A. A. Samchenko

In silico design of high-affinity ligands for the immobilization of inulinase

Using computer modeling, virtual screening of high-affinity ligands for immobilization of inulinase - an enzyme that cleaves inulin and fructose-containing polymers to fructose - has been performed. The inulinase molecule from Aspergillus ficuum (pdb: 3SC7) taken from the database of protein structures was used as a protein model and the target for flexible docking. The set of ligands studied included simple sugars (activators, inhibitors, products of enzymatic catalysis), as well as high-molecular weight compounds (polycation and polyanion exchange resins, glycoproteins, phenylalanine-proline peptide, polylactate, and caffeine). Based on the comparative analysis of the values of the total energy and the localization of ligand binding sites, we made several assumptions concerning the mechanisms of interaction of the suggested matrices for the immobilization of enzyme molecules and the structural features of such complexes. It was also assumed that the candidates for immobilization agents meeting the industrial requirements may be glycoproteins, for which we propose an additional incorporation of cysteine residues into their structure, aimed to create disulfide «anchors» to the surface.

Experience in simulating the structural and dynamic features of small proteins using table supercomputers

The results of theoretical studies of the structural and dynamic features of peptides and small proteins have been presented that were carried out by quantum chemical and molecular dynamics methods in high-performance graphic stations, “table supercomputers,” using distributed calculations by the CUDA technology.

The molecular mechanism of adsorption immobilization of inulinase on polymer matrices

The conditions and mechanisms of the immobilization of inulinase on polymeric carriers were studied using the VION KN-1 and KU-2 cation-exchangers, VION AN-1 and AV-17-2P anion-exchangers, and the ampholyte KOPAN-90. The calculated data showed a significant role of van der Waals interactions and hydrogen bonding in the formation of virtually all inulinase complexes with the immobilization matrices. The AV-17-2P anion-exchanger was the only one of the studied polymer matrices that was unable to form hydrogen bonds with inulinase. The mechanisms of the interaction between inulinase and various ampholytes and cation and anion exchange resins differ from each other. The strongest differences are observed in mechanisms of the sorption of inulinase on VION KN-1 and chitosan matrices. Approximately 87% of the identical amino-acid residues are involved in the interaction of the enzyme with the KU-2 and AV-17-2P resins and the VION AN-1 and KOPAN-90 fibers.

195 In silico design and virtual screening of inulinase immobilization ligands with highest affinity

The current approaches to discover new and efficient drugs to treat multi drug resistant (MDR) and extreme drug resistant (XDR) Tuberculosis (TB) are prohibitively expensive leading to a dry pipeline for new chemical entities (NCE). Newer strategies need to be developed for reducing long and protracting procedures of clinical development of new drugs. To minimize the cost of TB drug discovery, innovative approaches of designing NCE need to be devised utilizing a systems biology approach. Previously from our lab, critical and low concentration proteins required for the growth and survival of Mycobacterium tuberculosis (Mtb) was identified using a novel Systems Biology Spindle Map (SBSM) (Vashisht, 2014). The result of the in silico single gene knock out analysis was carried out on a total of 890 metabolic genes and 961 metabolites involved in 1152 reactions to identify putative drug targets. Out of the 116 lethal genes, 75 of these protein/enzymes had a lower concentration than the mean protein concentration making them effective drug targets. In the present work, these genes are being studied for their potential as putative, non-toxic and metabolically critical drug targets. Based on the existing knowledge, we also hypothesize that the most critical targets in Mtb should be evolutionarily conserved. Analysis of these targets for their conservation across the 1879 genomes of Mtb using GMTV database (Chernyaeva, 2014) was evaluated. Though, it is known that a large number of the sequences are conserved, only a small number actually remains invariant across the various strains of the bacteria. The initial analysis resulted in two genes, which showed no variation across the wide Mtb genome reported in the database. The two genes viz. Rv3607c (involved in folate biosynthesis) and Rv0321 (involved in interconversion of dCTP and dUTP) have an existing PDB structure. The former also has a reported GSK molecule proposed to be its inhibitor, generated as a result of a high-throughput screen (HTS) of two million compound library for anti-mycobacterial phenotypes further resulting into an open access list of 776 compounds with activity against tuberculosis (Jimenez, 2013). Based on the understanding of the active site of these proteins, and utilizing structure based drug design approaches as well as analyzing the SAR around the reported GSK molecule, we have generated a library of compounds from the existing chemical databases. The small molecules library has compounds, some of which are also the existing drugs for different diseases. Hence, together with recalibrating old drugs, utilizing small molecules databases and performing SAR on these, the generated library of compounds were docked (Glide tool of Schrodinger) against the two proteins of interest with improved binding affinities. These studies are expected to lead to the generation of a new antiTB drug candidate, primarily developed in silico. With these methodologies, it is proposed that, new ligands can be generated, with the success rate of 1/ 10 as compared to the existing 1/100 molecule entering clinical trials.

18 Possible extraterrestrial life: a quantum-chemical look on the silicon analogs of carbon biomolecules

The uniqueness of life on our planet has been an important topic of discussion in scientific literature for many decades. The most particular findings are in the fields of the structure of biomolecules and the mechanisms of their conformational and chemical transfers since they underlie all the biospheric processes of our planet. The compounds based on carbon are the subject of study of organic chemistry, which has an appropriate thoroughly developed classification of such substances; a number of approaches have been proposed for the analysis of composition and structure of the organic compounds, and a theoretical basis has been created, which describes the character of various chemical bonds involving carbon atoms. At the same time, since quite a while, there is a widely discussed hypothesis (Alison, 1968) concerning the possibility of existence of compounds, which are similar to organic, but are based on silicon atoms. Even in interstellar medium, among all the diversity of molecules detected, 84 are based on carbon, and 8 on silicon (Lazio, 2000), including four hybrid types, i.e. containing both silicon and carbon. According to approximate evaluations, the contents ratio of carbon to silicon in the space equals to 10:1, though the Earth’s crust consists of 87% of silicon in the form of oxides. In the Periodic Table, silicon is situated in the same group IV, like carbon. These two elements are largely similar in the structure of their valent electronic shells, and their noteworthy that previously it was stated (Lazio, 2000) that silicon-containing compounds are not as diverse in structure as carbon compounds. Despite having higher mass and radius, the atoms of silicon form double and triple covalent bonds (Wang et al., 2008). Therefore, the issue concerning the existence of silicon structures similar to carbon biomolecules, as well as the question of hypothetical “biochemical” processes involving non-carbonic analogs of aminoacids, carbohydrates, proteins, lipids, and other biomolecules, is still a matter of discussion in scientific and popular science literature. It is particularly notable that the modern methods of computational chemistry allow carrying out the estimating calculations of the structure and dynamics of such compounds, which is quite similar to the known approaches of substance modeling de novo in drug design. For instance, first by calculations (Nagase, Kudo, & Aoki, 1985), and later on experimentally (Abersfelder, White, Rzepa, & Scheschkewitz, 2010), aromaticity of cyclic carbohydrate-like derivatives of silicon was studied. In the present study, we used quantum-chemical semiempirical PM3 and ab initio B3LYP/6-311G(d,p) level of theory to investigate the peculiarities of several structural and thermodynamic parameters of molecules, which can be assumed as complete silicon analogs of carbonic L-amino acids and other biomolecules, so-called bricks of life: carbohydrates, nitrogenous bases, fatty acids, as well as vitamins and caffeine. The quantum-mechanical calculations that we made displayed that the molecules of silicon amino acids possess higher thermodynamic stability compared to carbon analogs. Thereby, silicon amino acids have a similar conformation freedom, increased values of dipole moment, as well as more pronounced electron-donor characteristics. Silicon analogs of carbohydrates, fatty acids, and nitrogenous bases are as well considered as heavier thermodynamically stable compounds, having special features in 3D-organization and worth further experimental study. The present work also deals with the question of the existence and stability of “alpha-helices” composed of silicon amino acids, because in the molecules of Si-analogs of aspartate and glutamate, we have discovered effective formation of intramolecular hydrogen bond (due to the side chain), which is highly important for Pauling–Corey alpha helix formation in natural L-amino acids (Kondratyev, Kabanov, & Komarov, 2010). Our estimations show that an “alpha helix” composed of 10 silicon alanine analogs is more stable in isolated state than a linear form of such macromolecule, which was not observed for a molecule of the same composition having a carbon backbone.

The electronic structure properties of 20 L-amino acids in neutral and zwitterion forms: Quantum-chemical calculations

The conformational diversity of the 20 DNA-encoded proteinogenic amino acids and their zwitterions in the gaseous state and in the state with the first hydration shell was analyzed using the PM3 and PM7 semi-empirical quantum-chemistry programs.

On the nature of the domination of oligomeric (dA:dT) n tracts in the structure of eukaryotic genomes

The comparative analysis of the frequency of oligomeric W- and S-tracts was conducted in the genomes of different eukaryotic species that differ in their GC-composition. The domination of mononucleotide and mixed (A/T)n-sequences compared with (G/C)n-sequences was detected in the studied eukaryotic genomes, including Dictyostelium discoideum (GC ~ 25.7%), Caenorhabditis elegans (GC ~ 36.9%), Arabidopsis thaliana (GC ~ 38.0%), Drosophila melanogaster (GC ~ 38.8%), Homo sapiens (GC ~ 40.0%), Gallus gallus (GC ~ 50.0%), Leishmania major (GC ~ 59.1%). Using the results of quantum–chemical calculations, a theoretical rationale of the important role of existing differences in the initial hidden structural polymorphism of the hydrogen bonding of the Watson–Crick AT and GC pairs in the development of this phenomenon is given. It is concluded that a decreased structural polymorphism of AT pairs compared with the high fourfold polymorphism of the main state of GC pairs may be the most probable source of the preference and reliability of the “use” of AT pairs by nature in genomic DNA of many species.

On the possible influence of different pathways of binding of amides with water on “Pyramidalization” of valence bonds of peptide group nitrogen

With the aim to study solvation effects in peptide structure organization, the behavior of the energy of different types of hydration in simple amines and amides has been analyzed. On the example of quantum-chemical DFT and PM3 calculations of amino derivatives of composition CH3-(CH2)3)-NH2, (CH3)2-NH, CH3-NH2, NH3, CH2=CH-NH2, H-CC-NH2, O=C(CH)3-N(CH3)2, O=C(CH3)-NH(CH3), O=C(CH3)-NH2, O=CH-N(CH3)H, and O=CH-NH2 it has been shown that: (1) in the given set of molecules, the proton acceptor N…H-O variant of hydrogen bonding of NH2 group with a water molecule is dominating only for the simplest amines. Being primordially weaker, the proton donor N-H…OH variant of water H-bonding gradually increases in energy in the given set as the basicity of the compound decreases, and for the case of amides of carboxylic acids it becomes already a significant channel of the hydration; (2) the intermolecular N-H…O=C bonding of trans-N-methylacetamides, which models the peptide hydrogen bonds in proteins, induces “planarization” of its initially nonplanar O=C-NH fragments. However, the addition of water molecules to the complex through the proton acceptor N…H-O variant of binding of N atom not only restores but even strengthens the “pyramidalization” of valence bonds of peptide groups.

Conformational mobility of the O=C−N−H fragments in isolated dipeptides of L-amino acids

Ab initio MP2 and semiempirical PM3 quantum-chemical calculations are used to discuss the bistability of the nonplanar O=C−N−H fragment in simple amides and dipeptides. The side group is shown to influence the structural polymorphism of the peptide group.