Molecular docking using surface complementarity

A method is described to dock a ligand into a binding site in a protein on the basis of the complementarity of the inter-molecular atomic contacts. Docking is performed by maximization of a complementarity function that is dependent on atomic contact surface area and the chemical properties of the contacting atoms. The generality and simplicity of the complementarity function ensure that a wide range of chemical structures can be handled. The ligand and the protein are treated as rigid bodies, but displacement of a small number of residues lining the ligand binding site can be taken into account. The method can assist in the design of improved ligands by indicating what changes in complementarity may occur as a result of the substitution of an atom in the ligand. The capabilities of the method are demonstrated by application to 14 protein–ligand complexes of known crystal structure. © 1996 Wiley Liss, Inc.     

Exploring the interaction between D-xylose isomerase and D-xylose by free energy calculation

The numerical quadrature thermodynamic integration method is used to investigate enzyme-substrate interaction of D-xylose isomerase. A screening function for the coulombic interaction is introduced into the simulation to correct the effect of finite cutoff radius for the non-bonded interaction. The binding free energy difference for D-xylose with D-xylose isomerase and its N184D mutant has been calculated, and the result 3.9 ± 1.2 kJ/mol agrees well with experimental data of 4.38 kJ/mol. In addition, the structure and dynamics of enzyme-substrate complex were simulated for mutant and wild-type enzyme, respectively. Analysis of the structures and intramolecular interactions of the complexes were found to be valuable for understanding the reaction mechanism of the enzyme D-xylose isomerase. © Wiley-Liss, Inc.     

Design,synthesis and biological evaluation of 1-Aryl-5-(4-arylpiperazine-1-carbonyl)-1H-tetrazols as novel microtubule destabilizers

A series of 1-aryl-5-(4-arylpiperazine-1-carbonyl)-1H-tetrazols as microtubule destabilizers were designed, synthesised and evaluated for anticancer activity. Based on bioisosterism, we introduced the tetrazole moiety containing the hydrogen-bond acceptors as B-ring of XRP44X analogues. The key intermediates ethyl 1-aryl-1H-tetrazole-5-carboxylates 10 can be simply and efficiently prepared via a microwave-assisted continuous operation process. Among the compounds synthesised, compound 6–31 showed noteworthy potency against SGC-7901, A549 and HeLa cell lines. In mechanism studies, compound 6–31 inhibited tubulin polymerisation and disorganised microtubule in SGC-7901 cells by binding to tubulin. Moreover, compound 6–31 arrested SGC-7901cells in G2/M phase. This study provided a new perspective for development of antitumor agents that target tubulin.     

Ancient DNA analysis of Fremont Amerindians of the Great Salt Lake Wetlands

Skeletal remains of 47 individuals from the Great Salt Lake Wetlands, affiliated principally with Bear River (A.D. 400—1000) and Levee Phase (A.D. 1000—1350) Fremont cultural elements, were assessed for four mitochondrial DNA (mtDNA) markers that, in particular association, define four haplogroups (A, B, C, and D) widely shared among contemporary Amerindians groups. The most striking result is the absence of haplogroup A in this Fremont series, despite its predominance in contemporary Amerindian groups. Additionally, haplogroup B, defined by the presence of a 9bp deletion in region V, is present at the moderately high frequency of 60%. Haplogroups C and D are present at low frequencies. An additional haplotype, "N, observed in some modern populations and two other prehistoric samples, is also present in this Fremont skeletal collection. © 1996 Wiley-Liss, Inc.     

Molecular similarity analysis on biologically active macrocyclic bis(bibenzyls)

Conformational analysis of marchantin A (1), a bis(diarylether) type, and riccardin A (2), a diarylether-biphenyl type macrocyclic bis(bibenzyl) was carried out by systematic unbounded multiple minimum search (SUMM). Mobility of the macrocyclic rings was analysed by variable temperature ¹H-NMR study. Molecular similarity analysis was performed on the minimum energy conformers of 1 and 2 comparing their steric, electrostatic and hydrophobic properties. Correlation between complexation properties and calmodulin inhibitor activity was established. Differences in steric and electrostatic profiles may be responsible for the reduced Ca²⁺ affinity and activity of 2.     

Application of force field calculations to the prediction of chirally discriminating chromatographic behaviour for β-CDs

β-Cyclodextrin and its derivatives have been utilised to effect chiral separation in HPLC and CZE, both as stationary phases and mobile phase additives. The basis of the method is assumed to depend upon the formation of inclusion complexes of differing stabilities between enantiomeric analytes and the cyclodextrin, resulting in a differential dynamic distribution between chromatographic phases. In this study, force field calculations have been employed to model the inclusion complexes of enantiomeric brompheniramine, ephedrine, pseudoephedrine, ibuprofen, mandelic acid, methylphenobarbitone, and hexobarbitone with β-cyclodextrin. The resulting values for Δ(ΔH), the difference in enthalpy of complex formation between enantiomeric pairs has been compared with literature chromatographic data to explain the ability of the systems to achieve enantiomeric separations. © 1996 Wiley-Liss, Inc.     

Molecular docking analysis of Clostridium perfringens beta toxin model with potential inhibitors from the ZINC database

Beta toxin from Clostridium perfringens after being secreted in gut is capable of causing necrotic enteritis in humans and several other animal species and does not respond to routinely used antibiotics. Therefore, there is a need to design an effective inhibitor for the Clostridium perfringens beta toxin (CPB) using cutting edge drug discovery technologies. Hence, potential CPB inhibitors were identified using computer aided screening of compounds from the ZINC database. Further, we document the molecular docking analysis of Clostridium perfringens beta toxin model (that revealed 4 binding pockets, A-D) with the identified potential inhibitors. We show that ZINC291192 [N-[(1-methylindol-3-yl) methyl eneamino]-7,10-dioxabicyclo[4.4.0]deca-2,4,11-triene-8- carboxamide] has optimal binding features with calculated binding energy of -10.38 kcal/mol and inhibition constant of 24.76 nM for further consideration.     

Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome

All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.     

Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage

In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3′untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.     

Multi-stage structure-based virtual screening approach towards identification of potential SARS-CoV-2 NSP13 helicase inhibitors

On account of its crucial role in the virus life cycle, SARS-COV-2 NSP13 helicase enzyme was exploited as a promising target to identify a novel potential inhibitor using multi-stage structure-based drug discovery approaches. Firstly, a 3D pharmacophore was generated based on the collected data from a protein-ligand interaction fingerprint (PLIF) study using key interactions between co-crystallised fragments and the NSP13 helicase active site. The ZINC database was screened through the generated 3D-pharmacophore retrieving 13 potential hits. All the retrieved hits exceeded the benchmark score of the co-crystallised fragments at the molecular docking step and the best five-hit compounds were selected for further analysis. Finally, a combination between molecular dynamics simulations and MM-PBSA based binding free energy calculations was conducted on the best hit (compound FWM-1) bound to NSP13 helicase enzyme, which identified FWM-1 as a potential potent NSP13 helicase inhibitor with binding free energy equals −328.6 ± 9.2 kcal/mol.