Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery

The anti-inflammatory potential of cefazolin as common gamma chain cytokine inhibitor

A continuing quest for specific inhibitors of proinflammatory cytokines brings promise for effective therapies designed for inflammatory and autoimmune disorders. Cefazolin, a safe, first-generation cephalosporin antibiotic, has been recently shown to specifically interact with interleukin 15 (IL-15) receptor subunit α (IL-15Rα) and to inhibit IL-15-dependent TNF-α and IL-17 synthesis. The aim of this study was to elucidate cefazolin activity against IL-2, IL-4, IL-15 and IL-21, i.e. four cytokines sharing the common cytokine receptor γ chain (γ_c). In silico, molecular docking unveiled two potential cefazolin binding sites within the IL-2/IL-15Rβ subunit and two within the γ_c subunit. In vitro, cefazolin decreased proliferation of PBMC (peripheral blood mononuclear cells) following IL-2, IL-4 and IL-15 stimulation, reduced production of IFN-γ, IL-17 and TNF-α in IL-2- and IL-15-treated PBMC and in IL-15 stimulated natural killer (NK) cells, attenuated IL-4-dependent expression of CD11c in monocyte-derived dendritic cells and suppressed phosphorylation of JAK3 in response to IL-2 and IL-15 in PBMC, to IL-4 in TF-1 (erythroleukemic cell line) and to IL-21 in NK-92 (NK cell line). The results of the study suggest that cefazolin may exert inhibitory activity against all of the γ_c receptor-dependent cytokines, i.e. IL-2, IL-4, IL-7, IL-9, IL-15 and IL-21.

Molecular dynamics simulation of Doxorubicin loading with N-isopropyl acrylamide carbon nanotube in a drug delivery system

BACKGROUND AND OBJECTIVE

Doxorubicin is one of the common drugs used for cancer therapy. Molecular dynamics were applied to investigate the loading of Doxorubicin with thermosensitive N-isopropyl acrylamide Carbon nanotube carrier.

METHODS

The results showed that the smaller polymer chain length has more decrease of gyration radius. A decrease of gyration radius resulted in more concentrated aggregation with stronger bonds. Therefore, the shorter the polymer chain lengths, the more stable polymer interaction and better Doxorubicin delivery. Smaller polymers also form more hydrogen bonds with the drug leading to stronger and more stable carriers.

RESULTS

A lower amount of wall shear stress was found near the inner wall of the artery, distal to the plaque region (stenosis), and in both percentages of stenosis the maximum wall shear stress will accrue in the middle of the stenosis; however it is much more in the higher rate of stenosis.

CONCLUSIONS

The results indicated that N-isopropyl acrylamide - Carbon nanotube is suitable for the delivery of Doxorubicin, and five mer N-isopropyl acrylamide is the optimum carrier for Doxorubicin loading.

Interaction between two essential, conserved bacterial proteins YeaZ and glycoprotease as a potential antibacterial target in multi-drug-resistant Staphylococcus aureus

Protein-protein interactions among highly conserved and essential proteins can serve as new targets for antibacterial therapies. One protein-protein interaction between two widely conserved and essential bacterial proteins, YeaZ and its paralog, a putative glycoprotease, is being looked into for its antimicrobial drug potential. These two proteins possess tandem functions, including repression of the branched-chain amino acids biosynthesis and induction of a tRNA modification important in enhancing translation fidelity through anticodon-codon base pairing. Heterodimer formation between these two proteins is essential for Staphylococcus aureus, and other bacterial species including Escherichia coli and Salmonella typhimurium. Such YeaZ-glycoprotease interaction could thus be a target for antimicrobial drugs designed for multi-drug-resistant S. aureus. In this review, we discuss the function, structure, and interaction between these two proteins and their orthologs in other bacteria.

From the Explored to the Unexplored: Computer-Tailored Drug Design Attempts in the Discovery of Selective Caspase Inhibitors

The pathophysiological roles of caspases have made them attractive targets in the treatment and amelioration of neurologic diseases. In normal conditions, the expression of caspases is regulated in the brain, while at the onset of neurodegeneration, such as in Alzheimer's disease, they are typically overexpressed. Till date, several therapeutic efforts that include the use of small endogenous binders have been put forward to curtail dysfunctionalities that drive aberrant death in neuronal cells. Caspases are highly homologous, both in structure and in sequence, which leaves us with the question: is it possible to specifically and individually target caspases, while multiple therapeutic attempts to achieve selective targeting have failed! Based on antecedent events, the use of Computer-Aided Drug Design (CADD) methods has significantly contributed to the design of small molecule inhibitors, especially with selective target ability and reduced off-target therapeutic effects. Interestingly, we found out that there still exists an enormous room for the integration of structure/ligand-based drug design techniques towards the development of highly specific reversible and irreversible caspase inhibitors. Therefore, in this review, we highlight drug discovery approaches that have been directed towards caspase inhibition in addition to an insightful focus on applicable CADD techniques for achieving selective targeting in caspase research.

Contriving a chimeric polyvalent vaccine to prevent infections caused by herpes simplex virus (type-1 and type-2): an exploratory immunoinformatic approach

Herpes simplex virus type 1 (HSV-1) and 2 (HSV-2) cause a variety of infections including oral-facial infections, genital herpes, herpes keratitis, cutaneous infection and so on. To date, FDA-approved licensed HSV vaccine is not available yet. Hence, the study was conducted to identify and characterize an effective epitope based polyvalent vaccine against both types of Herpes Simplex Virus. The selected proteins were retrieved from ViralZone and assessed to design highly antigenic epitopes by binding analyses of the peptides with MHC class-I and class-II molecules, antigenicity screening, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach. The final vaccine was constructed by the combination of top CTL, HTL and BCL epitopes from each protein along with suitable adjuvant and linkers. Physicochemical and secondary structure analysis, disulfide engineering, molecular dynamic simulation and codon adaptation were further employed to develop a unique multi-epitope peptide vaccine. Docking analysis of the refined vaccine structure with different MHC molecules and human immune TLR-2 receptor demonstrated higher interaction. Complexed structure of the modeled vaccine and TLR-2 showed minimal deformability at molecular level. Moreover, translational potency and microbial expression of the modeled vaccine was analyzed with pET28a(+) vector for E. coli strain K12 and the vaccine constructs had no similarity with entire human proteome. The study enabled design of a novel chimeric polyvalent vaccine to confer broad range immunity against both HSV serotypes. However, further wet lab based research using model animals are highly recommended to experimentally validate our findings.Communicated by Ramaswamy H. Sarma.

Are We Opening the Door to a New Era of Medicinal Chemistry or Being Collapsed to a Chemical Singularity?

The paradigm of "drug-like-ness" dramatically altered the behavior of the medicinal chemistry community for a long time. In recent years, scientists have empirically found a significant increase in key properties of drugs that have moved structures closer to the periphery or the outside of the rule-of-five "cage". Herein, we show that for the past decade, the number of molecules claimed in patent records by major pharmaceutical companies has dramatically decreased, which may lead to a "chemical singularity". New compounds containing fragments with increased 3D complexity are generally larger, slightly more lipophilic, and more polar. A core difference between this study and recently published papers is that we consider the nature and quality of sp³-rich frameworks rather than sp³ count. We introduce the original descriptor MCE-18, which stands for medicinal chemistry evolution, 2018, and this measure can effectively score molecules by novelty in terms of their cumulative sp³ complexity.

Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus)

Norovirus is known as a major cause of several acute gastroenteritis (AGE) outbreaks each year. A study was conducted to develop a unique multi epitope subunit vaccine against human norovirus by adopting reverse vaccinology approach. The entire viral proteome of Norwalk virus was retrieved and allowed for further in silico study to predict highly antigenic epitopes through antigenicity, transmembrane topology screening, allergenicity assessment, toxicity analysis, population coverage analysis and molecular docking approach. Capsid protein VP1 and protein VP2 were identified as most antigenic viral proteins which generated a plethora of antigenic epitopes. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, hydrophilicity, theoretical PI and structural behavior. Molecular docking analysis of the refined vaccine with different MHCs and human immune TLR8 receptor demonstrated higher binding interaction as well. Complexed structure of the modeled vaccine and TLR8 showed minimal deformability at molecular level. The designed construct was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for its heterologous cloning and expression, and sequence of vaccine constructs showed no similarity with human proteins. However, the study could initiate in vitro and in vivo studies regarding effective vaccine development against human norovirus.

Interaction sites of PEF proteins for recognition of their targets

The EF-hand is a helix-loop-helix motif observed mainly in intracellular calcium binding proteins. The EF-hand usually occurs as a pair, EF-lobe, which is a unit of evolution and structure. Penta EF-hand (PEF) proteins form a unique group including calpain, sorcin, grancalcin, ALG-2, and peflin. The fifth EF-hand of PEF proteins makes a pair with that of another PEF protein. The members of PEF family have diverse functions and their evolution is complex. The interaction of PEF proteins with target occurs at several sites. Here, we analyzed the ancestral sequences of each group of PEF proteins and determined the interfaces for the specific and selective interaction to the target among several PEF proteins. The shape of the groove for interaction at common site is different among PEF proteins. We found that the changes at limited sites induced the divergence of interaction sites that determines the selectivity of targets. The residues involved the changes at limited sites are important for the drug design selective to each PEF protein.

Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus

H7N9, a novel strain of avian origin influenza was the first recorded incidence where a human was transited by a N9 type influenza virus. Effective vaccination against influenza A (H7N9) is a major concern, since it has emerged as a life threatening viral pathogen. Here, an in silico reverse vaccinology strategy was adopted to design a unique chimeric subunit vaccine against avian influenza A (H7N9). Induction of humoral and cell-mediated immunity is the prime concerned characteristics for a peptide vaccine candidate, hence both T cell and B cell immunity of viral proteins were screened. Antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were adopted to generate the most antigenic epitopes of avian influenza A (H7N9) proteome. Further, a novel subunit vaccine was designed by the combination of highly immunogenic epitopes along with suitable adjuvant and linkers. Physicochemical properties and secondary structure of the designed vaccine were assessed to ensure its thermostability, h ydrophilicity, theoretical PI and structural behavior. Homology modeling, refinement and validation of the designed vaccine allowed to construct a three dimensional structure of the predicted vaccine, further employed to molecular docking analysis with different MHC molecules and human immune TLR8 receptor present on lymphocyte cells. Moreover, disulfide engineering was employed to lessen the high mobility region of the designed vaccine in order to extend its stability. Furthermore, we investigated the molecular dynamic simulation of the modeled subunit vaccine and TLR8 complexed molecule to strengthen our prediction. Finally, the suggested vaccine was reverse transcribed and adapted for E. coli strain K12 prior to insertion within pET28a(+) vector for checking translational potency and microbial expression.

Scalable Extraction of Big Macromolecular Data in Azure Data Lake Environment

Calculation of structural features of proteins, nucleic acids, and nucleic acid-protein complexes on the basis of their geometries and studying various interactions within these macromolecules, for which high-resolution structures are stored in Protein Data Bank (PDB), require parsing and extraction of suitable data stored in text files. To perform these operations on large scale in the face of the growing amount of macromolecular data in public repositories, we propose to perform them in the distributed environment of Azure Data Lake and scale the calculations on the Cloud. In this paper, we present dedicated data extractors for PDB files that can be used in various types of calculations performed over protein and nucleic acids structures in the Azure Data Lake. Results of our tests show that the Cloud storage space occupied by the macromolecular data can be successfully reduced by using compression of PDB files without significant loss of data processing efficiency. Moreover, our experiments show that the performed calculations can be significantly accelerated when using large sequential files for storing macromolecular data and by parallelizing the calculations and data extractions that precede them. Finally, the paper shows how all the calculations can be performed in a declarative way in U-SQL scripts for Data Lake Analytics.

Phenotype and target-based chemical biology investigations in cancers

Chemical biology has been attracting a lot of attention because of the key roles of chemical methods and techniques in helping to decipher and manipulate biological systems. Although chemical biology encompasses a broad field, this review will focus on chemical biology aimed at using exogenous chemical probes to interrogate, modify and manipulate biological processes, at the cellular and organismal levels, in a highly controlled and dynamic manner. In this area, many advances have been achieved for cancer biology and therapeutics, from target identification and validation based on active anticancer compounds (forward approaches) to discoveries of anticancer molecules based on some important targets including protein-protein interaction (reverse approaches). Herein we attempt to summarize some recent progresses mainly from China through applying chemical biology approaches to explore molecular mechanisms of carcinogenesis. Additionally, we also outline several new strategies for chemistry to probe cellular activities such as proximity-dependent labeling methods for identifying protein-protein interactions, genetically encoded sensors, and light activating or repressing gene expression system.