSD, RMSF, Rg, SASA, and H-bonding) have been conducted for the 2′OMTase—Ertapenem complex over 100 ns. The performed MD experiments verified the correct binding mode of Ertapenem against 2′OMTase exhibiting low energy and optimal dynamics. Finally, MM-PBSA studies indicated that Ertapenem bonded advantageously to the targeted protein with a free energy value of −43 KJ/mol. Furthermore, the binding free energy analysis revealed the essential amino acids of 2′OMTase that served positively to the binding. The achieved results bring hope to find a treatment for COVID-19 via in vitro and in vivo studies for the pointed compounds.

Mechanistic Insights Into Co-Administration of Allosteric and Orthosteric Drugs to Overcome Drug-Resistance in T315I BCR-ABL1

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm, driven by the BCR-ABL1 fusion oncoprotein. The discovery of orthosteric BCR-ABL1 tyrosine kinase inhibitors (TKIs) targeting its active ATP-binding pocket, such as first-generation Imatinib and second-generation Nilotinib (NIL), has profoundly revolutionized the therapeutic landscape of CML. However, currently targeted therapeutics still face considerable challenges with the inevitable emergence of drug-resistant mutations within BCR-ABL1. One of the most common resistant mutations in BCR-ABL1 is the T315I gatekeeper mutation, which confers resistance to most current TKIs in use. To resolve such conundrum, co-administration of orthosteric TKIs and allosteric drugs offers a novel paradigm to tackle drug resistance. Remarkably, previous studies have confirmed that the dual targeting BCR-ABL1 utilizing orthosteric TKI NIL and allosteric inhibitor ABL001 resulted in eradication of the CML xenograft tumors, exhibiting promising therapeutic potential. Previous studies have demonstrated the cooperated mechanism of two drugs. However, the conformational landscapes of synergistic effects remain unclear, hampering future efforts in optimizations and improvements. Hence, extensive large-scale molecular dynamics (MD) simulations of wide type (WT), WT-NIL, T315I, T315I-NIL, T315I-ABL001 and T315I-ABL001-NIL systems were carried out in an attempt to address such question. Simulation data revealed that the dynamic landscape of NIL-bound BCR-ABL1 was significantly reshaped upon ABL001 binding, as it shifted from an active conformation towards an inactive conformation. The community network of allosteric signaling was analyzed to elucidate the atomistic overview of allosteric regulation within BCR-ABL1. Moreover, binding free energy analysis unveiled that the affinity of NIL to BCR-ABL1 increased by the induction of ABL001, which led to its favorable binding and the release of drug resistance. The findings uncovered the in-depth structural mechanisms underpinning dual-targeting towards T315I BCR-ABL1 to overcome its drug resistance and will offer guidance for the rational design of next generations of BCR-ABL1 modulators and future combinatory therapeutic regimens.

Structural based investigation of novel pyrazole-thiazole Hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy

ABSTRACT CDK-1 and CDK-2 are two promising targets for cancer treatment as they are vital in tumor development, proliferation, and apoptosis during the cell cycle process. In treating cancers, CDK inhibitors (small molecules) are used to prevent the overproliferation and overexpression of cancer cells. Consequently, inhibiting CDKs is a promising treatment strategy in oncology. The limitations imposed by current CDK-1 and CDK-2 inhibitors, including neurotoxicity and the development of resistance, have prompted our group to use the novel synthesized pyrazole-thiazole hybrid analogues to investigate their possible potency against CDK-1 and CDK-2. The research study employed detailed computational approaches including molecular docking, molecular dynamics (MD) simulations, post-MD analyses such as RMSD, RMSF, RoG, per-residue energy decomposition, hydrogen bond lifetime analysis, and drug-likeness studies like ADME properties prediction and cytotoxicity, to predict the properties and inhibitory potentials of synthesized pyrazole-thiazole hybrid analogues against CDK-1 and CDK-2. The in silico binding free energy and other analysis reported in the study revealed that four (7 g, 8a, 8b, and 8 h) of the tested molecules against CDK-1 demonstrated a higher binding affinity and structural influence on the target protein than the known inhibitor, Roscovitine (RVT). Similarly, in the case of CDK-2, four (7b, 8a, 8b, and 8f) of the tested compounds showed better results than (RVT). Furthermore, structural examination of the two proteins after binding to the inhibitors revealed that the compounds form stable complexes with the targets and significantly reduced the structural flexibility of the proteins. Therefore, this study suggests the novel pyrazole-thiazole hybrid analogues as potential CDK-1 and CDK-2 inhibitors and could be potential lead compounds for target-based anticancer drugs inhibiting the important proteins, CDK-1 and CDK-2.

In silico and in vitro mapping of specificity patterns of glycosaminoglycans towards cysteine cathepsins B, L, K, S and V

Human cysteine cathepsins are lysosomal proteases, which are involved in different biological processes. Their enzymatic activity can be regulated by glycosaminoglycans (GAGs): long linear periodic negatively charged polysaccharides, which dimeric building blocks consist of uronic acid and hexosamine monosaccharide units. In this study, molecular docking simulations of chondroitin 4-sulfate, chondroitin 6-sulfate, heparin, heparan sulfate, dermatan sulfate and hyaluronic acid of various chain lengths were performed with cathepsins B, L, K, S and V and followed by molecular dynamics-based refinement and binding free energy analysis. We concluded that electrostatics might be a driving force for cathepsin-GAG interactions; indeed as in most of characterised systems, the increase of GAG chain length consequently leads to a more pronounced effect on the strength of cathepsin-GAG interactions. Results also suggest that binding of GAGs at different regions on cathepsins surface affect differently their enzymatic activity and could is dependent on cathepsin and GAG type. Present data contribute to systematic description of cathepsin-GAG interactions, which is helpful in understanding the subtle molecular mechanisms of protease regulation behind their biological functions.

High throughput virtual screening and molecular dynamics simulation analysis of phytomolecules against BfmR of Acinetobacter baumannii: anti-virulent drug development campaign

Acinetobacter baumannii is a notorious multidrug resistant bacterium responsible for several hospital acquired infections assisted by its capacity to develop biofilms. A. baumannii BfmR (RstA), a response regulator from the BfmR/S two-component signal transduction system, is the major controller of A. baumannii biofilm development and formation. As a result, BfmR represents a novel target for anti-biofilm treatment against A. baumannii. The discovery of the high-resolution crystal structure of BfmR provides a good chance for computational screening of its probable inhibitors. Therefore, in this study we aim to search new, less toxic, and natural BfmR inhibitors from 8450 phytomolecules available in the Indian Medicinal Plants, Phytochemistry and Therapeutic (IMPPAT) database by analyzing molecular docking against BfmR (PDB ID: 6BR7). Out of these 8450 phytomolecules 6742 molecules were successfully docked with BfmR with the docking score range −6.305 kcal/mol to +5.120 kcal/mol. Structure based-molecular docking (SB-MD) and ADMET (absorption, distribution, metabolism, excretion, & toxicity) profile examination revealed that Norepinephrine, Australine, Calystegine B3, 7,7 A-Diepialexine, and Alpha-Methylnoradrenaline phytocompounds strongly binds to the active site residues of BfmR. Furthermore, molecular dynamics simulation (MDS) studies for 100 ns and the binding free energy (MM/GBSA) analysis elucidated the binding mechanism of Calystegine B3, 7,7 A-Diepialexine, and Alpha-Methylnoradrenaline to BfmR. In summary, these phytocompounds seems to have the promising molecules against BfmR, and thus necessitates further verification by both in vitro and in vivo experiments. Highlights BfmR plays a key role in biofilm development and exopolysaccharide (EPS) synthesis in A. baumannii. Computational approach to search for promising BfmR inhibitors from IMPAAT database. The lead phytomolecules such as Calystegine B3, 7,7 A-Diepialexine, and Alpha-Methylnoradrenaline displayed significant binding with BfmR active site. The outcome of BfmR binding phytomolecules has broadened the scope of hit molecules validation. Communicated by Ramaswamy H. Sarma

Binding interaction of benzamide derivatives as inhibitors of DNA gyrase and Sec14p using Molegro Virtual Docker based on binding free energy

Abstract The docking simulation of benzamide derivatives as ligands and protein targets (DNA–gyrase) was performed and Sec14p binding mode interaction was predicted based on binding free energy analysis. Software Molegro Virtual Docking (MVD) was used to visualize the ligand–protein binding interactions. The results indicated the prevalence of steric or hydrophobic interactions among all the benzamide ligands besides hydrogen bonding or electrostatic interactions. The compounds B2, B4 against DNA gyrase, and compounds B3, B5 against Sec14p showed an uncompetitive pattern of inhibition as compared with the reference molecule. While compounds B1, B5 exhibited the best MolDock scores, i.e., −109.736 and −114.391 kcal/mol respectively for DNA gyrase, also compounds B1 and B2 against Sec14p displayed −100.105 and −119.451 kcal/mol sequentially. It was evident from the comparison of MolDock score for both the bacterial and fungal protein receptors that all the ligands were found to be more potent against DNA gyrase than Sec14p. However, only compound B2 with MolDock score −119.451 kcal/mol showed exceptional activity against Sec14p and was predicted to have potency as a lead compound to find a new anti-fungal therapeutic agent. Docking studies further highlighted the unique interactions such as tail-end hydrophobic rings of benzamide inhibitors with catalytically important amino acid residues, allowing flexibility in binding to both the receptors different from other inhibitors. These findings showed us that B1, B2 against Staphylococcus aureus and B5 against Saccharomyces cerevisiae could be leading compounds to discover new multidrug-resistant strains.

A multi-targeted approach to identify potential flavonoids against three targets in the SARS-CoV-2 life cycle

The advent and persistence of the Severe Acute Respiratory Syndrome Coronavirus – 2 (SARS-CoV-2)-induced Coronavirus Disease (COVID-19) pandemic since December 2019 has created the largest public health emergency in over a century. Despite the administration of multiple vaccines across the globe, there continues to be a lack of approved efficacious non-prophylactic interventions for the disease. Flavonoids are a class of phytochemicals with historically established antiviral, anti-inflammatory and antioxidative properties that are effective against cancers, type 2 diabetes mellitus, and even other human coronaviruses. To identify the most promising bioactive flavonoids against the SARS-CoV-2, this article screened a virtual library of 46 bioactive flavonoids against three promising targets in the SARS-CoV-2 life cycle: human TMPRSS2 protein, 3CLpro, and PLpro. By examining the effects of glycosylation and other structural-activity relationships, the presence of sugar moiety in flavonoids significantly reduces its binding energy. It increases the solubility of flavonoids leading to reduced toxicity and higher bioavailability. Through protein-ligand contact profiling, it was concluded that naringin formed more hydrogen bonds with TMPRSS2 and 3CLpro.In contrast, hesperidin formed a more significant number of hydrogen bonds with PLpro. These observations were complimented by the 100 ns molecular dynamics simulation and binding free energy analysis, which showed a considerable stability of docked bioflavonoids in the active site of SARS-CoV-2 target proteins. Finally, the binding affinity and stability of the selected docked complexes were compared with the reference ligands (camostat for TMPRSS2, GC376 for 3CLpro, and GRL0617 for PLpro) that strongly inhibit their respective SARS-COV-2 targets. Overall analysis revealed that the selected flavonoids could be potential therapeutic agents against SARS-CoV-2. Naringin showed better affinity and stability for TMPRSS2 and 3CLpro, whereas hesperidin showed a better binding relationship and stability for PLpro.

Pharmacophore-guided virtual screening and dynamic simulation of Kallikrein-5 inhibitor: Discovery of potential molecules for rosacea therapy

Rosacea is a common chronic inflammatory skin disease characterized by flushing, transient erythema, persistent erythema, telangiectasia, papules, pustules, phymata, edema, pain, stinging, or burning, and its treatment is still being developed. Rosacea is known to be regulated by excessive activation of Kallikrein-5 (KLK5). This research aimed to discover potent compounds for rosacea therapy based on virtual screening guided by pharmacophore and molecular dynamic simulation targeting KLK5. First, we generated and validated the pharmacophore model for target using the model to screen the compounds from the ZINC database and then conducted molecular docking and molecular dynamic simulations on KLK5. The generated pharmacophore model of KLK5 inhibitor has several features, such as F1: aromatic, F2: aromatic, F3: aromatic, F4: aromatic and hydrophobic, and F5: hydrogen bonding acceptors and donors. Subsequently, we used the pharmacophore model to screen the ZINC database and obtained 102 hits. Six best hits were obtained based on the docking score of KLK5, and the molecular interactions were revealed. Furthermore, the molecular dynamic simulation was conducted for 50 ns, and the system stability was assessed via RMSD, RMSF, MM-PBSA binding free energy, Rg, SASA, and PCA analyses. ZINC000022339916 was found to exhibit better stability compared with other hit compounds, azelaic acid, and native ligand of co-crystal KLK5 inhibitor. The compound is currently in the ordering process, and the study of biological activity will be held and reported soon.

N-Acetyldopamine dimers from Oxya chinensis sinuosa attenuates lipopolysaccharides induced inflammation and inhibits cathepsin C activity

Oxya chinensis sinuosa (rice field grasshopper) is an edible insect with numerous health beneficial properties, traditionally being used to treat many ailments in Korea and other countries. O. chinensis sinuosa has been used from centuries, however, a little is known about the chemical functionality of its bioactive compounds. Therefore, this study examined the anti-inflammatory and cathepsin C inhibitory activities of N-acetyldopamine dimer (2R, 3S)-2-(3′,4′-dihydroxyphenyl)-3-acetylamino-7-(N-acetyl-2″-aminoethyl)-1,4-benzodioxane (DAB1) isolated from O. chinensis sinuosa. Results showed that DAB1 reduced the expression of pro-inflammatory mediator (iNOS, COX-2) and cytokines (TNF-α, IL-1β, and IL-6), and curtailed the nuclear translocation of NF-κB by inhibiting the phosphorylation of IκBα in lipopolysaccharide stimulated macrophages. Additionally, DAB1 inhibited cathepsin C activity at the cellular level, supported by in vitro assay (Ki, 71.56 ± 10.21 µM and Kis, 133.55 ± 18.2 µM). Moreover, combinatorial molecular simulation and binding free energy analysis suggested a significant stability and binding affinity of cathepsin C-DAB1 complex via formation of hydrogen bond and hydrophobic interactions with the catalytic residues (Gln228, Thr379, Asn380, and Hie381). Also, essential dynamics analysis showed DAB1 induced non-functional motions in cathepsin C structure. Collectively, DAB1 was concluded as anti-inflammatory and cathepsin C inhibiting agent and could be used in the drug development against respective diseases.

Ligand-Induced Conformational and Dynamical Changes in a GT-B Glycosyltransferase: Molecular Dynamics Simulations of Heptosyltransferase I Complexes.

Understanding the dynamical motions and ligand recognition motifs of heptosyltransferase I (HepI) can be critical to discerning the behavior of other glycosyltransferase (GT) enzymes. Prior studies in our lab have demonstrated that GTs in the GT-B structural class, which are characterized by their connection of two Rossman-like domains by a linker region, have conserved structural fold and dynamical motions, despite low sequence homology, therefore making discoveries found in HepI transferable to other GT-B enzymes. Through molecular dynamics simulations and ligand binding free energy analysis of HepI in the apo and bound complexes (for all kinetically relevant combinations of the native substrates/products), we have determined the energetically favored enzymatic pathway for ligand binding and release. Our principal component, dynamic cross correlation, and network analyses of the simulations have revealed correlated motions involving residues within the N-terminal domain communicating with C-terminal domain residues via both proximal amino acid residues and also functional groups of the bound substrates. Analyses of the structural changes, energetics of substrate/product binding, and changes in pKa have elucidated a variety of inter and intradomain interactions that are critical for enzyme catalysis. These data corroborate our experimental observations of protein conformational changes observed in both presteady state kinetic and circular dichroism analyses of HepI. These simulations provided invaluable structural insights into the regions involved in HepI conformational rearrangement upon ligand binding. Understanding the specific interactions governing conformational changes is likely to enhance our efforts to develop novel dynamics disrupting inhibitors against GT-B structural enzymes in the future.

Molecular dynamics investigation of ivermectin bound to importin alpha/beta heterodimer

ABSTRACT Ivermectin (D1), an FDA-approved drug, is mainly used as an inhibitor for the treatment of parasitic infections. This drug was drawn attention due to its effectiveness in COVID-19 treatment. In this work, we investigated how ivermectin and its analogues are interacted with Impα/β1 heterodimer by molecular docking, steered molecular dynamics (SMD), classical molecular dynamics (MD), and MM/PBSA binding free energy analysis. Docking results showed that ivermectin dimer showed the highest binding affinity of −12.2 kcal/mol compared to its monomer. In SMD, the highest acceleration of 600 pm/ps2 is noticed for D1-Impα/β1 complex in the distance from 18.27 to 18.36 Å. The pulling force of 1745.86 pN is also detected for D1-Impα/β1. To validate the docking and SMD results, 100 ns molecular dynamics (MD) simulation is performed on the D1-Impα/β1 complex. The average RMSD value indicates a good structural stability of the complex despite some significant changes at the beginning. It is noted that most of the residues are stable over the simulation time with an average RMSF value of less than 2.65 Å. The MM/PBSA free energy of ivermectin also shows strong and spontaneous binding with the Impα/β1.

Structural and functional insights into the major mutations of SARS-CoV-2 Spike RBD and its interaction with human ACE2 receptor

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread around the world jeopardizing the global economy and health. The rapid proliferation and infectivity of the virus can be attributed to many accumulating mutations in the spike protein leading to continuous generation of variants. The spike protein is a glycoprotein that recognizes and binds to cell surface receptor known as angiotensin-converting enzyme 2 (ACE2) leading to the fusion of the viral and host cell membranes and entry into the host cells. These circulating variants in the population have greatly impacted the virulence, transmissibility, and immunological evasion of the host. The present study is aimed at understanding the impact of the major mutations (L452R, T478K and N501Y) in the receptor-binding domain (RBD) of spike protein and their consequences on the binding affinity to human ACE2 through protein–protein docking and molecular dynamics simulation approaches. Protein-protein docking and Molecular mechanics with generalised Born and surface area solvation (MM/GBSA) binding free energy analysis reveal that the spike mutants-L452R, T478K and N501Y have a higher binding affinity to human ACE2 as compared to the native spike protein. The increase in the number of interface residues, interface area and intermolecular forces such as hydrogen bonds, salt bridges and non-bonded contacts corroborated with the increase in the binding affinity of the spike mutants to ACE2. Further, 75 ns all-atom molecular dynamics simulation investigations show variations in the geometric properties such as root mean square deviation (RMSD), radius of gyration (Rg), total solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs) in the mutant spike:ACE2 complexes with respect to the native spike:ACE2 complex. Therefore, the findings of this study unravel plausible molecular mechanisms of increase in binding affinity of spike mutants (L452R, T478K and N501Y) to human ACE2 leading to higher virulence and infectivity of emerging SARS-CoV-2 variants. The study will further aid in designing novel therapeutics targeting the interface residues between spike protein and ACE2 receptor.

Sulfonylbis(acylhydrazones) as anticholinesterase inhibitors: Synthesis, in vitro biological evaluation and computational studies

This current research work is focused on the synthesis of sulfonyl-mediated hydrazones, its exploration as anticholinesterase inhibitors, in vitro biological evaluation, and computational studies. A series of 21 novel bis(acylhydrazones) (4a-u) have been synthesized in good to excellent yields using 4,4ꞌ-sulfonyldiphenol as the precursor. Characterization of the synthesized compounds was achieved via spectroscopic techniques i.e. UV, FT-IR, NMR (1H and 13C), and HRMS. In vitro anticholinesterase activity of these compounds was performed using acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) as cholinesterase enzymes. Among all the compounds tested, compounds 4 g and 4 h were found to be the most significant AChE inhibitions with IC50 values of 101.4 and 102.7 µM as compared to the standard cholinesterase inhibitor i.e., galantamine (IC50 = 104.5 µM). Additionally, compound 4 g was also found to be an excellent inhibitor of BChE with an IC50 value of 136.0 µM as compared to the standard galantamine (IC50 = 156.8 µM). Molecular docking of the most active compounds 4 g and 4 h also supported their potential to interact with cholinesterase enzymes. Further affirmation on the intermolecular stability of the docked complexes was achieved by molecular dynamics simulation for 100 ns with mean deviations ∼2 Å. Residue level fluctuations analysis also interpreted the good stability of compounds interacting pocket residues. Lastly, binding free energy analysis was performed that decipher the intermolecular interactions that are dominated by both van der Waals and electrostatic energies. In short, both theoretical and experimental studies unveiled the compounds as potent blockers of cholinesterase enzymes.

Novel acylpiperidine analogues as potential aphid repellent agents: Rational design, synthesis and repellent activity

Odorant-binding protein (OBP) is a promising potential target and can be used as a template for developing insect control agents due to its ability to bind to and transport semiochemicals to olfactory receptors, thus triggering behavioural responses among insects. In this study, 27 novel acylpiperidine analogues were designed and synthesised by introducing the hydrophobic long chain of the aphid alarm pheromone (E)-β-farnesene (EβF) into the polar acylpiperidine group of the commercial insect repellent icaridine based on the binding cavity characteristics of an OBP of the pea aphid Acyrthosiphon pisum, ApisOBP3. Compound 14c displayed good repellent activity against the pea aphids with a repellence rate of 61.5% at a concentration of 6 μg/μL. The equilibrium dissociation constant (Ki) of compound 14c against ApisOBP3 was 20.92 μM in competitive fluorescence binding assays; this value is similar to the Ki of the commercial insect repellent icaridine (20.56 μM). Molecular dynamics simulation revealed that the EβF long chain of compound 14c showed considerable hydrophobic interactions with the binding domain of ApisOBP3. Moreover, the acylpiperidine moiety of compound 14c formed one hydrogen bond and multiple carbon–hydrogen bonds with the Phe2 and Asn109 residues, respectively. The binding free energy analysis indicated that the contribution of the van der Waals force to the binding affinity was approximately twice as great as that of the electrostatic force. These studies provide significant guidance for the rational designing and efficient identification of novel insect repellent agents.

Molecular simulations reveal the impact of RAMP1 on ligand binding and dynamics of calcitonin gene-related peptide receptor (CGRPR) heterodimer

Calcitonin gene-related peptide receptor (CGRPR) is a heterodimer protein complex consisting of a class-B G protein-coupled receptor (GPCR) named calcitonin receptor-like receptor (CLR) and an accessory protein, receptor activity modifying protein type 1 (RAMP1). Here in this study, with several molecular modeling approaches and molecular dynamics (MD) simulations, the structural and dynamical effects of RAMP1 on the binding of small molecule CGRPR inhibitors (namely rimegepant and telcagepant) to the CGRPR extracellular ectodomain complex site (site 1) and transmembrane binding site (site 2) are investigated. Results showed that although these molecules stay stable at site 1, they can also bind to site 2, which may be interpreted as non-specificity of the ligands, however, most of these interactions at transmembrane binding site are not sustainable or are weak. Furthermore, to examine the site 2 for gepant binding, different in silico experiments (i.e., alanine scanning mutagenesis, SiteMap, ligand decomposition binding free energy analyses) are also conducted and the results confirmed the putative binding pocket (site 2) of the gepants at the CGRPRs.

Screening of phytochemicals as potential anti-breast cancer agents targeting HER2: an in-silico approach

Breast cancer is the most common cancer among women around the world. Human Epidermal growth factor Receptor-2 (HER2) is a membrane tyrosine kinase overexpressed in 30% of human breast cancers; thus, it serves as an important drug target. Currently available HER2 inhibitor lapatinib targets the ATP binding site of the cytoplasmic kinase domain, blocking autophosphorylation and activation of HER-2. However, it causes side effects like diarrhea, nausea, rash and possible liver toxicity. As phytochemicals have fewer side effects and are relatively affordable, they offer an effective alternative. Hence, we aimed to identify potential phytochemicals that could act as HER2 inhibitors employing computational methods such as molecular docking, molecular dynamic simulation, and ADMET prediction. Out of 1500 phytochemicals docked to the ATP binding site of the HER2 kinase domain, luxenchalcone, rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone exhibited higher binding affinity than the reference inhibitor and satisfied the Lipinski’s rule of five. Analysis of molecular dynamics simulation trajectory showed that Rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone formed a stable and compact complex without vast conformational fluctuations. MM/PBSA binding free energy analysis revealed that Rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone have high binding affinity to HER2. Therefore, Rhinacanthin Q, subtrifloralacton D, and 7,7″-dimethyllanaraflavone could be potential bioactive molecules to act as inhibitor of HER2 protein. Eventually, experimental studies are needed to evaluate the potentials of these phytochemicals further. The development of drug for HER2 positive breast cancer could be accelerated with the findings of our research. Communicated by Ramaswamy H. Sarma

Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study.

The papain-like protease (PLpro) of the coronavirus (CoV) family plays an essential role in processing the viral polyprotein and immune evasion. Additional proteolytic activities of PLpro include deubiquitination and deISGylation, which can reverse the post-translational modification of cellular proteins conjugated with ubiquitin or (Ub) or Ub-like interferon-stimulated gene product 15 (ISG15). These activities regulate innate immune responses against viral infection. Thus, PLpro is a potential antiviral target. Here, we have described the structural and energetic basis of recognition of PLpro by the human ISG15 protein (hISG15) using atomistic molecular dynamics simulation across the CoV family, i.e., MERS-CoV (MCoV), SARS-CoV (SCoV), and SARS-CoV-2 (SCoV2). The cumulative simulation length for all trajectories was 32.0 μs. In the absence of the complete crystal structure of complexes, protein–protein docking was used. A mutation (R167E) was introduced across all three PLpro to study the effect of mutation on the protein–protein binding. Our study reveals that the apo-ISG15 protein remains closed while it adopts an open conformation when bound to PLpro, although the degree of openness varies across the CoV family. The binding free energy analysis suggests that hISG15 binds more strongly with SCoV2-PLpro compared to SCoV or MCoV. The intermolecular electrostatic interaction drives the hISG15-PLpro complexation. Our study showed that SCoV or MCoV-PLpro binds more strongly with the C-domain of hISG15, while SCoV2-PLpro binds more favorably the N-domain of hISG15. Overall, our study explains the molecular basis of differential deISGylating activities of PLpro among the CoV family and the specificity of SCoV2-PLpro toward hISG15.

Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.

Riboswitches are naturally occurring RNA elements that control bacterial gene expression by binding to specific small molecules. They serve as important models for RNA-small molecule recognition and have also become a novel class of targets for developing antibiotics. Here, we carried out conventional and enhanced-sampling molecular dynamics (MD) simulations, totaling 153.5 μs, to characterize the determinants of binding free energies and unbinding paths for the cognate and synthetic ligands of a PreQ1 riboswitch. Binding free energy analysis showed that two triplets of nucleotides, U6-C15-A29 and G5-G11-C16, contribute the most to the binding of the cognate ligands, by hydrogen bonding and by base stacking, respectively. Mg2+ ions are essential in stabilizing the binding pocket. For the synthetic ligands, the hydrogen-bonding contributions of the U6-C15-A29 triplet are significantly compromised, and the bound state resembles the apo state in several respects, including the disengagement of the C15-A14-A13 and A32-G33 base stacks. The bulkier synthetic ligands lead to significantly loosening of the binding pocket, including extrusion of the C15 nucleobase and a widening of the C15-C30 groove. Enhanced-sampling simulations further revealed that the cognate and synthetic ligands unbind in almost opposite directions. Our work offers new insight for designing riboswitch ligands.

Characterization of the insecticide detoxification carboxylesterase Boest1 from Bradysia odoriphaga Yang et Zhang (Diptera: Sciaridae).

In insects, carboxylesterases (CarEs) are enzymes involved in the detoxification of insecticides. However, the molecular mechanism of CarE-mediated insecticide metabolism in Bradysia odoriphaga, a serious agricultural pest, remains unclear. The aim of this study is to investigate the detoxification process of malathion, bifenthrin, and imidacloprid by B. odoriphaga carboxylesterase (Boest1). An alpha class CarE gene Boest1 was cloned from B. odoriphaga. The results of real-time quantitative polymerase chain reaction showed that Boest1 is up-regulated with age during the larval stage, and the level of transcription of Boest1 is higher in the midgut and Malpighian tubule than in other tissues. The expression level of Boest1 was significantly increased after exposure to malathion and bifenthrin. Recombinant BoEST1 expressed in vitro showed high catalytic activity toward α-naphthyl acetate, which was substantially inhibited by malathion and triphenyl phosphate. The in vitro metabolism assays showed that BoEST1 demonstrates hydrolytic capacity toward malathion and bifenthrin but not imidacloprid. The binding free energy analysis indicates that BoEST1 has a higher affinity for malathion and bifenthrin than imidacloprid. These results suggest that BoEST1 plays a role in the breakdown of insecticides and may be involved in the development of resistance in the Chinese chive pest B. odoriphaga; our findings also provide data for better pest management and perspectives for new pesticides development. © 2021 Society of Chemical Industry.

Difference in the binding mechanisms of ABT-263/43b with Bcl-xL/Bcl-2: computational perspective on the accurate binding free energy analysis.

B-cell lymphoma/leukemia gene-2(Bcl-2) protein family known for regulating cell cycle arrest and subsequent cell death is highly expressed in a variety of cancers. Among them, the Bcl-xL and Bcl-2 are two essential proteins in the Bcl-2 family. In the present work, the differences in binding modes as between the two proteins and two ligands ABT-263/43b were investigated and compared. And the computational alanine scanning combined with the recently developed interaction entropy (AS-IE) method was employed for predicting their binding free energies and finding those amino acids that were more critical during the binding process. The result showed that the binding free energy calculated by the AS-IE method was more in line with experimental values than the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. Besides, no significant difference was found between Bcl-xL and ABT-263/43b in the binding free energy, which Bcl-xL showed slightly weaker binding free energy to 43b because of the fewer number of key residues with interactions. Nonetheless, compared with the Bcl-2 and 43b complex, the Bcl-2 and ABT-263 system had greater number of key residues interacting with ABT-263, in particular, contribute favorably, resulting in a stronger binding ability for the Bcl-2 and ABT-263 systems. The van der Waals and hydrogen bond contributions were significant in the four protein-ligand complexes. Overall, Tyr108 was found to be the common key residues in the Bcl-xL-ligand complex, while Tyr105, Glu100, and Glu143 were established as the common key residue in the Bcl-2-ligand systems. We hope that the predicted hot spot residues and their energy distributions can guide the design of peptide and small-molecule drugs targeting Bcl-xL and Bcl-2.