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The severe acute respiratory syndrome coronavirus (SARS‐CoV‐2) pandemic has triggered a significant impact on global public health security, it is urgent to develop effective antiviral drugs. Previous studies have found that binding to ACE2 is a key step in the invasion of SARS‐CoV‐2 into host cells, so virus invasion can be inhibited by blocking ACE2, but there are few reports on this kind of specific inhibitor. Our previous study found that Harringtonine (HT) can inhibit the entry of SARS‐CoV‐2 spike pseudovirus into ACE2h cells, but its relatively high cytotoxicity limits its further development. Amino acid modification of the active components can increase their solubility and reduce their cytotoxicity. Therefore, in this study, seven new derivatives were synthesized by amino acid modification of its core structure Cephalotaxine. The target compounds were evaluated by cell viability assay and the SARS‐CoV‐2 spike pseudovirus entry assay. Compound CET‐1 significantly inhibited the entry of pseudovirus into ACE2h cells and showed less cytotoxicity than HT. Molecular docking results showed that CET‐1 could bind TYR83, an important residue of ACE2, just like HT. In conclusion, our study provided a novel compound with more potential activity and lower toxicity than HT on inhibiting the SARS‐CoV‐2 spike pseudovirus infection, which makes it possible to be a lead compound as an antiviral drug in the future. [ABSTRACT FROM AUTHOR]

Taxol (paclitaxel) is the first approved microtubule‐stabilizing agent (MSA) by binding stoichiometrically to tubulin, which is considered to be one of the most significant advances in first‐line chemotherapy against diverse tumors. However, a large number of residue missence mutations harboring in the tubulin have been observed to cause acquired drug resistance, largely limiting the clinical application of Taxol and its analogs in chemotherapy. A systematic investigation of the intermolecular interactions between the Taxol and various tubulin mutants would help to establish a comprehensive picture of drug response to tubulin mutations in clinical treatment of cancer, and to design new MSA agents with high potency and selectivity to overcome drug resistance. In this study, we described an integration of in silico analysis and in vitro assay (iSiV) to profile Taxol against a panel of 149 clinically observed, cancer‐associated missence mutations in β‐tubulin at molecular and cellular levels, aiming to a systematic understanding of molecular mechanism and biological implication underlying drug resistance and sensitivity conferring from tubulin mutations. It is revealed that the Taxol‐resistant mutations can be classified into three types: (I) nonbonded interaction broken due to mutation, (II) steric hindrance caused by mutation, and (III) conformational change upon mutation. In addition, we identified three new Taxol‐resistant mutations (C239Y, T274I, and R320P) that can largely reduce the binding affinity of Taxol to tubulin at molecular level, in which the T274I and R320P were observed to considerably impair the antitumor activity of Taxol at cellular level. Moreover, a novel drug‐susceptible mutation (M363T) was also identified, which improves Taxol affinity by 2.6‐fold and decreases Taxol antitumor EC50 values from 29.4 to 18.7 μM. [ABSTRACT FROM AUTHOR]

The α‐amylase, SusG, is a principal component of the Bacteroides thetaiotaomicron (Bt) starch utilization system (Sus) used to metabolize complex starch molecules in the human gastrointestinal (GI) tract. We previously reported the non‐microbicidal growth inhibition of Bt by the acarbose‐mediated arrest of the Sus as a potential therapeutic strategy. Herein, we report a computational approach using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation to explore the interactive mechanism between acarbose and SusG at the atomic level in an effort to understand how acarbose shuts down the Bt Sus. The docking analysis reveals that acarbose binds orthosterically to SusG with a binding affinity of −8.3 kcal/mol. The MD simulation provides evidence of conformational variability of acarbose at the active site of SusG and also suggests that acarbose interacts with the main catalytic residues via a general acid–base double‐displacement catalytic mechanism. These results suggest that small molecule competitive inhibition against the SusG protein could impact the entire Bt Sus and eliminate or reduce the system's ability to metabolize starch. This computational strategy could serve as a potential avenue for structure‐based drug design to discover other small molecules capable of inhibiting the Sus of Bt with high potency, thus providing a holistic approach for selective modulation of the GI microbiota. [ABSTRACT FROM AUTHOR]

A series of novel noncovalent glycine/β‐alanine anilide derivatives possessing 2‐chloronaphthoquinone structure as a pharmacophoric unit were designed, synthesized, and evaluated for their antiproliferative and antiproteasomal activities against MCF‐7 cell line, in vitro. According to biological activity results, all the target compounds showed antiproliferative activity in the range of IC50 = 7.10 ± 0.10–41.08 ± 0.14 μM and most of them exhibited inhibitory efficacy with varying ratios against the three catalytic subunits (β1, β2, and β5) presenting caspase‐like (C‐L), trypsin‐like (T‐L) and chymotrypsin‐like (ChT‐L) activities of proteasome. The antiproteasomal activity evaluations revealed that compounds preferentially inhibited the β5 subunit compared with β1 and β2 subunits of the proteasome. Among the compounds, compounds 7 and 9 showed the highest antiproliferative activity with an IC50 value of 7.10 ± 0.10 and 7.43 ± 0.25 μM, respectively. Additionally, compound 7 displayed comparable potency to PI‐083 lead compound in terms of β5 antiproteasomal activity with an inhibition percentage of 34.67 at 10 μM. This compound showed an IC50 value of 32.30 ± 0.45 μM against β5 subunit. Furthermore, molecular modeling studies of the most active compound 7 revealed key interactions with β5 subunit. The results suggest that this class of compounds may be beneficial for the development of new potent proteasome inhibitors. [ABSTRACT FROM AUTHOR]

The nitric oxide/cyclic guanosine monophosphate (NO/cGMP) signaling pathway is an effective mechanism involved in the treatment of hypertension. In our search for potential antihypertensive agents, a series of novel NO‐donor derivatives of the 4‐chromanone skeleton were designed and synthesized by coupling furoxans or nitrooxy NO‐donor moieties. All derivatives showed enhanced nitric oxide releasing capacity and vasodilator activity with EC50 values ranging from 0.0215 μM to 1.46 μM, obviously superior to those of precursor 3. These biological evaluations indicated that all compounds displayed an important vasorelaxant effect, and several compounds (9c, 14b, 14c, 14d) presented good vasodilator activity, with 14c being the best. Furthermore, molecular modeling studies revealed that compound 14c occupied the pocket well with the phosphodiesterase 5 domain in a favorable conformation. In conclusion, we observed that these novel compounds can act as structural templates for the design and subsequent development of new vasodilators and antihypertensive drugs. [ABSTRACT FROM AUTHOR]

Cheminformatics utilizing machine learning (ML) techniques have opened up a new horizon in drug discovery. This is owing to vast chemical space expansion with rocketing numbers of expected hits and lead compounds that match druggable macromolecular targets, in particular from natural compounds. Due to the natural products' (NP) structural complexity, uniqueness, and diversity, they could occupy a bigger space in pharmaceuticals, allowing the industry to pursue more selective leads in the nanomolar range of binding affinity. ML is an essential part of each step of the drug design pipeline, such as target prediction, compound library preparation, and lead optimization. Notably, molecular mechanic and dynamic simulations, induced docking, and free energy perturbations are essential in predicting best binding poses, binding free energy values, and molecular mechanics force fields. Those applications have leveraged from artificial intelligence (AI), which decreases the computational costs required for such costly simulations. This review aimed to describe chemical space and compound libraries related to NPs. High‐throughput screening utilized for fractionating NPs and high‐throughput virtual screening and their strategies, and significance, are reviewed. Particular emphasis was given to AI approaches, ML tools, algorithms, and techniques, especially in drug discovery of macrocyclic compounds and approaches in computer‐aided and ML‐based drug discovery. Anthraquinone derivatives were discussed as a source of new lead compounds that can be developed using ML tools for diverse medicinal uses such as cancer, infectious diseases, and metabolic disorders. Furthermore, the power of principal component analysis in understanding relevant protein conformations, and molecular modeling of protein–ligand interaction were also presented. Apart from being a concise reference for cheminformatics, this review is a useful text to understand the application of ML‐based algorithms to molecular dynamics simulation and in silico absorption, distribution, metabolism, excretion, and toxicity prediction. [ABSTRACT FROM AUTHOR]

Interleukin‐17 (IL‐17) is a family of pro‐inflammatory cytokines and has been involved in the pathogenesis of chronic inflammatory and autoimmune diseases. The IL‐17E, also known as IL‐25, is a distinct member of this family that binds to its unique receptor IL‐17Rb to induce the activation of nuclear factor kappa‐light‐chain enhancer of activated B cells. Here, we systematically examined the intermolecular recognition and association of IL‐25 with IL‐17Rb and demonstrated that the IL‐25 primarily adopts two discrete linear and cyclic epitopes to interact with IL‐17Rb. The two epitopes are separately located in the monomers 1 and 2 of IL‐25 homodimer and cover sequences 125DPRGNSELLYHN136 and 77ELDRDLNRLPQDLY90. They totally contribute 71.6% binding energy to the full‐length IL‐25. The linear epitope targets a site spanning over the extracellular fnIIID1 and fnIIID2 domains of IL‐17Rb, while the cyclic epitope primarily binds at the fnIIID1 domain. In addition, we also found that the linear and cyclic epitopes are natively folded into ordered single‐stranded and double‐stranded conformations in IL‐25 protein context, respectively, but would become largely disordered when splitting from the context to be free peptides, which, however, cannot bind effectively to IL‐17Rb as them in the native state. In this respect, we extended the cyclic epitope to cover the whole IL‐25 double‐stranded region and added a disulfide bridge across its two strands at three selected anchor residue pairs. It is revealed that the disulfide‐stapled peptides can be constrained into a native‐like conformation and thus exhibit an improved binding potency to IL‐17Rb as compared to their unstapled counterpart. [ABSTRACT FROM AUTHOR]

With the rise in antibiotic resistance, there is interest in discovering new drugs active against new targets. Here, we investigate the dynamic structures of three isoprenoid synthases from Mycobacterium tuberculosis using molecular dynamics (MD) methods with a view to discovering new drug leads. Two of the enzymes, cis-farnesyl diphosphate synthase (cis-FPPS) and cis-decaprenyl diphosphate synthase (cis-DPPS), are involved in bacterial cell wall biosynthesis, while the third, tuberculosinyl adenosine synthase (Rv3378c), is involved in virulence factor formation. The MD results for these three enzymes were then compared with previous results on undecaprenyl diphosphate synthase (UPPS) by means of active site volume fluctuation and principal component analyses. In addition, an analysis of the binding of prenyl diphosphates to cis-FPPS, cis-DPPS, and UPPS utilizing the new MD results is reported. We also screened libraries of inhibitors against cis-DPPS, finding ~1 μm inhibitors, and used the receiver operating characteristic-area under the curve (ROC-AUC) method to test the predictive power of X-ray and MD-derived cis-DPPS receptors. We found that one compound with potent M. tuberculosis cell growth inhibition activity was an IC(50) ~0.5- to 20-μm inhibitor (depending on substrate) of cis-DPPS, a ~660-nm inhibitor of Rv3378c as well as a 4.8-μm inhibitor of cis-FPPS, opening up the possibility of multitarget inhibition involving both cell wall biosynthesis and virulence factor formation.

In the fight against heart failure, therapeutics that have the ability to increase the contractile power of the heart are urgently needed. One possible route of action to improve heart contractile power is increasing the calcium sensitivity of the thin filament. From a pharmaceutical standpoint, calcium sensitizers have the distinct advantage of not altering cardiomyocyte calcium levels and thus have lower potential for side-effects. Small chemical molecules have been shown to bind to the interface between cTnC and the cTnI switch peptide and exhibit calcium-sensitizing properties, possibly by stabilizing cTnC in an open conformation. Building on existing structural data of a known calcium sensitizer bound to cardiac troponin, we combined computational structure-based virtual screening drug discovery methods and solution NMR titration assays to identify a novel calcium sensitizer 4-(4-(2,5-dimethylphenyl)-1-piperazinyl)-3-pyridinamine (NSC147866) which binds to cTnC and the cTnC-cTnI147-163 complex. Its presence increases the affinity of switch peptide to cTnC by approximately a factor of two. This action is comparable to that of known levosimendan analogues.

In most eubacteria, apicomplexans, and most plants, including the causal agents for diseases such as malaria, leprosy, and tuberculosis, the methylerythritol phosphate pathway is the route for the biosynthesis of the C(5) precursors to the essential isoprenoid class of compounds. Owing to their absence in humans, the enzymes of the methylerythritol phosphate pathway have become attractive targets for drug discovery. This work investigates a new class of inhibitors against the second enzyme of the pathway, 1-deoxy-D-xylulose 5-phosphate reductoisomerase. Inhibition of this enzyme may involve the chelation of a crucial active site Mn ion, and the metal-chelating moieties studied here have previously been shown to be successful in application to the zinc-dependent metalloproteinases. Quantum mechanics and docking calculations presented in this work suggest the transferability of these metal-chelating compounds to Mn-containing 1-deoxy-D-xylulose 5-phosphate reductoisomerase enzyme, as a promising starting point to the development of potent inhibitors.

Systemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis; however, non‐albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first‐choice antifungal drugs for candidiasis; however, they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane permeability. In this study, we screened for antifungal activity of an in‐house azole library of 65 compounds to identify hit matter followed by a molecular modeling study for their CYP51 inhibition mechanism. Antifungal susceptibility tests against standard Candida spp. including C. albicans revealed derivatives 12 and 13 as highly active. Furthermore, they showed potent antibiofilm activity as well as neglectable cytotoxicity in a mouse fibroblast assay. According to molecular docking studies, 12 and 13 have the necessary binding characteristics for effective inhibition of CYP51. Finally, molecular dynamics simulations of the C. albicans CYP51 (CACYP51) homology model's catalytic site complexed with 13 were stable demonstrating excellent binding. [ABSTRACT FROM AUTHOR]

(R/S)‐Salsolinol is a full agonist of the μ‐opioid receptor (μOR) Gi protein pathway via its (S)‐enantiomer and is functionally selective as it does not promote β‐arrestin recruitment. Compared to (S)‐salsolinol, the (R)‐enantiomer is a less potent agonist of the Gi protein pathway. We have now studied the interactions of the salsolinol enantiomers docked in the binding pocket of the μOR to determine the molecular interactions that promote enantiomeric specificity and functional selectivity of (R/S)‐salsolinol. Molecular dynamics simulations showed that (S)‐salsolinol interacted with 8 of the 11 residues of the μOR binding site, enough to stabilize the molecule. (R)‐Salsolinol showed higher mobility with fewer prevalent bonds. Hence, the methyl group bound to the (S)‐stereogenic center promoted more favorable interactions in the μOR binding site than in the (R)‐orientation. Because (S)‐salsolinol is a small molecule (179.2 Da), it did not interact with residues implicated in the binding of larger morphinan agonists that are located toward the extracellular portion of the binding pocket: W3187.35, I3227.39, and Y3267.43. Our results suggest that contact with residues which (S)‐salsolinol interacts with are enough to elicit Gi protein activation, and possibly define a minimum set required by μOR ligands to promote activation of the Gi protein pathway. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are small molecules present in all living beings. Despite their huge sequence variability, AMPs present great structural conservation, mainly in cysteine‐stabilized families. Moreover, in non‐model plants, it is possible to detect cysteine‐stabilized AMPs (cs‐AMPs) with different sequences not covered by conventional searches. Here, we described a threading application for cs‐AMP identification in the non‐model arum lily (Zantedeschia aethiopica) plant, exploring the spathe transcriptome. By using the predicted proteins from the Z. aethiopica transcriptome as our primary source of sequences, we have filtered by using structural alignments of 12 putative cs‐AMP sequences. The two unreported sequences were submitted to PCR validation, and ZaLTP7 gene was confirmed. By using the structure alignments, we classified ZaLTP7 as an LTP type 2‐like. The successful threading application for cs‐AMP identification is an important advance in transcriptomic and proteomic data mining. Besides, the same approach could be applied to the use of NGS public data to discover molecules to combat multidrug‐resistant bacteria. [ABSTRACT FROM AUTHOR]

The antimicrobial activities of natural products have attracted much attention due to the increasing incidence of pathogens that have become resistant to drugs. Thus, it has been attempted to promisingly manage infectious diseases via a new group of therapeutic agents called antimicrobial peptides. In this study, a novel antifungal peptide, MCh‐AMP1, was purified by reverse phase HPLC and sequenced by de novo sequencing and Edman degradation. The antifungal activity, safety, thermal, and pH stability of MCh‐AMP1 were determined. This peptide demonstrated an antifungal activity against the tested Candida and Aspergillus species with MIC values in the range of 3.33–6.66 μM and 6.66–13.32 μM, respectively. Further, physicochemical properties and molecular modeling of MCh‐AMP1 were evaluated. MCh‐AMP1 demonstrated 3.65% hemolytic activity at the concentration of 13.32 μM on human red blood cells and 10% toxicity after 48 hr at the same concentration on HEK293 cell lines. The antifungal activity of MCh‐AMP1 against Candida albicans was stable at a temperature range of 30–50°C and at the pH level of 7–11. The present study indicates that MCh‐AMP1 may be considered as a new antifungal agent with therapeutic potential against major human pathogenic fungi. [ABSTRACT FROM AUTHOR]

The estimation of the correct binding mode and affinity of a ligand into a target protein using computational methods is challenging. However, docking can introduce poses from which the correct binding mode could be identified using other methods. Here, we analyzed the reliability of binding energy estimation using the molecular mechanics‐generalized Born surface area (MMGBSA) method without and with energy minimization to identify the likely ligand binding modes within docking results. MMGBSA workflow (a) outperformed docking in recognizing the correct binding modes of androgen receptor ligands and (b) improved the correlation coefficient of computational and experimental results of rescored docking poses to phosphodiesterase 4B. Combined with stability and atomic distance analysis, MMGBSA helped to (c) identify the binding modes and sites of metabolism of cytochrome P450 2A6 substrates. The standard deviation of estimated binding energy within one simulation was lowered by minimization in all three example cases. Minimization improved the identification of the correct binding modes of androgen receptor ligands. Although only three case studies are shown, the results are analogous and indicate that these behaviors could be generalized. Such identified binding modes could be further used, for example, with free energy perturbation methods to understand binding energetics more accurately. MMGBSA can be efficiently used to select the correct binding pose for ligands. The results are further improved by energy minimization of complexes from molecular dynamics simulations. Also, the correlation coefficient between experimental and calculated data is improved. [ABSTRACT FROM AUTHOR]

A respected number of drugs suffer from bitter taste which results in patient incompliance. With the aim of solving the bitterness of guaifenesin, dimethyl maleate, maleate, glutarate, succinate, and dimethyl succinate prodrugs were designed and synthesized. Molecular orbital methods were utilized for the design of the ester prodrugs. The density functional theory (DFT) calculations revealed that the hydrolysis efficiency of the synthesized prodrugs is significantly sensitive to the pattern of substitution on C=C bond and distance between the nucleophile and the electrophile. The hydrolysis of the prodrugs was largely affected by the pH of the medium. The experimental t1/2 for the hydrolysis of guaifenesin dimaleate ester prodrugs in 1N HCl was the least and for guaifenesin dimethyl succinate was the highest. Functional heterologous expression of TAS2R14, a broadly tuned bitter taste receptor responding to guaifenesin, and experiments using these prodrugs revealed that, while some of the prodrugs still activated the receptor similarly or even stronger than the parent substance, succinate derivatization resulted in the complete loss of receptor responses. The predicted binding modes of guaifenesin and its prodrugs to the TAS2R14 homology model suggest that the decreased activity of the succinate derivatives may be caused by a clash with Phe247. A number of novel bitterless ester guaifenesin prodrugs were designed, synthesized, and characterized. The prodrugs have shown sufficient stability at neutral pH values and rapid release under low pH conditions (stomach). Using bitter taste receptor assays, it was confirmed that the most promiscuous human bitter taste receptor responsible for the bitter perception of many drugs, the TAS2R14, is not activated by some of the prodrugs. We conclude that our approach could be used to mask the bitterness of other similar drugs. [ABSTRACT FROM AUTHOR]

This study describes the activity of five natural hydroxycinnamic acids and derived compound: caffeic (1), rosmarinic (2), chlorogenic (3), and cryptochlorogenic (4), acids and isoverbascoside (5). All compounds inhibited Leishmania amazonensis arginase with IC50 —in range of 1.5—11 μM. Compounds 2 and 5 also showed activity against promastigotes of L. amazonensis with IC50 = 61 (28–133) μM and IC50 = 14 (9–24) μM, respectively. Further computational studies applying molecular docking simulations were performed on the competitive inhibitors to gain insight into the molecular basis for arginase inhibition and could be exploited to the development of new antileishmanials drug targeting parasite arginase. Cinnamic acids derived compounds inhibited Leishmania arginase. Free binding energies (ΔGbind) indicate higher affinity with the parasite arginase rather than human arginase. Compound 5 showed better result against promastigotes. [ABSTRACT FROM AUTHOR]

π–π interactions are common and important noncovalent interactions that contribute to biochemical molecular interactions, but the tools for the convenient 3D visualization of π–π interactions are lacking. We have developed an open‐source and easy‐to‐use tool for the automated identification and display of π–π stacking in 3D. It can percept the aromaticity of rings from any selected ligand and the surrounding residues, calculate the distances and dihedral angles between each pair of aromatic ring planes, as well as can highlight the various configurations of π–π interactions in 3D: the sandwich configuration, the T‐shaped configuration, and the parallel‐displaced configuration. In addition, the users can easily adjust or set their own criteria for π–π stacking. [ABSTRACT FROM AUTHOR]

The human cannabinoid G‐protein‐coupled receptor 1 (CB1) is highly expressed in central nervous system. CB1‐selective antagonists show therapeutic promise in a wide range of disorders, such as obesity‐related metabolic disorders, dyslipidemia, drug abuse, and type 2 diabetes. Rimonabant (SR141716A), MJ08, and MJ15 are selective CB1 antagonists with selectivity >1,000‐folds over CB2 despite 42% sequence identity between CB1 and CB2. The integration of homology modeling, automated molecular docking, and molecular dynamics simulation were used to investigate the binding modes of these selective inverse agonists/antagonists with CB1 and CB2 and their selectivity. Our analyses showed that the hydrophobic interactions between ligands and hydrophobic pockets of CB1 account for the main binding affinity. In addition, instead of interacting with ligands directly as previously reported, the Lys1923.28 in CB1 was engaged in indirect interactions with ligands to keep inactive‐state CB1 stable by forming the salt bridge with Asp1762.63. Lastly, our analyses indicated that the selectivity of these antagonists came from the difference in geometry shapes of binding pockets of CB1 and CB2. The present study could guide future experimental works on these receptors and has the guiding significance for the design of functionally selective drugs targeting CB1 or CB2 receptors. [ABSTRACT FROM AUTHOR]

Abstract: We synthesized a series of novel thioether pleuromutilin derivatives incorporating 2‐aminothiophenol moieties into the C14 side chain via acylation reactions under mild conditions. We evaluated the in‐vitro antibacterial activities of the derivatives against methicillin‐resistant Staphylococcus aureus (MRSA, ATCC 43300), Staphylococcus aureus (ATCC 29213) and Escherichia coli (ATCC 25922). The majority of the synthesized derivatives possessed moderate antibacterial activities. Compound 8 was found to be the most active antibacterial derivative against MRSA. We conducted docking experiments to understand the possible mode of interactions between compounds 8, 9b, 11a and 50S ribosomal subunit. The docking results proved that there is a reasonable correlation between the binding free energy and the antibacterial activity. Compound 8 was evaluated for its in‐vivo antibacterial activity and showed higher efficacy than tiamulin against MRSA in mouse infection model. [ABSTRACT FROM AUTHOR]

Laulimalide (LAU) and Peloruside A (PLA) are non‐taxane microtubule stabilizing agents with promising antimitotic properties. These ligands promote the assembly of microtubules (MTs) by targeting a unique binding site on β‐tubulin. The X‐ray structure for LAU/PLA‐tubulin association was recently elucidated, but little information is available regarding the role of these ligands as modulators of interdimeric interactions across MTs. Herein, we report the use of molecular dynamics (MD), principal component analysis (PCA), MM/GBSA‐binding free energy calculations, and computational alanine scanning mutagenesis (ASM) to examine effect of LAU/PLA association on lateral and longitudinal contacts between tubulin dimers in reduced MT models. MD and PCA results revealed that LAU/PLA exerts a strong restriction of lateral and longitudinal interdimeric motions, thus enabling the stabilization of the MT lattice. Besides structural effects, LAU/PLA induces a substantial strengthening of longitudinal interdimeric interactions, whereas lateral contacts are less affected by these ligands, as revealed by MM/GBSA and ASM calculations. These results are valuable to increase understanding about the molecular features involved in MT stabilization by LAU/PLA, and to design novel compounds capable of emulating the mode of action of these ligands. [ABSTRACT FROM AUTHOR]

New synthesized series of 9‐amino‐1,2,3,4‐tetrahydroacridine derivatives with iodobenzoic acid moiety were studied for their inhibitory activity toward cholinesterase and against β‐amyloid aggregation. All novel molecules 3a–3i interacted with both cholinesterases—acetylcholinesterase and butyrylcholinesterase—delivered nanomolar IC50 values. The structure–activity relationship showed that N‐butyl moiety derivatives are stronger inhibitors toward AChE and BuChE than N‐ethyl and N‐propyl moieties compounds. The most potent compound toward acetylcholinesterase was inhibitor 3f (IC50 = 31.2 n m), and it was more active than reference drug, tacrine (IC50 = 100.2 n m). Compound 3f showed strong inhibition of butyrylcholinesterase (IC50 = 8.0 n m), also higher than tacrine (IC50 = 16.3 n m). In the kinetic studies, compound 3f revealed mixed type of acetylcholinesterase inhibition. The computer modeling was carried out. The most active compound 3f was confirmed as peripheral anionic site inhibitor of acetylcholinesterase. Moreover, molecule 3f inhibited β‐amyloid aggregation (at the concentration 10 μ m—24.96% of inhibition, 25 μ m—72%, 50 μ m—78.44%, and 100 μ m—84.92%). Therefore, among all examined, compound 3f is the most promising molecule for further, more detailed research of novel multifunctional agents in the therapy of Alzheimer's disease. [ABSTRACT FROM AUTHOR]

The ability to design and fine‐tune non‐covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand–protein interfaces. In this communication, we employ a two‐parameter geometric model to conduct a large‐scale statistical analysis of aromatic contacts in the experimental and computer‐generated structures of ligand–protein complexes, considering various combinations of aromatic amino acid residues and ligand rings. The geometry of interfacial π–π stacking in crystal structures accords with experimental and theoretical data collected for simple systems, such as the benzene dimer. Many contemporary ligand docking programs implicitly treat aromatic stacking with van der Waals and Coulombic potentials. Although this approach generally provides a sufficient specificity to model aromatic interactions, the geometry of π–π contacts in high‐scoring docking conformations could still be improved. The comprehensive analysis of aromatic geometries at ligand–protein interfaces lies the foundation for the development of type‐specific statistical potentials to more accurately describe aromatic interactions in molecular docking. A Perl script to detect and calculate the geometric parameters of aromatic interactions in ligand–protein complexes is available at https://github.com/michal-brylinski/earomatic. The dataset comprising experimental complex structures and computer‐generated models is available at https://osf.io/rztha/. [ABSTRACT FROM AUTHOR]

Since the first major outbreak of Zika virus (ZIKV) in 2007, ZIKV is spreading explosively through South and Central America, and recent reports in highly populated developing countries alarm the possibility of a more catastrophic outbreak. ZIKV infection in pregnant women leads to embryonic microcephaly and Guillain-Barré syndrome in adults. At present, there is limited understanding of the infectious mechanism, and no approved therapy has been reported. Despite the withdrawal of public health emergency, the WHO still considers the ZIKV as a highly significant and long-term public health challenge that the situation has to be addressed rapidly. Non-structural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase and RNA-dependent RNA polymerase (RdRp) domain. We used molecular modeling to obtain the structure of ZIKV RdRp, and by molecular docking and phylogeny analysis, we here demonstrate the potential sites for drug screening. Two metal binding sites and an NS3-interacting region in ZIKV RdRp are demonstrated as potential drug screening sites. The docked structures reveal a remarkable degree of conservation at the substrate binding site and the potential drug screening sites. A phylogeny-based approach is provided for an emergency preparedness, where similar class of ligands could target phylogenetically related proteins. [ABSTRACT FROM AUTHOR]

Curcumin has shown pharmacological properties against different phenotypes of various disease models. Different synthetic routes have been employed to develop its numerous derivatives for diverse and improved therapeutic roles. In this study, we have synthesized curcumin derivatives containing isoxazole, pyrazoles, and pyrimidines and then the synthesized molecules were evaluated for their anti-inflammatory and antinociceptive activities in experimental animal models. Acute toxicity of synthesized molecules was evaluated in albino mice by oral administration. Any behavioral and neurological changes were observed at dose of 10 mg/kg body weight. Additionally, cyclooxygenase-2 ( COX-2) enzyme inhibition studies were performed through in vitro assays. In vivo anti-inflammatory studies showed that curcumin with pyrimidines was the most potent anti-inflammatory agent which inhibited induced edema from 74.7% to 75.9%. Compounds 7, 9, and 12 exhibited relatively higher prevention of writhing episodes than any other compound with antinociceptive activity of 73.2%, 74.9%, and 71.8%, respectively. This was better than diclofenac sodium (reference drug, 67.1% inhibition). Similarly, COX-2 in vitro inhibition assays results revealed that compound 12 (75.3% inhibition) was the most potent compound. Molecular docking studies of 10, 11, and 12 compounds in human COX-2 binding site revealed the similar binding modes as that of other COX-2-selective inhibitors. [ABSTRACT FROM AUTHOR]

Molecular dynamics ( MD) simulations were employed to study the tubulin-binding modes of 20 epothilone derivatives spanning a wide range of antitumor activity. Trajectory analysis revealed that active ligands shared a common region of association and similar binding poses compared to the high-resolution crystal structure of the tubulin complex with epothilone A, the stathmin-like protein RB3, and tubulin tyrosine ligase ( PDB code 4I50). Conformational analysis of epothilones in aqueous solution and tubulin-bound states indicated that the bound conformations of active species can be found to a significant extent within the ensemble of conformers available in aqueous solution. On the other hand, inactive derivatives were unable to adopt bound-like conformations in aqueous solution, thus requiring an extensive conformational pre-organization to accomplish an effective interaction with the tubulin receptor. Additionally, MD results revealed that epothilone binding-induced structuring of the M-loop and local flexibility changes in protein regions involved in interdimeric contacts that are relevant for microtubule stabilization. These results provide novel, valuable structural information to increase understanding about the underlying molecular aspects of epothilones activity and support further work on the search for new active tubulin-binding agents. [ABSTRACT FROM AUTHOR]

A series of racemic unnatural amino acids was rationally designed on the basis of recently published X-ray structures of the GluA2 LBD with bound phenylalanine-based antagonists. Twelve new diaryl- or aryl/heteroaryl-substituted phenylalanine derivatives were synthesized and evaluated in vitro in radioligand binding assays at native rat ionotropic glutamate receptors. The most interesting compound in this series, ( RS)-2-amino-3-(3′-hydroxy-5-(1 H-pyrazol-4-yl)-[1,1′-biphenyl]-3-yl)propanoic acid 7e, showed the binding affinity of 4.6 μ m for native AMPA receptors and over fourfold lower affinity for kainic acid receptors. Furthermore, 7e was evaluated at recombinant homomeric rat GluA2 and GluA3 receptors. Recently reported X-ray structures 5 CBR and 5 CBS, representing two distinct antagonist binding modes, were used as templates for molecular docking of the synthesized series. Binding data supported with molecular modeling confirmed that aryl/heteroaryl-substituted phenylalanine analogues effectively bind to AMPA receptors with low micromolar affinity and high selectivity over native NMDA and kainate receptors. These properties make 7e a promising lead for the further development of new AMPA receptor ligands. [ABSTRACT FROM AUTHOR]

Virtual molecular catalogs have limited utility if member compounds are (i) difficult to synthesize or (ii) unlikely to have biological activity. The Distributed Drug Discovery (D3) program addresses the synthesis challenge by providing scientists with a free virtual D3 catalog of 73,024 easy-to-synthesize N-acyl unnatural α-amino acids, their methyl esters, and primary amides. The remaining challenge is to document and exploit the bioactivity potential of these compounds. In the current work, a search process is described that retrospectively identifies all virtual D3 compounds classified as bioactive hits in PubChem-cataloged experimental assays. The results provide insight into the broad range of drug-target classes amenable to inhibition and/or agonism by D3-accessible molecules. To encourage computer-aided drug discovery centered on these compounds, a publicly available virtual database of D3 molecules prepared for use with popular computer docking programs is also presented. [ABSTRACT FROM AUTHOR]

Inhibition of mushroom tyrosinase was observed with synthetic dihydropyrano[3,2- b]chromenediones. Among them, DHPC04 displayed the most potent tyrosinase inhibitory activity with a K i value of 4 μ m, comparable to the reference standard inhibitor kojic acid. A kinetic study suggested that these synthetic heterocyclic compounds behave as competitive inhibitors for the L- DOPA binding site of the enzyme. Furthermore, molecular modeling provided important insight into the mechanism of binding interactions with the tyrosinase copper active site. [ABSTRACT FROM AUTHOR]

Macrolides, one of the most prescribed classes of antibiotics, bind in the bacterial ribosome's polypeptide exit tunnel and inhibit translation. However, mutations and other ribosomal modifications, especially to the base A2058 of the 23S rRNA, have led to a growing resistance problem. Here, we have used molecular dynamics simulations to study the macrolides erythromycin and azithromycin in wild-type, A2058G-mutated, and singly or doubly A2058-methylated Escherichia coli ribosomes. We find that the ribosomal modifications result in less favorable interactions between the base 2058 and the desosamine sugar of the macrolides, as well as greater displacement of the macrolides from their crystal structure position, illuminating the causes of resistance. We have also examined four azithromycin derivatives containing aromatic indole-analog moieties, which were previously designed based on simulations of the stalling peptide SecM in the ribosome. Surprisingly, we found that the studied moieties could adopt very different geometries when interacting with a key base in the tunnel, A751, possibly explaining their distinct activities. Based on our simulations, we propose modifications to the indole-analog moieties that should increase their interactions with A751 and, consequently, enhance the potency of future azithromycin derivatives. [ABSTRACT FROM AUTHOR]

An in silico method has been used to discover N-hydroxy-substituted 2-aryl acetamide analogs as a new class of HIV-1 integrase inhibitors. Based on the molecular requirements of the binding pocket of catalytic active site, two molecules (compounds 2 and 4b) were designed as fragments. These were further synthesized and biologically evaluated. In vitro potency along with docking studies highlighted compound 4b as an active fragment which was further used to synthesize new leads as HIV-1 integrase inhibitors. Finally, six promising compounds (compounds 5b, 5c, 5e, 6-2c, 6-3b, and 6-5b) were identified by integrase inhibition assay (>50% inhibition). Based on in vitro anti- HIV-1 activity in a reporter gene-based cell assay system, compounds 5d, 6s, and 6k were found as novel HIV-1 integrase inhibitors due to its better selectivity index. Additionally, docking study revealed the importance of H-bond as well as hydrophobic interactions with Asn155, Lys156, and Lys159 which were required for their anti- HIV-1 activity. [ABSTRACT FROM AUTHOR]

The bromodomain ( BRD) and extra-terminal domain ( BET) protein family bind to acetylated histones on lysine residues and act as epigenetic readers. Recently, the role of this protein family in bone loss has been gaining attention. Earlier studies have reported that benzotriazepine (Bzt) derivatives could be effective inhibitors of BET proteins. In this study, using in silico tools we designed three Bzt analogs (W49, W51, and W52). By docking, molecular simulations, and chemiluminescent Alpha Screen binding assay, we show that the studied analogs were selective at inhibiting BRD4 when compared to BRD2. Furthermore, we tested the effectiveness of these analogs on osteoclast formation and function. Among the examined analogs, Bzt-W49 and Bzt-W52 were found to be the most potent inhibitors of osteoclastogenesis without cytotoxicity in murine RAW264.7 osteoclast progenitors. Both the compounds also inhibited osteoclast formation without affecting cell viability in human CD14+ monocytes. Moreover, owing to attenuated osteoclastogenesis, actin ring formation and bone resorptive function of osteoclasts were severely perturbed. In conclusion, these results suggest that the novel BRD4-selective Bzt analogs designed in this study could be explored further for developing therapeutics against bone loss diseases characterized by excessive osteoclast activity. [ABSTRACT FROM AUTHOR]

A series of 18 novel N-Mannich bases derived from 5-adamantyl-1,2,4-triazole-3-thione was synthesized and characterized using NMR spectroscopy and X-ray diffraction technique. All derivatives were evaluated for their anticancer potential against four human cancer cell lines. Several tested compounds exerted good cytotoxic activities on K562 and HL-60 cell lines, along with pronounced selectivity, showing lower cytotoxicity against normal fibroblasts MRC-5 compared to cancer cells. The effects of compounds 5b, 5e, and 5j on the cell cycle were investigated by flow cytometric analysis. It was found that these compounds cause the accumulation of cells in the subG1 and G1 phases of the cell cycle and induce caspase-dependent apoptosis, while the anti-angiogenic effects of 5b, 5e, and 5j have been confirmed in EA.hy926 cells using a tube formation assay. Further, the interaction of Bax protein with compound 5b was investigated by means of molecular modeling, applying the combined molecular docking/molecular dynamics approach. [ABSTRACT FROM AUTHOR]

UDP- N-acetylglucosamine enolpyruvyl transferase (MurA) is one of the key enzymes involved in peptidoglycan biosynthesis. The peptide HESFWYLPHQSY (called PEP 1354) is an inhibitor of MurA with an IC50 value of 200 μ m. In this article, we have used the FlexPepDock ab-initio protocol from the Rosetta program homology modeling and molecular dynamics simulations to analyze, for the first time, the interaction of the PEP 1354 peptide with MurA enzyme from Pseudomonas aeruginosa (MurA- PA). Our modeling results suggest that the peptide binds to the same active site as the natural substrate UDP- N-acetylglucosamine (UNAG). Additionally, the MurA-peptide complex revealed that the peptide seems to prevent the closure of the Pro114-123 loop and, consequently, the open-closed transition of the MurA structure. [ABSTRACT FROM AUTHOR]

The human cytomegalovirus-encoded G protein-coupled receptor US28 is a constitutively active receptor, which can recognize various chemokines. Despite the recent determination of its 2.9 Å crystal structure, potent and US28-specific tool compounds are still scarce. Here, we used structural information from a refined US28: VUF2274 complex for virtual screening of >12 million commercially available small molecule compounds. Using a combined receptor- and ligand-based approach, we tested 98 of the top 0.1% ranked compounds, revealing novel chemotypes as compared to the ~1.45 million known ligands in the Ch EMBL database. Two compounds were confirmed as agonist and inverse agonist, respectively, in both IP accumulation and Ca2+ mobilization assays. The screening setup presented in this work is computationally inexpensive and therefore particularly useful in an academic setting as it enables simultaneous testing in binding as well as in different functional assays and/or species without actual chemical synthesis. [ABSTRACT FROM AUTHOR]

A series of isonicotinohydrazide derivatives was synthesized and tested against recombinant human and rat ecto-5′-nucleotidases ( h-e5′ NT and r-e5′ NT) and alkaline phosphatase isozymes including both bovine tissue-non-specific alkaline phosphatase ( b- TNAP) and tissue-specific calf intestinal alkaline phosphatase ( c- IAP). These enzymes are implicated in vascular calcifications, hypophosphatasia, solid tumors, and cancers, such as colon, lung, breast, pancreas, and ovary. All tested compounds were active against both enzymes. The most potent inhibitor of h-e5′ NT was derivative (E)-N′-(1-(3-(4-fluorophenyl)-5-phenyl-4,5-dihydro-1 H-pyrazol-1-yl)ethylidene)isonicotinohydrazide ( 3j), whereas derivative ( E)- N′-(4-hydroxy-3-methoxybenzylidene)isonicotinohydrazide ( 3g) exhibited significant inhibitory activity against r-e5′ NT . In addition, the derivative (E)-N′-(4′-chlorobenzylidene)isonicotinohydrazide ( 3a) was most potent inhibitor against calf intestinal alkaline phosphatase and the derivative ( E)- N′-(4-hydroxy-3-methoxybenzylidene)isonicotinohydrazide ( 3g) was found to be most potent inhibitor of bovine tissue-non-specific alkaline phosphatase. Furthermore, putative binding modes of potent compounds against e5′ NT (human and rat e5′ NT) and AP (including b- TNAP and c- IAP) were determined computationally. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations and binding free energy calculations were employed to examine the interaction between E-selectin and six structurally related oligosaccharides including the physiological ligand sialyl Lewis x. Molecular dynamics simulations revealed that sialyl Lewis x and its mimics share a common binding region and similar interactions with E-selectin involving the formation of hydrogen bonds with Glu80, Asn82, Asn83, Arg97, Asn105, Asp106, and Glu107 residues and electrostatic contacts with Ca2+ and the positively charged Lys111 and Lys 113 residues. Regarding binding free energy calculations, the performance of the rigorous but computationally expensive pathway methods TI, BAR, and MBAR was compared to the less rigorous but faster end-point methods MM/ PBSA and MM/ GBSA aimed at identifying a suitable approach to deal with the very subtle binding free energy differences within the ligands under study. All methods succeeded in predicting increased binding affinities for sialyl Lewis x analogs compared to the native ligand with absolute errors <1 kcal/mol. The best correlation with experimental data was obtained by TI ( r2 = 0.84), followed by MBAR ( r2 = 0.80), BAR ( r2 = 0.73), MM/ PBSA ( r2 = 0.73) and MM/ GBSA ( r2 = 0.47). These results provide valuable information to increase understanding about E-selectin-oligosaccharide interactions and conduct further research aimed at designing novel ligands targeting this protein. [ABSTRACT FROM AUTHOR]

Experimental evidence suggests that hERG and hEAG potassium channels may serve as important cancer therapy targets because either of the channel blockade or inactivation by different methods leads to inhibition of cancer cells growth and proliferation. However, there is no known hEAG specific blocker, and hERG blockade leads to adverse cardiac side effects, although it is currently used in treating certain types of arrhythmias. There have been some attempts to explain the channels blockade by clofilium, an antiarrhythmic agent, and the results lead to different possible binding modes. This study investigates for the first time the potential of using clofilium as a lead compound for finding a novel cancer therapy agent which may target ion channels. The implied findings from a comparative assessment of literature studies were verified using molecular dynamics simulations. The results indicate a particular structural difference between the two channels that could provide a novel and realistic way of using clofilium analogs which may target the hEAG1 ion channel in cancer therapy. [ABSTRACT FROM AUTHOR]

A series of novel pleuromutilin derivatives possessing piperazine moieties were synthesized under mild conditions. The in vitro antibacterial activities of these derivatives against Staphylococcus aureus and Escherichia coli were tested by the agar dilution method. Structure-activity relationship studies resulted in compounds 11b, 13b, and 14a with the most potent in vitro antibacterial activity among the series (minimal inhibitory concentration = 0.0625-0.125 μg/mL). The binding of compounds 11b, 13b, and 14a to the E. coli ribosome was investigated by molecular modeling, and it was found that there is a reasonable correlation between the binding free energy and the antibacterial activity. [ABSTRACT FROM AUTHOR]

Synthesis, in vitro cytotoxic activity, and interaction with tubulin of oxidized, isomeric 1-(5-alkoxybenzo[ d][1,3]oxathiol-6-yl)-3-phenylprop-2-en-1-ones and 1-(6-alkoxybenzo[ d][1,3]oxathiol-5-yl)-3-phenylprop-2-en-1-ones are described. Most of the compounds demonstrated cytotoxic activity at submicromolar concentrations. It was found that oxidation of sulfur atom of the oxathiole-fused chalcones strongly influenced activity of the parent compounds, and that depending on relative position of the sulfur atom in the molecule, the activity was either increased or diminished. For isomers with sulfur atom para to the chalcone carbonyl group, oxidation led to increase in activity, while for isomers with sulfur atom meta to the carbonyl the activity dropped down. It was demonstrated that the compounds interact with tubulin at the colchicine binding site, and the interaction was evaluated using molecular modeling. It was concluded that the observed profound influence of oxidation of the sulfur atom on cytotoxic activity cannot be solely related to interaction of the compounds with tubulin. [ABSTRACT FROM AUTHOR]

With the continuation of our unremitting efforts toward the discovery of potent HIV-1 NNRTIs, a series of novel imidazo[4,5-b]pyridin-2-ylthioacetanilides were designed, synthesized, and evaluated for their antiviral activities through combining bioisosteric replacement and structure-based drug design. Almost all of the title compounds displayed moderate to good activities against wild-type (wt) HIV-1 strain with EC50 values ranging from 0.059 to 1.41 μ m in a cell-based antiviral assay. Thereinto, compounds 12 and 13 were the most active two analogues possessing an EC50 value of 0.059 and 0.073 μ m against wt HIV-1, respectively, which was much more effective than the control drug nevirapine (EC50 = 0.26 μ m) and comparable to delavirdine (EC50 = 0.038 μ m). In addition, one selected compound showed a remarkable reverse transcriptase inhibitory activity compared to nevirapine and etravirine. In the end of this manuscript, preliminary structure-activity relationships (SARs) and molecular modeling studies were detailedly discussed, which may provide valuable insights for further optimization. [ABSTRACT FROM AUTHOR]

A general pharmachophore model for various types of Ser/ Thr kinases was developed. Search for the molecules fitting to this pharmacophore among ASINEX proprietary library revealed a number of compounds, which were tested and appeared to possess some activity against several Ser/ Thr kinases such as Aurora A, Aurora B and Haspin. The possibility of performing the fine-tuning of the general Ser/ Thr pharmacophore to desired types of kinase to get active and selective inhibitors was exemplified by Aurora A kinase. As a result, several hits in 3-5 n m range of activity against Aurora A kinase with rather good selectivity and ADME properties were obtained. [ABSTRACT FROM AUTHOR]

The present work reports the synthesis of several 2-iminothiazoline derivatives of sulfanilamide ( 3a- j) as inhibitors of jack bean ureases. The title compounds were synthesized by the heterocyclization of sulfanilamide thioureas with propragyl bromide in dry ethanol in the presence of 1,8-Diazabicyclo[5.4.0]undec-7-ene as a base. All of the compounds showed higher urease inhibitory activity than the standard thiourea. The compounds ( 3h) and ( 3i) exhibited excellent enzyme inhibitory activity with IC50 0.064 and 0.058 μ m, respectively, while IC50 of thiourea is 20.9 μ m. The kinetic mechanism analyzed by Dixon plot showed that compound ( 3h) is a mixed-type inhibitor while ( 3i) is a competitive one. Docking studies suggested that Asp633, Ala636, His492, Ala440, Lue523, Asp494 and Arg439 are the major interacting residues in the binding site of the protein and may have an instrumental role in the inhibition of enzyme's function. 2-iminothiazoline analogues ( 3a- j) showed good docking score (−10.6466 to −8.7215 Kcal/mol) and binding energy (London dG ranging from −14.4825 to −10.4087 Kcal/mol) which is far better than the standard thiourea (binding score in S field −4.5790 Kcal/mol London dG −4.7726 Kcal/mol). Our results inferred compound ( 3i) may serve as a structural model for the design of most potent urease inhibitors. [ABSTRACT FROM AUTHOR]

A new series of-fluoro chalcones-substituted amino-alkyl derivatives ( 3a˜3l) were designed, synthesized, characterized and evaluated for the inhibitory activity against acetylcholinesterase and butyrylcholinesterase. The results showed that the alteration of fluorine atom position and amino-alkyl groups markedly influenced the activity and the selectivity of chalcone derivates in inhibiting acetylcholinesterase and butyrylcholinesterase. Among them, compound 3l possesses the most potent inhibitory against acetylcholinesterase ( IC50 = 0.21 ± 0.03 μmol/L), and the highest selectivity for acetylcholinesterase over butyrylcholinesterase ( IC50 (BuChE)/ IC50 ( AChE) = 65.0). Molecular modeling and enzyme kinetic study on compound 3l supported its dual acetylcholinesterase inhibitory profile, simultaneously binding at the catalytic active and peripheral anionic site of the enzyme. [ABSTRACT FROM AUTHOR]

Antibiotic resistance has been the subject of interest in clinical practice due to high prevalence of antibiotic-resistant pathogenic organisms. In view of the prevalence of lesser resistance in antibiotics belonging to aminoglycoside class of compounds viz. Food and Drug Administration-approved gentamicin for the treatment of Staphylococcus infections, which also has instances of resistance in the clinical isolates of Staphylococcus aureus, a series of novel glycoconjugates of 8-fluoro norfloxacin analogues with high regio-selectivity by employing copper (I)-catalyzed 1, 3-dipolar cycloaddition of 1-O-propargyl monosaccharides has been synthesized and evaluated for the antibacterial activity against gentamicin resistance Staphylococcus aureus. Among these compounds, the compound 10g showed better antibacterial activity ( MIC = 3.12 μg/ml) than gentamicin ( Escherichia coli (12.5 μg/ml), Staphylococcus aureus (6.25 μg/ml) and Klebsiella pneumonia (6.25 μg/ml), including gentamicin resistant (>50 μg/ml) strain in vitro). The docking studies suggest DNA gyrase of Staphylococcus aureus as a probable target for the antibacterial action of compound 10g. [ABSTRACT FROM AUTHOR]

A series of benzoyl diarylamine/ether derivatives were designed, synthesized, and evaluated for their activity against human immunodeficiency virus ( HIV) in MT-4 cells. Three compounds ( 3b, 5a, and 6a1) exhibited moderate activities against wild-type (wt) HIV-1 with EC50 values ranging from 11 to 56 μ m. Among them, compound 5a was the most potent inhibitor with a novel chemical skeleton, affording a new lead compound for further molecular optimization. An enzyme assay was also implemented to confirm the binding target of the active compounds represented by 6a1. Molecular simulation studies on compound 5a, 6a1, and 7a4 were carried out to understand their binding mode with wt HIV-1 reverse transcriptase ( RT) and provided useful information for further rational design of NNRTIs. [ABSTRACT FROM AUTHOR]

Taking into account the uncertainties involved in 3D model of biomolecule developed by homology modeling ( HM), it is important to opportunely validate the initial structure before employing for different purposes such as drug design. Extended simulation times and the necessity of correct representation of interactions within the protein and the nearby molecules impose significant limitations on molecular dynamics ( MD)-based refinement of structures developed by HM. Consequently, there is a pressing requirement for more efficient methods for HM and subsequent validation of developed structure. Multiple MD simulation runs are well suited for producing ensembles of structures. In this context, a computational investigation was presented to study the structure of melanocortin 4 receptor (MC4R) using molecular dynamics ( MD) simulations in explicit phospholipids bilayer. Several MD runs with different initial velocities were employed to sample conformations in the neighborhood of the native structure of receptor, collecting trajectories spanning 0.21 ms. The coherence between the results, different structural analysis, and the convergence of parameters derived by principal component analysis ( PCA) shows that an accurate description of the MC4R conformational space around the native state was achieved by multiple MD trajectories. [ABSTRACT FROM AUTHOR]

Alzheimer's disease is the major cause of senile dementia, flewing out 10% of 65 years old and 50% of 85 years old global population. The major fisiopathologic characteristics of Alzheimer's disease are the deposition of extracellular neuritic plaques and the presence of intracellular neurofibrillary tangles in memory-related areas of the brain. The plaques are composed by the β-amyloid peptide with 40 or 42 residues, result from hydrolysis of the amyloid precursor protein by the β-secretase 1 ( BACE-1) on the amyloidogenic pathway, that begins with the BACE-1 and which inhibition is considered one of the most promising treatments available of Alzheimer's disease. In this work, molecular modeling techniques such as virtual screening of compound libraries, pharmacophore-based virtual screening, molecular interaction fields, ADME/Tox predictions, and similarity search were used to design novel inhibitors of BACE-1, starting from structures available in the Protein Data Bank. The results obtained from all virtual screening techniques leaded to 10 promising compounds, which were then evaluated by enzymatic assays, and, three of them showed inhibitory activity of BACE-1 at a 1 μ m range. [ABSTRACT FROM AUTHOR]

Laulimalide, a cancer chemotherapeutic in preclinical development, has a unique binding site located on two adjacent β-tubulin units between tubulin protofilaments of a microtubule. Our extended protein model more accurately mimics the microtubule environment, and together with a 135 ns molecular dynamics simulation, identifies a new binding mode for laulimalide, which differs from the modes presented in work using smaller protein models. The new laulimalide-residue interactions that are computationally revealed explain the contacts observed via independent mass shift perturbation experiments. The inclusion of explicit solvent shows that many laulimalide-tubulin interactions are water mediated. The new contacts between the drug and the microtubule structure not only improve our understanding of laulimalide binding but also will be essential for efficient derivatization and optimization of this prospective cancer chemotherapy agent. Observed changes in secondary protein structure implicate the S7-H9 loop ( M-loop) and H1′-S2 loop in the mechanism by which laulimalide stabilizes microtubules to exert its cytotoxic effects. [ABSTRACT FROM AUTHOR]

Novel curcumin analogs with 4-piperidone ring were designed, synthesized, and evaluated for their cytotoxic activities against five different cancer cell lines. 3,5-bis(4-Hydroxy-3-methoxybenzylidene)-4-oxo- N-phenylpiperidine-1-carbothioamide ( XIIe) exhibited considerable cytotoxic activity with IC50 values in 1-2.5 μ m range. In silico and in vitro, studies were also performed to predict the binding affinity of the target compounds to the β-chain of tubulin receptor ( PDB code 1 SA1) and their abilities to affect microtubules polymerization cycle. 3,5-bis(3-Iodo-5-methoxy-4-propoxybenzylidene)- N-acetylpiperidin-4-one ( VIIa) was found to exert 93.3% inhibition of tubulin and destabilization of microtubules in vitro compared to vincristine while, 3,5-bis(3,4,5-trimethoxybenzylidene)- N-benzoylpiperidin-4-one ( XIIc) showed high potency in a different way where it exerted 94.8% stabilization of microtubules in vitro compared to positive control paclitaxel. [ABSTRACT FROM AUTHOR]