Quantifying Functional-Group-like Structural Fragments in Molecules and Its Applications in Drug Design.

A functional group in a molecule is a structural fragment consisting of a few atoms or a single atom that imparts reactivity to a molecule. Hence, defining functional groups is crucial in chemistry to predict the properties and reactivities of molecules. However, there is no established method in the literature for defining functional groups based on reactivity parameters. In this work, we addressed this issue by designing a set of predefined structural fragments along with reactivity parameters like electron conjugation and ring strain. This approach uses bond orders and atom connectivities to quantify the presence of these fragments within an organic molecule based on a given input molecular coordinate. To assess the effectiveness of this approach, we performed a case study to show the benefits of using these newly designed structural fragments instead of traditional fingerprint-based methods for grouping potential COX1/COX2 inhibitors by screening an approved drug library against aspirin molecule. The structural fragment-based model for ternary classification of rat oral LD50 of chemicals showed performance similar to the fingerprint-based models. In evaluating the regression model performance for aqueous solubility, log(S), predictions, our approach outperformed the fingerprint-based model.

Role of electron and hole doping in the NdNi1-xVxO3 nanostructure.

Neodymium nickelate, NdNiO3, attracts attention due to the simultaneous occurrence of several phase transitions around the same temperature. The electronic properties of NdNiO3 are extremely complex as structural distortion, electron correlation, charge ordering, and orbital overlapping play significant roles in the transitions. We report the effects of electron and hole injection via doping a single 3d metal, V, in the NdNiO3 nanostructure to understand the variations in the electronic properties without any structural distortion. A reversible resistivity modulation of more than five orders of magnitude via hole doping and complete suppression of the metal to insulator transition via electron doping is observed along with the switching of major charge carriers. The modulation of electronic properties without any structural distortion and external strain opens up new directions to consider the NdNi1-xVxO3 nanostructures applicable as emerging electronic devices.

Cloning, expression and characterization of PURase gene from Pseudomonas sp. AKS31.

Polyurethane (PUR) is a soil and aquatic contaminant throughout the world. Towards bioremediation, in a previous study, a soil bacterium, Pseudomonas sp. AKS31, capable of efficiently degrading PUR was isolated. Polyurethanase (PURase) enzyme is capable of cleaving the ester bond of PUR and is considered as a key regulator of PUR biodegradation. Hence, for a high yield, easy purification, and further characterization, the aim of this study was to clone and overexpress the PURase gene of this isolate. The current study also investigated structural aspects of this enzyme through predictive bioinformatics analyses. In this context, the PURase gene of the isolate was cloned and expressed in E. coli using pET28(a)+ vector. The obtained recombinant protein was found insoluble. Therefore, first, the protein was made soluble with urea and purified using nickel-NTA beads. The purified enzyme exhibited substantial activities when tested on the LA-PUR plate. Bioinformatics-based analysis of the protein revealed the presence of a lipase serine active site and indicated that this PURase belongs to the Family 1.3 lipase. Hence, the present study shows that active PURase can be produced in large quantities using a prokaryotic expression system and thus, provides an effective strategy for in-vitro PUR-degradation.

Inhibiting fungal multidrug resistance by disrupting an activator-Mediator interaction.

Eukaryotic transcription activators stimulate the expression of specific sets of target genes through recruitment of co-activators such as the RNA polymerase II-interacting Mediator complex. Aberrant function of transcription activators has been implicated in several diseases. However, therapeutic targeting efforts have been hampered by a lack of detailed molecular knowledge of the mechanisms of gene activation by disease-associated transcription activators. We previously identified an activator-targeted three-helix bundle KIX domain in the human MED15 Mediator subunit that is structurally conserved in Gal11/Med15 Mediator subunits in fungi. The Gal11/Med15 KIX domain engages pleiotropic drug resistance transcription factor (Pdr1) orthologues, which are key regulators of the multidrug resistance pathway in Saccharomyces cerevisiae and in the clinically important human pathogen Candida glabrata. The prevalence of C. glabrata is rising, partly owing to its low intrinsic susceptibility to azoles, the most widely used antifungal agent. Drug-resistant clinical isolates of C. glabrata most commonly contain point mutations in Pdr1 that render it constitutively active, suggesting that this transcriptional activation pathway represents a linchpin in C. glabrata multidrug resistance. Here we perform sequential biochemical and in vivo high-throughput screens to identify small-molecule inhibitors of the interaction of the C. glabrata Pdr1 activation domain with the C. glabrata Gal11A KIX domain. The lead compound (iKIX1) inhibits Pdr1-dependent gene activation and re-sensitizes drug-resistant C. glabrata to azole antifungals in vitro and in animal models for disseminated and urinary tract C. glabrata infection. Determining the NMR structure of the C. glabrata Gal11A KIX domain provides a detailed understanding of the molecular mechanism of Pdr1 gene activation and multidrug resistance inhibition by iKIX1. We have demonstrated the feasibility of small-molecule targeting of a transcription factor-binding site in Mediator as a novel therapeutic strategy in fungal infectious disease.

A Prelude to Biogermylene Chemistry*.

The biological applications of germylenes remain unrealised owing to their unstable nature. We report the isolation of air-, water-, and culture-medium-stable germylene DPMGeOH (3; DPM=dipyrromethene ligand) and its potential biological application. Compound 3 exhibits antiproliferative effects comparable to that of cisplatin in human cancer cells. The cytotoxicity of compound 3 on normal epithelial cells is minimal and is similar to that of the currently used anticancer drugs. These findings provide a framework for a plethora of biological studies using germylenes and have important implications for low-valent main-group chemistry.

The Preparation of Complexes of Germanone from a Germanium µ-Oxo Dimer.

Complexes of germanone containing formal Ge=O→M bonds (M=Zn, B, Ge, Sn) were isolated and characterized. The compounds were prepared through a novel synthetic route using a germanium µ-oxo dimer 3 as the starting material. This method circumvents the need to employ germanones to prepare complexes of germanones.

Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins.

BACKGROUND: The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals. RESULTS: Bhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥ 0.5 in 91% of the cases and Cα RMSDs ≤ 5 Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution. CONCLUSION: Bhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment.

Use of thio and seleno germanones as ligands: silver(I) halide complexes with Ge═E→Ag-I (E = S, Se) moieties and chalcogen-dependent argentophilic interaction.

The potential of thio and seleno germanones [LPhGe═E] (L = aminotroponiminate (ATI) ligand, E = S 3, Se 4) to function as ligands has been demonstrated through the isolation of their silver(I) iodide complexes [{(t-Bu)2ATIGe(E)Ph}2(Ag2I2)] (E = S 5, Se 6) with a planar and discrete Ag2I2 core. Compounds 5 and 6 possess the hitherto unknown Ge═E→Ag-I moieties and the crystallographic data reveals the presence of a strong argentophilic interaction (2.950(1) Å) in complex 6, but is inconclusive in complex 5 (3.470(1) Å). Using theoretical studies, proof for the presence and absence of argentophilic interactions in complexes 6 and 5 was obtained, respectively. Further, it is disclosed that the donor ability of the chalcogen atoms in the Ge═E→Ag-I moieties dictate the Ag···Ag interaction in these complexes.

Are ligand-stabilized carboxylic acid derivatives with Ge═Te bonds isolable?

The stability of ligand-stabilized carboxylic acid derivatives (such as esters, amides, anhydrides, and acid halides) with terminal Ge═Te bonds is highly questionable as there is no report on such compounds. Nevertheless, we are able to isolate germatelluroester [LGe(Te)Ot-Bu] (4), germatelluroamide [LGe(Te)N(SiMe3)2] (5), and germatelluroacid anhydride [LGe(Te)OGe(Te)L] (6) complexes (L = aminotroponiminate (ATI)) as stable species. Consequently, the synthetic details, structural characterization, and UV-vis spectroscopic and theoretical studies on them are reported for the first time.

Raman scattering study of InAs nanowires under high pressure.

The pressure-dependent phonon modes of InAs nanowires have been investigated by Raman spectroscopy under high pressure up to ∼58 GPa. X-ray diffraction measurements show that InAs nanowires at 21 GPa exhibit a phase transition from a wurtzite to an orthorhombic crystal structure, with a corresponding drastic change in the first-order Raman spectra. In the low-pressure regime, a linear increase in phonon frequencies is observed, whereas splitting between longitudinal and transversal optical phonon modes decreases as a function of applied pressure. The calculated mode Grüneisen parameters and Born's transverse effective charge indicate that the wurtzite InAs nanowires exhibit a more covalent nature under compression.

Hyperthermophilic asparaginase mutants with enhanced substrate affinity and antineoplastic activity: structural insights on their mechanism of action.

Thermophilic l-asparaginases display high stability and activity at elevated temperatures. However, they are of limited use in leukemia therapy because of their low substrate affinity and reduced activity under physiological conditions. In an attempt to combine stability with activity at physiological conditions, 3 active-site mutants of Pyrococcus furiosus l-asparaginase (PfA) were developed. The mutants, specifically K274E, showed improved enzymatic properties at physiological conditions as compared to the wild type. All variants were thermodynamically stable and resistant to proteolytic digestion. None of the enzymes displayed glutaminase activity, a highly desirable therapeutic property. All variants showed higher and significant killing of human cell lines HL60, MCF7, and K562 as compared to the Escherichia coli l-asparaginase. Our study revealed that increased substrate accessibility through the active site loop plays a major role in determining activity. A new mechanistic insight has been proposed based on molecular dynamics simulated structures, where dynamic flipping of a critical Tyr residue is responsible for the activity of thermophilic l-asparaginases. Our study not only resulted in development of PfA mutants with combination of desirable properties but also gave a mechanistic insight about their activity.

Digermylene oxide complexes: facile synthesis and reactivity.

A simple heating of aminotroponiminate (ATI) ligand stabilized germylene monochlorides [(R)2ATIGeCl] (R = t-Bu 1, i-Bu 2) with an excess of potassium hydroxide in toluene resulted in the first ATI ligand stabilized digermylene oxides [{(R)2ATIGe}2O] (R = t-Bu 3, i-Bu 4), respectively. Reaction of compound 3 with elemental sulfur and selenium gave the first germaacid anhydride complexes [{(t-Bu)2ATIGe(E)}2O] (E = S 5, Se 6) with (S)Ge-O-Ge(S) and (Se)Ge-O-Ge(Se) moieties, respectively. The digermylene oxide complexes 3 and 4 and germaacid anhydride complexes 5 and 6 were characterized by multinuclear NMR spectroscopy and single-crystal X-ray diffraction analysis. In its (77)Se NMR spectrum, compound 6 showed a resonance at -78.9 ppm. The Ge-O-Ge bond angles in compounds 5 and 6 are 178.66(2)° and 179.81(2)°, respectively. To understand further the bonding features, DFT calculations followed by MO, AIM, and NBO analysis were carried out on compounds 3, 5, and 6. The computed Wiberg bond indices of Ge-O bonds are slightly less than 0.5 in all the aforementioned compounds, and the same for the Ge═E bonds in compounds 5 and 6 are close to 1.4.

A rapid identification of hit molecules for target proteins via physico-chemical descriptors.

We report here a novel computationally fast protocol (RASPD) for identifying good candidates for any target protein from any molecule/million molecule database. A QSAR-type equation sets up the extent of complementarity of the physico-chemical properties of the target protein and the candidate molecule and an estimate of the binding energy is generated. A correlation coefficient of 0.84 and an average error ±1.45 kcal mol(-1) are obtained for the calculated protein-ligand binding energies against experiment for more than 380 protein-ligand complexes. RASPD is seen to perform better than other popular scoring functions in predicting binding energies. The most interesting feature of this methodology is that it takes only a fraction of a second for calculating the binding energy of any ligand without docking in the active site of the target protein as opposed to several minutes for regular docking and scoring methods, while the accuracy in sorting good candidates remains comparable to that of conventional techniques. An entire million compound library, a (~10(5) compound) natural product library and a (~10(5) compound) NCI database can be scanned against a specified target protein within a few minutes for identifying hit molecules. The RASPD methodology is freely accessible at .

Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance.

The propensity of poorly water-soluble drugs to aggregate at supersaturation impedes their bioavailability. Supersaturated amorphous drug-salt-polymer systems provide an emergent approach to this problem. However, the effects of polymers on drug-drug interactions in aqueous phase are largely unexplored and it is unclear how to choose an optimal salt-polymer combination for a particular drug. Here, we describe a comparative experimental and computational characterization of amorphous solid dispersions containing the drug celecoxib, and a polymer, polyvinylpyrrolidone vinyl acetate (PVP-VA) or hydroxypropyl methylcellulose acetate succinate, with or without Na+/K+ salts. Classical models for drug-polymer interactions fail to identify the best drug-salt-polymer combination. In contrast, more stable drug-polymer interaction energies computed from molecular dynamics simulations correlate with prolonged stability of supersaturated amorphous drug-salt-polymer systems, along with better dissolution and pharmacokinetic profiles. The celecoxib-salt-PVP-VA formulations exhibit excellent biopharmaceutical performance, offering the prospect of a low-dosage regimen for this widely used anti-inflammatory, thereby increasing cost-effectiveness, and reducing side-effects.

Sanjeevini: a freely accessible web-server for target directed lead molecule discovery.

BACKGROUND: Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to design improved lead molecules for the target. RESULTS: Sanjeevini represents a massive on-going scientific endeavor to provide to the user, a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. It builds in several features, including automated detection of active sites, scanning against a million compound library for identifying hit molecules, all atom based docking and scoring and various other utilities to design molecules with desired affinity and specificity against biomolecular targets. Each of the modules is thoroughly validated on a large dataset of protein/DNA drug targets. CONCLUSIONS: The article presents Sanjeevini, a freely accessible user friendly web-server, to aid in drug discovery. It is implemented on a tera flop cluster and made accessible via a web-interface at http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp. A brief description of various modules, their scientific basis, validation, and how to use the server to develop in silico suggestions of lead molecules is provided.

Aminotroponiminatogermaacid halides with a Ge(E)X moiety (E = S, Se; X = F, Cl).

Fluorination of aminotroponiminate (ATI) ligand-stabilized germylene monochloride [(t-Bu)(2)ATI]GeCl (1) with CsF gave the aminotroponiminatogermylene monofluoride [(t-Bu)(2)ATI]GeF (2). Oxidative addition reaction of compound 2 with elemental sulfur and selenium led to isolation of the corresponding germathioacid fluoride [(t-Bu)(2)ATI]Ge(S)F (3) and germaselenoacid fluoride [(t-Bu)(2)ATI]Ge(Se)F (4), respectively. Similarly, reaction of aminotroponiminatogermylene monochloride [(i-Bu)(2)ATI]GeCl (9) with elemental sulfur and selenium gave the aminotroponiminatogermathioacid chloride [(i-Bu)(2)ATI]Ge(S)Cl (11) and aminotroponiminatogermaselenoacid chloride [(i-Bu)(2)ATI]Ge(Se)Cl (12), respectively. Compound 9 has been prepared through a multistep synthetic route starting from 2-(tosyloxy)tropone 5. All compounds (2-4 and 6-12) were characterized through the multinuclear NMR spectroscopy, and single-crystal X-ray diffraction studies were performed on compounds 2, 4, and 8-12. The germaselenoacid halide complexes 4 and 12 showed doublet (-142.37 ppm) and singlet (-213.13 ppm) resonances in their (77)Se NMR spectra, respectively. Germylene monohalide complexes 2 and 9 have a germanium center in distorted trigonal pyramidal geometry, whereas a distorted tetrahedral geometry is seen around the germanium center in germaacid halide complexes 4, 11, and 12. The length of the Ge═E bond in germathioacid chloride (11) and germaselenoacid halide (4 and 12) complexes is 2.065(1) and 2.194(av) Å, respectively. Theoretical studies (based on the DFT methods) on complexes 4, 11, and 12 reveal the nature of the Ge═E multiple bond in these germaacid halide complexes with computed Wiberg bond indices (WBI) being 1.480, 1.508, and 1.541, respectively.

Selenadiazolopyridine: a synthon for supramolecular assembly and complexes with metallophilic interactions.

The synthesis and characterization of the complexes of Cu(I), Ag(I), Cu(II), and Co(II) ions with 1,2,5-selenadiazolopyridine (psd) is reported. The following complexes have been prepared: [Cu(2)(psd)(3)(CH(3)CN)(2)](2+)2(PF(6)(-)); [(CuCl)(2)(psd)(3)]; [Cu(2)(psd)(6)](2+)2(ClO(4))(-); [Ag(2)(psd)(2)](2+)2(NO(3))(-); [Ag(2)(psd)(2)](2+)2(CF(3)COO)(-); [Cu(psd)(2)(H(2)O)(3)](2+)2(ClO(4))(-)·(psd)(2); [Cu(psd)(4)(H(2)O)](2+)2(ClO(4))(-)·(CHCl(3)); [Cu(psd)(2)(H(2)O)(3)](2+)2(NO(3))(-)·(H(2)O)·(psd)(2), and [Co(psd)(2)(H(2)O)(4)](2+)2(ClO(4))(-)·(psd)(2). The electronic structure of ligand psd, in particular the bond order of Se-N bonds, has been probed by X-ray diffraction, (77)Se NMR, and computational studies. A detailed analysis of the crystal structures of the ligand and the complexes revealed interesting supramolecular assembly. The assembly was further facilitated by the presence of neutral ligands for some complexes (Cu(II) and Co(II)). The molecular structure of the ligand showed that it was present as a dimer in the solid state where the monomers were linked by strong secondary bonding Se···N interactions. The crystal structures of Cu(I) and Ag(I) complexes revealed the dinuclear nature with characteristic metallophilic interactions [M···M] (M = Cu, Ag), while the Cu(II) and Co(II) complexes were mononuclear. The presence of M···M interactions has been further probed by Atoms in Molecules (AIM) calculations. The paramagnetic Cu(II) and Co(II) complexes have been characterized by UV-vis, ESI spectroscopy, and room temperature magnetic measurements.

Air and water stable germacarbonyl compounds.

Germacarbonyl compounds are the germanium analogs of carbonyl compounds requiring an inert atmosphere for stability. Making these compounds survive the ambient conditions was not feasible given the lability of the Ge[double bond, length as m-dash]E bonds (E = O, S, Se, Te). However, the first examples of germacarbonyl compounds synthesized under ambient conditions by taking advantage of dipyrromethene ligand stabilization are detailed here; the isolated compounds are thiogermanone 3, selenogermanone 4, thiogermacarboxylic acid 6, selenogermacarboxylic acid 7, thiogermaester 9, selenogermaester 10, thiogermaamide 12, and selenogermaamide 13 with Ge[double bond, length as m-dash]E bonds (E = S, Se). Compounds 12 and 13 can react under atmospheric conditions with copper(i) halides offering air and water stable monomeric 14-15 and dimeric 16-19 copper(i) complexes (halide = Cl, Br, I). Apart from just binding, selectivity was also observed; thiogermaamide 12 and selenogermaamide 13 bind CuCl and CuBr, respectively, when treated with a mixture of copper(i) halides.

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.

We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-à-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp.

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase.

Cytochrome P450 (CYP) heme monooxygenases require two electrons for their catalytic cycle. For mammalian microsomal CYPs, key enzymes for xenobiotic metabolism and steroidogenesis and important drug targets and biocatalysts, the electrons are transferred by NADPH-cytochrome P450 oxidoreductase (CPR). No structure of a mammalian CYP-CPR complex has been solved experimentally, hindering understanding of the determinants of electron transfer (ET), which is often rate-limiting for CYP reactions. Here, we investigated the interactions between membrane-bound CYP 1A1, an antitumor drug target, and CPR by a multiresolution computational approach. We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage to the CYP active site. Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET. In the complexes, the interactions of the CPR FMN domain with the proximal side of CYP 1A1 are supplemented by more transient interactions of the CPR NADP domain with the distal side of CYP 1A1. Computed ET rates and pathways agree well with available experimental data and suggest why the CYP-CPR ET rates are low compared to those of soluble bacterial CYPs.