Combining in silico and in vitro approaches to identification of potent inhibitor against phospholipase A2 (PLA2).

Phospholipase A2 (PLA2) is the main constituent of snake venom. PLA2 enzymes catalyze the Ca dependent hydrolysis of 2-acyl ester bonds of 3-sn-phospholipids, releasing fatty acids and lysophospholipids. Inside the body of the victim, PLA2 from snake venom induces either direct or indirect pathophysiological effects, including anticoagulant, inflammatory, neurotoxic, cardiotoxic, edematogenic, and myotoxic activities.

An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15.

G protein-coupled receptor 15 (GPR15, also known as BOB) is an extensively studied orphan G protein-coupled receptors (GPCRs) involving human immunodeficiency virus (HIV) infection, colonic inflammation, and smoking-related diseases. Recently, GPR15 was deorphanized and its corresponding natural ligand demonstrated an ability to inhibit cancer cell growth. However, no study reported the potential role of GPR15 in a pan-cancer manner.

CytoMegaloVirus Infection Database: A Public Omics Database for Systematic and Comparable Information of CMV.

CytoMegaloVirus (CMV) is known to cause infection in humans and may remain dormant throughout the life span of an individual. CMV infection has been reported to be fatal in patients with weak immunity. It is transmitted through blood, saliva, urine, semen and breast milk.

STS-NLSP: A Network-Based Label Space Partition Method for Predicting the Specificity of Membrane Transporter Substrates Using a Hybrid Feature of Structural and Semantic Similarity.

Membrane transport proteins play crucial roles in the pharmacokinetics of substrate drugs, the drug resistance in cancer and are vital to the process of drug discovery, development and anti-cancer therapeutics. However, experimental methods to profile a substrate drug against a panel of transporters to determine its specificity are labor intensive and time consuming. In this article, we aim to develop an multi-label classification approach to predict whether a substrate can specifically recognize one of the 13 categories of drug transporters ranging from ATP-binding cassette to solute carrier families using both structural fingerprints and chemical ontologies information of substrates.

Free Energy Calculations on the Water-Chain-Assisted and the Dehydration Mechanisms of Transmembrane Ion Permeation.

Two permeation mechanisms, namely the water-chain-assisted mechanism and the dehydration mechanism, have been proposed for ions through lipid membranes. In previous studies, multiple reaction coordinates and potential of mean force calculations have been applied in studying such complex transmembrane processes of ions. To reduce the expensive computational cost, we develop two new reaction coordinates in our recent work and in this work to study the two permeation mechanisms.

Identification of chlorprothixene as a potential drug that induces apoptosis and autophagic cell death in acute myeloid leukemia cells.

Although acute myeloid leukemia (AML) is a highly heterogeneous malignance, the common molecular mechanisms shared by different AML subtypes play critical roles in AML development. It is possible to identify new drugs that are effective for various AML subtypes based on the common molecular mechanisms. Therefore, we developed a hypothesis-driven bioinformatic drug screening framework by integrating multiple omics data.

Prediction of CYP450 Enzyme-Substrate Selectivity Based on the Network-Based Label Space Division Method.

A drug may be metabolized by multiple cytochrome P450 (CYP450) isoforms. Predicting the metabolic fate of drugs is very important to prevent drug-drug interactions in the development of novel pharmaceuticals. Prediction of CYP450 enzyme-substrate selectivity is formulized as a multilabel learning task in this study.

Bioinformatics Approaches for Anti-cancer Drug Discovery.

Drug discovery is important in cancer therapy and precision medicines. Traditional approaches of drug discovery are mainly based on in vivo animal experiments and in vitro drug screening, but these methods are usually expensive and laborious. In the last decade, omics data explosion provides an opportunity for computational prediction of anti-cancer drugs, improving the efficiency of drug discovery.

ATC-NLSP: Prediction of the Classes of Anatomical Therapeutic Chemicals Using a Network-Based Label Space Partition Method.

Anatomical Therapeutic Chemical (ATC) classification system proposed by the World Health Organization is a widely accepted drug classification scheme in both academic and industrial realm. It is a multilabeling system which categorizes drugs into multiple classes according to their therapeutic, pharmacological, and chemical attributes. In this study, we adopted a data-driven network-based label space partition (NLSP) method for prediction of ATC classes of a given compound within the multilabel learning framework.

Ion Channels as Therapeutic Targets for Type 1 Diabetes Mellitus.

Ion channels are integral proteins expressed in almost all living cells and are involved in muscle contraction and nutrient transport. They play a critical role in the normal functioning of the excitable tissues of the nervous system and regulate the action potential and contraction events. Dysfunction of genes encodes ion channel proteins, which disrupt the channel function and lead to a number of diseases, among which is type 1 diabetes mellitus (T1DM).

Immunoinformatics approaches to explore Helicobacter Pylori proteome (Virulence Factors) to design B and T cell multi-epitope subunit vaccine.

Helicobacter Pylori is a known causal agent of gastric malignancies and peptic ulcers. The extremophile nature of this bacterium is protecting it from designing a potent drug against it. Therefore, the use of computational approaches to design antigenic, stable and safe vaccine against this pathogen could help to control the infections associated with it.

Stoichioproteomics reveal oxygen usage bias, key proteins and pathways in glioma.

Background: The five-year survival rate and therapeutic effect of malignant glioma is low. Identification of key/associated proteins and pathways in glioma is necessary for developing effective diagnosis and targeted therapy of glioma. In addition, Glioma involves hypoxia-specific microenvironment, whether hypoxia restriction influences the stoichioproteomic characteristics of expressed proteins is unknown.

Prediction and validation of potent peptides against herpes simplex virus type 1 via immunoinformatic and systems biology approach.

The human herpes simplex virus type 1 (HSV-1) is an extremely rampant human pathogen, and its infection could cause life-long diseases, including the central nervous system disorders. The glycoproteins of HSV-1 such as glycoprotein B, glycoprotein C, glycoprotein D, glycoprotein H, and glycoprotein L are highly involved in mediating the viral attachment and infection of the host cell. Therefore, immunoinformatic approaches followed by molecular dynamics simulation and systems biology has been used to analyze these glycoproteins in order to propose effective peptide-based vaccine candidates against the HSV-1 infection.

New strategy for identifying potential natural HIV-1 non-nucleoside reverse transcriptase inhibitors against drug-resistance: an study.

Non-nucleosides reverse transcriptase inhibitors (NNRTIs), specifically targeting the HIV-1 reverse transcriptase (RT), play a unique role in anti-AIDS agents due to their high antiviral potency, structural diversity, and low toxicity in antiretroviral combination therapies used to treat HIV. However, due to the emergence of new drug-resistant strains, the development of novel NNRTIs with adequate potency, improved resistance profiles and less toxicity is highly required. In this work, a novel virtual screening strategy combined with structure-based drug design was proposed to discover the potential inhibitors against drug-resistant HIV strains.

Estimation of Probability Distribution and Its Application in Bayesian Classification and Maximum Likelihood Regression.

Nonparametric estimation of cumulative distribution function and probability density function of continuous random variables is a basic and central problem in probability theory and statistics. Although many methods such as kernel density estimation have been presented, it is still quite a challenging problem to be addressed to researchers. In this paper, we proposed a new method of spline regression, in which the spline function could consist of totally different types of functions for each segment with the result of Monte Carlo simulation.

Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer.

The lung metastasis of breast cancer involves complicated regulatory changes driven by chromatin remodelling. However, the epigenetic reprogramming and regulatory mechanisms in lung metastasis of breast cancer remain unclear. Here, we generated and analysed genome-wide profiles of multiple histone modifications (H3K4me3, H3K27ac, H3K27me3, H3K4me1 and H3K9me3), as well as transcriptome data in lung-metastatic and non-lung-metastatic breast cancer cells.

Sustainable production of biomass and industrially important secondary metabolites in cell cultures of selfheal ( L.) elicited by silver and gold nanoparticles.

Elicited artificial cultures are gaining more interest due to their uniform biosynthesis of industrially valuable secondary metabolites. In this study, a unique methodology was applied, in which different ratios of gold (Au) and silver (Ag) nanoparticles (NPs) were supplemented to submerge cultures to investigate sustainable production of biomass and antioxidant secondary metabolites. Cell suspension cultures were exposed to Ag and AuNPs alone or different ratios of AgAuNPs (1:2; 1:3; 2:1; 3:1) in combination with NAA.

Evaluation of anti-EGFR-iRGD recombinant protein with GOLD nanoparticles: synergistic effect on antitumor efficiency using optimized deep neural networks.

The epidermal growth factor receptor, also known as EGFR, is a tyrosine kinase receptor commonly found in epithelial tumors. As part of the first target for cancer treatment, EGFR has been the subject of intense research for more than 20 years; as a result, there are a number of anti-EGFR agents currently available. More recently, with our basic understanding of mechanisms related to receptor activation and function, both the secondary and primary forms of EGFR somatic mutations have led to the discovery of new anti-EGFR agents aimed at providing new insights into the clinical targeting of this receptor and possibly acting as an ideal model for developing strategies to target other types of receptors.

Protection of Primary Dopaminergic Midbrain Neurons Through Impact of Small Molecules Using Virtual Screening of GPR139 Supported by Molecular Dynamic Simulation and Systems Biology.

Introduction: GPCR share a common structural feature, i.e., the presence of seven trans-membrane helices having three intracellular and three extracellular loops.

Immunoinformatics and structural vaccinology driven prediction of multi-epitope vaccine against Mayaro virus and validation through in-silico expression.

The Mayaro virus (MAYV) belongs to genus "Alphavirus" and family "Togaviridae". MAYV has distribution in the Amazonia, Central and Northeastern regions of Brazil. The abundance of mosquito vector Haemagogus janthinomys has major role in the outbreaks of arthralgia disease in Brazil.

CEBPE expression is an independent prognostic factor for acute myeloid leukemia.

Background: Identifying reliable predictive markers is important to make therapeutic decisions, and determine the prognosis for acute myeloid leukemia (AML) patients. However, approximately 50% patients could not be accurately predicted by existing risk factors. It is necessary to identify novel prognostic factors to subdivide the intermediate-risk group or patients without any cytogenetic and molecular abnormalities.

Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2.

Half of the world population is infected by the Gram-negative bacterium Helicobacter pylori (H. pylori). It colonizes in the stomach and is associated with severe gastric pathologies including gastric cancer and peptic ulceration.