V. Shanthi

In silico analysis of drug-resistant mutant of neuraminidase (N294S) against oseltamivir

The recent H1N1 influenza pandemic has attracted worldwide attention due to the high infection rate. Oseltamivir is a new class of anti-viral agent approved for the treatment and prevention of influenza infections. The principal target for this drug is a virus surface glycoprotein, neuraminidase (NA), which facilitates the release of nascent virus and thus spreads infection. Until recently, only a low prevalence of neuraminidase inhibitor (NAI) resistance (<1 %) had been detected in circulating viruses. However, there have been reports of significant numbers of A (H1N1) influenza strains with a N294S neuraminidase mutation that was highly resistant to the NAI, oseltamivir. Hence, in the present study, we highlight the effect of point mutation-induced oseltamivir resistance in H1N1 subtype neuraminidases by molecular simulation approach. The docking analysis reveals that mutation (N294S) significantly affects the binding affinity of oseltamivir with mutant type NA. This is mainly due to the decrease in the flexibility of binding site residues and the difference in prevalence of hydrogen bonds in the wild and mutant structures. This study throws light on the possible effects of drug-resistant mutations on the large functionally important collective motions in biological systems.

Exploring the Role of C–H….π Interactions on the Structural Stability of Single Chain “All-Alpha” Proteins

C–H….π interactions are known to be important contributors to protein stability. In this study, we have analyzed the influence of C–H….π interactions in single chain “all-alpha” proteins. In the data set, a total of 181 C–H….π interactions were observed. The most prominent representatives are the interactions between aromatic C–H donor groups and aromatic π acceptors. Eighty-one percent of the C–H….π interactions between side chain to side chain and remaining19% of the C–H….π interactions were observed between side-chain to side-chain five-member aromatic ring. The donor atom contribution to C–H….π interactions was mainly from Phe, Tyr, and Trp residues. The acceptor atom contribution to C–H….π interactions was mainly from Phe, Tyr, Trp, and His. The highest percentage of C–H….π interactions were observed form Phe residue. The secondary structure preference analysis of all C–H….π interacting residues showed that Phe, Tyr, Trp, and His preferred to be in helix. Long-range C–H….π interactions are the predominant type of interactions in single chain all-alpha proteins data set. All the C–H….π interactions forming residues in the data set preferred to be in the buried region. Seventy-three percent of the donor residues and 65% of the acceptor residues are highly conserved.

Identification of Potential Inhibitors of H5N1 Influenza A Virus Neuraminidase by Ligand-Based Virtual Screening Approach

The neuraminidase (NA) of the influenza virus is the target of antiviral drug, oseltamivir. Recently, cases were reported that influenza virus becoming resistant to oseltamivir, necessitating the development of new long-acting antiviral compounds. In this report, a novel class of lead molecule with potential NA inhibitory activity was identified using a combination of virtual screening (VS), molecular docking, and molecular dynamic approach. The PubChem database was used to perform the VS analysis by employing oseltamivir as query. Subsequently, the data reduction was carried out by employing molecular docking study. Furthermore, the screened lead molecules were analyzed with respect to the Lipinski rule of five, drug-likeness, toxicity profiles, and other physico-chemical properties of drugs by suitable software program. Final screening was carried out by normal mode analysis and molecular dynamic simulation approach. The result indicates that CID 25145634, deuterium-enriched oseltamivir, become a promising lead compound and be effective in treating oseltamivir sensitive as well as resistant influenza virus strains.

Contribution of unconventional C-H...O bonds to the structural stability of antimicrobial peptides.

The native structure of Antimicrobial peptides is stabilized by a large number of individually weak forces; a complete understanding of folding implies the need to evaluate the contribution of each of these, including nonconventional hydrogen bonds. In this work, we have analyzed the influence of C-H…O interactions in the structural stability of Antimicrobial peptides by comparison with conventional hydrogen bond. There are a number of amino acid residues that can form hydrogen bonds via their side chains in addition to their peptide group. Perhaps highest contribution in this category is polar residue (Cys) and charged residues such as Lys and Arg. A total of 2513 C-H…O interactions were found in a data set of 53 Antimicrobial peptides. Among the 2513 nonconventional interactions observed in the data set, 40% of interactions are bonded to α carbon. This is consistent with the fact that the hydrogens are more acidic than others. Most prominent were side-chain to main-chain C-H…O interactions (SM-C-H…O). 92% of the stabilizing centers in the Antimicrobial peptides were found to be involved in C-H…O interactions. These interactions are mainly formed by short range contacts. Moreover, the study shows that, there is an average of more than one C-H…O interactions observed for every single residue in the Antimicrobial peptides data set. It is concluded that the C-H…O interaction can, indeed, be categorized as a true stabilizing force like hydrogen bond in Antimicrobial peptides.

Investigation of Nalidixic Acid Resistance Mechanism in Salmonella enterica Using Molecular Simulation Techniques

The emergence of nalidixic acid-resistant strains of Salmonella typhimurium remains to be a major public health problem. In particular, the substitution of Asn in place of Asp at the 87 loci in the GyrA of S. typhimurium was experimentally stated for nalidixic acid resistance. However, the data on the possible mechanism of nalidixic acid resistance are limited. In this study, I-Mutant2.0 and DUET program were employed to explore the impact of mutation on the stability of GyrA protein. Subsequently, molecular simulation techniques were employed to provide detailed information on the nalidixic acid-resistant associates with the D87N mutation in the GyrA of S. typhimurium. The binding free energy data depicts that nalidixic acid forms stable complex only with native-type GyrA than mutant (D87N) type GyrA protein. Moreover, our results theoretically suggest that hydrogen bonding formed by the Arg91 is certainly responsible for the GyrA of S. typhimurium drug selectivity. It is hoped that these evidences are immensely important for the development of new antibiotic and to overcome the nalidixic acid resistance in the near future.

In silico identification of catalytic residues in azobenzene reductase from Bacillus subtilis and its docking studies with azo dyes.

Prediction of catalytic residues of an enzyme molecule is of great importance for a range of applications including molecular docking, drug design, structural identification and comparison of binding sites. Over the last decades, many studies have been conducted to identify the enzyme catalytic site. But, the catalytic residues of the azobenzene reductase from bacillus subtilis are still unknown. Investigation shows that under anaerobic conditions, azo dyes can be reduced by this enzyme and other environmental microorganisms to colorless amines, which may be toxic, mutagenic, and carcinogenic to humans and animals. To assess and estimate the toxicity, it is essential to identify the catalytic residues of this enzyme. The computational methods developed that address this issue are few. In this approach, we identify the catalytic residues of azobenzene reductase from bacillus subtilis, which were then analyzed in terms of properties including function, conservation, hydrogen bonding, B-factor, solvent accessibility, and flexibility. The results indicate that, Lys (83) and Tyr (74) play an important role as catalytic site residues in the azobenzene reductase from bacillus subtilis. It is hoped that this information will provide a better understanding of the molecular mechanisms involved in catalysis and a heuristic basis for predicting the catalytic residues in enzymes of unknown function. In this study, our approach mainly looks for a better understanding of the biodegradation of the Sudan I, Sudan II, Sudan III and Sudan IV dyes mediated by azobenzene reductase from bacillus subtilis. Further more, the catalytic site residues information is essential for understanding and altering substrate specificity and for the design of enzyme inhibitors.

In silico analysis of detrimental mutations in ADD domain of chromatin remodeling protein ATRX that cause ATR-X syndrome: X-linked disorder

Many biological functions involve specific interactions of proteins. Mutations in ATRX gene can change the sequence and structure of a protein thereby impairing its function. Thus, the dysfunction of chromatin remodeling protein ATRX as a result of amino acid substitution in ADD domain often underlies the human disease, ATR-X syndrome. In general, it is mainly caused by amino acid substitution that interfered with the interactions of interest at the interface level. Hence, the study of protein–protein interactions and the interface that mediate the interactions stand important for understanding of biological function. In this work, we address the loss of function in chromatin remodeling protein ATRX due to loss of structural stability that affect the functional activity in mutant ADD domain by 17 missense mutations viz., G175E, N179S, P190A, P190L, P190S, L192F, V194I, C200S, Q219P, C220R, C220Y, W222S, C243F, R246C, R246L, G249C, and G249D. Furthermore, the loss of binding affinity of ADD domain with their interacting partner namely histone H3-peptide were investigated by (1) computing the RMSD (root mean square deviation) for the ADD domain of native with all the 17 mutants, (2) computing intra-molecular interactions in ADD domain of native with all the mutants, (3) computing binding affinity of native and mutant structures of ADD domain with histone H3-peptide through docking studies, and (4) cross validating the loss of function on binding affinity through inter-molecular interactions and normal mode analysis. Finally, as from our computational result, we concluded that all the parameters mentioned above used for studying ADD domain of mutant structures showed the decreased potential values compared to native structure that underlie ATR-X syndrome.

Predicting Therapeutic Template by Evaluating the Structural Stability of Anti-Cancer Peptides—A Computational Approach

Clinically significant antibiotic resistance has evolved against virtually every antibiotic deployed. Yet the development of new classes of antibiotics has lagged far behind our growing need for such drugs. Antimicrobial peptides (AMPs) have emerged as novel therapeutics hailed for their bactericidal and immunomodulatory properties. However, the process of optimizing antimicrobial peptide stability, using large peptide libraries is both tedious and expensive. The intent of this study is to analyze computationally the stability of anti-cancer peptides (ACPs) and to discover a potential template from a pool of ACPs for therapeutic use. Consequently we highlighted that ACP, NK-Lysin appears advantageous over the other ACPs with respect to stability, and may provide a convenient platform for the development of anticancer therapeutic peptide.

A compact review on the comparison of conventional and non-conventional interactions on the structural stability of therapeutic proteins

Therapeutic proteins carry out the most difficult tasks in living cells. They do so by interacting specifically with other molecules. This requires that they fold to a unique and more stable conformation. A prerequisite for comprehending the folding processes in their immense complexity entails a thorough understanding of many weak interactions. The purpose of this review is to systematically study the role of weak interactions such as cation-π, C-H......π, N-H......π and O-H......π, in the set of 49 therapeutic proteins. The importance of many of these interactions (for example, cationic residues interacting with π system) is revealed by the higher degree of conservation observed for them in protein structures. These interactions are mainly formed by long-range contacts and significant percentage of cation-π, C-H......π, N-H......π and O-H......π interacting residues had one or more stabilization centers. Further, a comparison of conventional and nonconventional interactions in the present data set unambiguously highlights the significance of these weak interactions in the structural stability of therapeutic proteins. We propose that the incorporation of the entirety of these interactions leads to a more complete description of the problem, and that this could provide new perspectives and new possible answers.

In silico studies of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) of NRL gene

Abstract Single Nuclear Polymorphisms (SNPs) are the majority of genetic variations occurring in a genome and help in understanding the genetics behind many complex diseases. By knowing the function of SNPs, the human phenotypic variations can be well known. Identification of functional SNPs in a disease-related gene is still a challenge. In this work, using computational methods, we have analyzed the genetic variations which can affect the expression and functionality of NRL gene leading to many diseases. Out of 376 SNPs, 21 SNPs were filtered as non-synonymous missense mutations related with humans in the particular gene. The tools used were SIFT, Polyphen-2, I-Mutant 2.0, SNPs&GO, PHD-SNP. Among these 21, 5 SNPs were predicted to be deleterious by all the tools. 5 mutations out of 21 were predicted deleterious by all servers with amino acid changes D15A, R66W, F21S, L160P and L194P while S50T is predicted tolerated by SIFT. L160P and S50T have been reported in some cases of retinitis pigmentosa.