Computational Screening of Newly Designed Compounds against Coxsackievirus A16 and Enterovirus A71

Outbreaks of hand, foot, and mouth disease (HFMD) that occur worldwide are mainly caused by the Coxsackievirus-A16 (CV-A16) and Enterovirus-A71 (EV-A71). Unfortunately, neither an anti-HFMD drug nor a vaccine is currently available. Rupintrivir in phase II clinical trial candidate for rhinovirus showed highly potent antiviral activities against enteroviruses as an inhibitor for 3C protease (3Cpro). In the present study, we focused on designing 50 novel rupintrivir analogs against CV-A16 and EV-A71 3Cpro using computational tools. From their predicted binding affinities, the five compounds with functional group modifications at P1′, P2, P3, and P4 sites, namely P1′-1, P2-m3, P3-4, P4-5, and P4-19, could bind with both CV-A16 and EV-A71 3Cpro better than rupintrivir. Subsequently, these five analogs were studied by 500 ns molecular dynamics simulations. Among them, P2-m3, the derivative with meta-aminomethyl-benzyl group at the P2 site, showed the greatest potential to interact with the 3Cpro target by delivering the highest number of intermolecular hydrogen bonds and contact atoms. It formed the hydrogen bonds with L127 and K130 residues at the P2 site stronger than rupintrivir, supported by significantly lower MM/PB(GB)SA binding free energies. Elucidation of designed rupintrivir analogs in our study provides the basis for developing compounds that can be candidate compounds for further HFMD treatment.     

六钼酸盐有机胺杂化衍生物与SARS-CoV 3CLpro相互作用的分子动力学模拟

采用分子动力学模拟方法, 在分子水平上探讨六钼酸盐有机杂化衍生物潜在的抗SARS病毒活性. 3CLpro主蛋白酶是冠状病毒复制和转录过程中起关键作用的功能蛋白, 因此采用SARS-CoV 3CLpro作为靶标进行抗SARS病毒的药物设计. 使用Insight II软件包中的Biopolymer, Discover 3, Profile-3D和Affinity等模块, 研究 POMs/3CLpro相互作用的结合位点和作用性质. 研究其能量变化规律, 探讨了多酸化合物对SARS病毒可能的抑制机理. 研究结果表明, POMs与3CLpro在酶的催化活性位点处有较强的结合力. 形成的复合物主要以静电相互作用相结合, 氢键相互作用对复合物的相对稳定性有一定影响. 对于POMs/3CLpro复合物, 有机胺基团取代的POMs所带负电荷比未取代体系的高, 比3CLpro的结合能更高, 这与POMs的相关量子化学计算结果吻合.     

Macrophage activation in vitro by chemically cross-linked (1----3)-beta-D-glucans

The chemical cross-linking of soluble (1----3)-beta-D-glucans having molecular weights of 21000 (CL 3 h) and 6400 (CL 6 h), and laminarin (CL LAMI), which showed negligible biological activity, by epichlorohydrin provided rigid particles. These particles showed no gel-to-sol transition upon the addition of sodium hydroxide. We compared the effects of chemical cross-linking on the biological activities of glucans. The alternative complement pathway was not activated by any of the cross-linked glucans. Glucose consumption, lysosomal enzyme release, and interleukin-1 production by mouse resident peritoneal macrophages incubated in vitro were strongly induced by CL 3 h, CL 6 h and CL LAMI. However, cross-linked dextran, Sephadex, did not exhibit any of these biological activities. These results suggested that chemical cross-linking of (1----3)-beta-D-glucans enhances macrophage activities without opsonization by complement components.     

Drug design with a new transition state analog of the hydrated carbonyl: silicon-based inhibitors of the HIV protease

BACKGROUND: Silicon is the element most similar to carbon, and bioactive organosilanes have therefore been of longstanding interest. Design of bioactive organosilanes has often involved a systematic replacement of a bioactive molecule's stable carbon atoms with silicon. Silanediols, which are best known as unstable precursors of the robust and ubiquitous silicone polymers, have the potential to mimic an unstable carbon, the hydrated carbonyl. As a bioisostere of the tetrahedral intermediate of amide hydrolysis, a silanediol could act as a transition state analog inhibitor of protease enzymes. RESULTS: Silanediol analogs of a carbinol-based inhibitor of the HIV protease were prepared as single enantiomers, with up to six stereogenic centers. As inhibitors of this aspartic protease, the silanediols were nearly equivalent to both their carbinol analogs and indinavir, a current treatment for AIDS, with low nanomolar K(i) values. IC(90) data from a cell culture assay mirrored the K(i) data, demonstrating that the silanediols can also cross cell membranes and deliver their antiviral effects. CONCLUSIONS: In their first evaluation as inhibitors of an aspartic protease, silanediol peptidomimetics have been found to be nearly as potent as currently available pharmaceutical agents, in enzyme and cell protection assays. These neutral, cell-permeable transition state analogs therefore provide a novel foundation for the design of therapeutic agents.     

The role of photosensitizer molecular charge and structure on the efficacy of photodynamic therapy against Leishmania parasites

Photodynamic therapy (PDT) is emerging as a potential therapeutic modality in the clinical management of cutaneous leishmaniasis (CL). In order to establish a rationale for effective PDT of CL, we investigated the impact of the molecular charge and structure of photosensitizers on the parasitic phototoxic response. Two photosensitizers from the benzophenoxazine family that bear an overall cationic charge and two anionic porphyrinoid molecules were evaluated. The photodynamic activity of the photosensitizers decreases in the following order: EtNBSe > EtNBS > BpD > PpIX. The studies suggest that compared to hydrophobic anionic photosensitizers, the hydrophilic cationic benzophenoxazine analogs provide high effectiveness of PDT possibly due to (1) their strong attraction to the negatively charged parasitic membrane, (2) their hydrophilicity, (3) their high singlet oxygen quantum yield, and (4) their efficacy in targeting intracellular organelles.     

Structural Characterization, Biological Effects, and Synthetic Studies on Xanthones from Mangosteen (Garcinia mangostana), a Popular Botanical Dietary Supplement

Mangosteen (Garcinia mangostana L., Clusiaceae) is a popular botanical dietary supplement in the United States, where it is used principally as an antioxidant. It is referred to as the "queen of fruits" in Thailand, a country of origin. The major secondary metabolites of mangosteen, the xanthones, exhibit a variety of biological activities including antibacterial, antifungal, antiinflammatory, antioxidant, antiplasmodial, cytotoxic, and potential cancer chemopreventive activities. Moreover, some of the xanthones from mangosteen have been found to influence specific enzyme activities, such as aromatase, HIV-1 protease, inhibitor κB kinase, quinone reductase, sphingomyelinase, topoisomerase and several protein kinases, and they also modulate histamine H(1) and 5-hydroxytryptamine(2A) receptor binding. Several synthetic procedures for active xanthones and their analogs have been conducted to obtain a better insight into structure-activity relationships for this compound class. This short review deals with progress made in the structural characterization of the chemical constituents of mangosteen, as well as the biological activity of pure constituents of this species and synthetic methods for the mangosteen xanthones.     

Synthesis,Antimicrobial, Anticancer,PASS, Molecular Docking,Molecular Dynamic Simulations & Pharmacokinetic Predictions of Some Methyl β-D-Galactopyranoside Analogs

A series of methyl β-D-galactopyranoside (MGP, 1) analogs were selectively acylated with cinnamoyl chloride in anhydrous N,N-dimethylformamide/triethylamine to yield 6-O-substitution products, which was subsequently converted into 2,3,4-tri-O-acyl analogs with different acyl halides. Analysis of the physicochemical, elemental, and spectroscopic data of these analogs revealed their chemical structures. In vitro antimicrobial testing against five bacteria and two fungi and the prediction of activity spectra for substances (PASS) showed promising antifungal functionality comparing to their antibacterial activities. Minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) tests were conducted for four compounds (4, 5, 6, and 9) based on their activity. MTT assay showed low antiproliferative activity of compound 9 against Ehrlich’s ascites carcinoma (EAC) cells with an IC₅₀ value of 2961.06 µg/mL. Density functional theory (DFT) was used to calculate the thermodynamic and physicochemical properties whereas molecular docking identified potential inhibitors of the SARS-CoV-2 main protease (6Y84). A 150-ns molecular dynamics simulation study revealed the stable conformation and binding patterns in a stimulating environment. In-silico ADMET study suggested all the designed molecules to be non-carcinogenic, with low aquatic and non-aquatic toxicity. In summary, all these antimicrobial, anticancer and in silico studies revealed that newly synthesized MGP analogs possess promising antiviral activity, to serve as a therapeutic target for COVID-19.     

Structural and kinetic analysis of the unnatural fusion protein 4-coumaroyl-CoA ligase::stilbene synthase

To increase the biochemical efficiency of biosynthetic systems, metabolic engineers have explored different approaches for organizing enzymes, including the generation of unnatural fusion proteins. Previous work aimed at improving the biosynthesis of resveratrol, a stilbene associated a range of health-promoting activities, in yeast used an unnatural engineered fusion protein of Arabidopsis thaliana (thale cress) 4-coumaroyl-CoA ligase (At4CL1) and Vitis vinifera (grape) stilbene synthase (VvSTS) to increase resveratrol levels 15-fold relative to yeast expressing the individual enzymes. Here we present the crystallographic and biochemical analysis of the 4CL::STS fusion protein. Determination of the X-ray crystal structure of 4CL::STS provides the first molecular view of an artificial didomain adenylation/ketosynthase fusion protein. Comparison of the steady-state kinetic properties of At4CL1, VvSTS, and 4CL::STS demonstrates that the fusion protein improves catalytic efficiency of either reaction less than 3-fold. Structural and kinetic analysis suggests that colocalization of the two enzyme active sites within 70 ? of each other provides the basis for enhanced in vivo synthesis of resveratrol.     

新型烟酰胺腺嘌呤二核苷酸(NAD)类似物的合成及其辅酶活性

尝试4种形成焦磷酸键的方法合成了5种结构新颖的新型烟酰胺腺嘌呤二核苷酸(NAD)类似物.初步考察了类似物的生物活性,发现苹果酸酶和醇脱氢酶以类似物3b和3d为辅酶时,活性只有以NAD为辅酶时的13%～30%;而以类似物3a,3c和3e为辅酶时,这些酶的活性均极低.     

Trichogin GA IV: a versatile template for the synthesis of novel peptaibiotics

Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 3(10)-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 3(10)- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.     

Synthesis and antibacterial activities of novel oxazine and thiazine ring-fused tricyclic quinolonecarboxylic acids: 10-(Alicyclic amino)-9-fluoro-7-oxo-7H-pyrido[1,2,3-de][1,4]benzoxazine-6-carboxylic acids and the corresponding 1-thia congeners

Several analogs 4 and 5 of Ofloxacin ( 1 ) which contain the oxazine and thiazine rings fused with a quinolone carboxylic acid moiety, respectively, were prepared and their in vitro and in vivo antibacterial activities were compared with those of 1 and its previously prepared 3-exo-methylene analogs 2 and 3 . Unlike 1, 2 , and 3 , analogs 4 and 5 possess an antiaromatic oxazine and thiazine moiety and show markedly lower antibacterial activities. Alteration of their C-10 amino-substituent groups from piperazine to azetidine significantly improved the in vitro antibacterial activities, particularly in the case of the thiazine derivative 5 , but not the in vivo ones. The antibacterial activities of these three types of tricyclic quinolonecarboxylic acids are briefly discussed on the basis of the molecular properties revealed by molecular orbital calculation. The molecular dipole moment was suggested to be one possible factor controlling the binding affinity of these compounds with DNA gyrase.     

A comparison of polymerization characteristics and mechanisms of ε-caprolactone and trimethylene-carbonate with rare earth halides

Characteristics and mechanisms of the ring opening-polymerizations of ε-caprolactone (CL) and trimethylene carbonate (TMC) with rare earth halides have been compared for the first time. It has been found that rare earth halides show high catalytic activities for the polymerization of TMC, but very low activities for that of CL polymerization. The copolymerization of CL and TMC can proceed only in the presence of high contents of TMC in the comonomer feed. The copolymerization rate decreases rapidly with increasing molar fraction of CL in the feed. The mechanism study by IR, ¹H-, ¹³C-, and ³¹P-NMR spectra shows that the first step reaction of the polymerization of TMC or CL with rare earth halide is the complexation of monomer to the rare earth ion. The strong coordination of TMC to rare earth ion induces the ring-cleavage of TMC and generation of the cationic species, which initiate the polymerization of TMC via a cationic process. However, the polymerization of CL with rare earth halide is an “activated-hydrolysis” process, in which rare earth catalyst does not initiate the polymerization but serves as an activator of CL. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35 : 1339–1352, 1997     

Novel [D-Arg2]dermorphin(1-4) analogs with mu-opioid receptor antagonist activity

Ten Tyr-D-Arg-Phe-betaAla-NH(2) (YRFB) analogs in which specific amino acid side chains are shifted to the N(alpha)-position were synthesized, and the binding to these analogs to the mu receptor and their in vitro biological properties were evaluated. Some analogs in which a N,N-bis(p-hydroxybenzyl)-Gly residue was substituted for Tyr(1) exhibited mu receptor antagonist activities (pA(2)) between 5.3 and 6.1. Of these analogs, [N,N-bis(p-hydroxybenzyl)-Gly(1)]YRFB was found to be the most potent specific antagonist for the mu-opioid receptor.     

Facile synthesis of hollow Co3O4 microspheres and its use as a rapid responsive CL sensor of combustible gases

The hollow Co(3)O(4) microspheres (HCMs) were prepared by the carbonaceous templates, which did not need the surface pretreatment. The chemiluminescence (CL) and catalytic properties for CO oxidation over these hollow samples were evaluated. The samples were characterized by scanning electron microscopy (SEM), energy disperse spectra (EDS), transmission electron microscopy (TEM), selected area electron diffraction (ED), X-ray diffraction (XRD), temperature-programmed desorption (TPD) and N(2) adsorption. The influences of filter' band length, flow rate of gas, test temperature, and particle structure on CL intensities were mainly investigated. It was found that compared with the solid Co(3)O(4) particles (SCPs), HCMs had a stronger CL intensity, which was ascribed to its hollow structure; and that CL properties of the catalysts were well correlated with their reaction activities. Moreover, HCMs were used to fabricate a highly sensitive gas detector, which is a rapid and effective method for the selection of catalysts or the detection of environmental deleterious gases.     

An approach to sequence-specific antibody proteases

We describe here a novel strategy for the isolation of antibodies with sequence-specific protease activity: the synthesis of dipeptide haptens in which the targeted peptide bond has been replaced by a ring-strained or torsionally strained hydroxyethylene transition-state analog. Thus, the analogs mimic both a peptide bond in a distorted, reactive conformation and the transition state for peptide bond hydrolysis. In order to obtain sequence-specific antibody proteases, these analogs have been flanked with additional amino acid residues in preparation for immunization. In particular, we have synthesized peptides containing analogs such as 2-cis-amino-3-cis-hydroxycyclobutane carboxylic acid andendo-(3-amino-2-hydroxy)bicyclo[2.2.1]heptane-7-anti-carboxylic acid. We have also prepared a series of peptide derivatives containing analogs, such as 2-[3-amino-2-oxo-1-azetidinyl]-3-methylbutanoic acid, in which the targeted peptide bond has been incorporated into a β-lactam ring. Since the “peptide bond” has been left intact, these species mimic only a distorted ground state. At present, antibodies are being elicited against a number of the above peptide derivatives.     

Synthesis of New Brassinosteroid 24-Norcholane Type Analogs Conjugated in C-3 with Benzoate Groups

The metabolism of brassinosteroid leads to structural modifications in the ring skeleton or the side alkyl chain. The esterification and glycosylation at C-3 are the most common metabolic pathways, and it has been suggested that conjugate brassinosteroids are less active or inactive. In this way, plants regulate the content of active brassinosteroids. In this work, the synthesis of brassinosteroid 24-norcholane type analogs conjugated at C-3 with benzoate groups, carrying electron donor and electron attractant substituents on the aromatic ring, is described. Additionally, their growth-promoting activities were evaluated using the Rice Lamina Inclination Test (RLIT) and compared with that exhibited by brassinolide (used as positive control) and non-conjugated analogs. The results indicate that at the lowest tested concentrations (10⁻⁸–10⁻⁷ M), all analogs conjugated at C-3 exhibit similar or higher activities than brassinolide, and the diasteroisomers with S configuration at C-22 are the more active ones. Increasing concentration (10⁻⁶ M) reduces the biological activities of analogs as compared to brassinolide.     

Fluorinated peptidomimetics: synthesis, conformational and biological features

Peptides modified with fluoroalkyl functions in key backbone positions have been scarcely studied so far. Thus, little is known about their synthesis, their structural and physico-chemical properties, and their biological features. Our interest in this field of research led to the development of stereocontrolled synthetic protocols, both in solution and in solid phase, for many different fluoroalkyl peptidomimetics, some of which are overviewed in this paper: (a) ψ[CH(CF₃)NH]-peptide mimics holding a great potential as hybrids between natural peptides and hydrolytic transition state analogs; (b) trifluoromethyl (Tfm) malic peptidomimetics as micromolar inhibitors of some matrix metalloproteinases; (c) bis-Tfm analogs of Pepstatin A, that are nanomolar and selective inhibitors of the protozoal aspartyl protease Plasmepsin II.     

Synthesis of 1,4-dihydropyridine-5-phosphonates and their calcium-antagonistic and antihypertensive activities: novel calcium-antagonist 2-[benzyl(phenyl)amino]ethyl 5-(5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorinan-2-yl)-1,4-dihydro-2,6-dim ethyl-4-(3-nitrophenyl)-3-pyridinecarboxylate hydrochloride ethanol (NZ-105) and its crystal structure.

The effect of the 3-carboxylic-ester variation in 2,2-dimethyltrimethylene 3-alkoxycarbonyl-4-aryl-1,4-dihydro-2,6-dimethyl-5-pyridinephosphonat es (1) was investigated with relation to the calcium-antagonistic and antihypertensive activities: the analogs containing the alkyl groups of not more than 12 carbons and an amino functionality in the carboxylic-ester moiety were synthesized to be examined for biological activities. Among them, 2-[benzyl(phenyl)amino]-ethyl 5-(5,5-dimethyl-2-oxo-1,3,2-dioxaphosphorinan-2-yl)-1,4-dihydro-2, 6-dimethyl-4-(3-nitrophenyl)-3-pyridine-carboxylate hydrochloride ethanol (NZ-105) showed particularly beneficial activities and was selected for further pharmacological studies and clinical development. Some aspects of the structure-activity relationships and solid-state structure of NZ-105 by X-ray crystallographic analysis were described.     

Stereo structure-controlled and electronic structure-controlled estrogen-like chemicals to design and develop non-estrogenic bisphenol A analogs based on chemical hardness concept

The aim of this study was to elucidate the structure-activity relationship of bisphenol A (BPA) analogs using absolute hardness (eta) and absolute electronegativity (chi) (chemical hardness) and to design a non-estrogen active BPA. To determine the structure-activity relationships of BPA analogs, we investigated MCF-7 cell proliferation stimulated by BPA analogs and an eta-chi diagram based on the electronic structure of the BPA analogs. The results show that the actions of the environmental hormones BPA analogs have two chemical properties; (i) 'stereo structure-controlled' and (ii) 'electronic structure-controlled' estrogen-like chemical activities. Therefore, we designed and synthesized BPA analogs which do not possess these 2 characteristics, ((i) and (ii)), and demonstrate the non-estrogen activity of the analog.