Ligand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors

Abbreviations ADME absorption, distribution, metabolism, and excretion

MMGB/SA molecular mechanics generalized born surface area

IFD induced fit docking

RTK receptor tyrosine kinase

NSCLC non-small-cell lung cancer

ATP adenosine triphosphate

OPLS optimized potential for liquid stimulation

RMSD root mean square deviation

HTVS high-throughput virtual screening

SP standard precision

XP extra precision

OPLS-AA optimized potential for liquid stimulation-all atom

MD molecular simulation

MME molecular mechanics energies

SGB surface generalized born

POPC membrane 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine membrane

PDB Protein Data Bank

DDR1 discoidin domain receptor 1

DDR2 discoidin domain receptor 2

DDRs discoidin domain receptors

ECM extracellular matrix

TIP4P transferable intermolecular potential 4 point

NPT constant particle number, pressure and temperature

RMSF root mean square fluctuation

Communicated by Ramaswamy H. Sarma     

Soft regions of protein surface are potent for stable dimer formation

Abstract

By having knowledge about the characteristics of protein interaction interfaces, we will be able to manipulate protein complexes for therapies. Dimer state is considered as the primary alphabet of the most proteins’ quaternary structure. The properties of binding interface between subunits and of noninterface region define the specificity and stability of the intended protein complex. Considering some topological properties and amino acids’ affinity for binding in interfaces of protein dimers, we construct the interface-specific recurrence plots. The data obtained from recurrence quantitative analysis, and accessibility-related metrics help us to classify the protein dimers into four distinct classes. Some mechanical properties of binding interfaces are computed for each predefined class of the dimers. The computed mechanical characteristics of binding patch region are compared with those of nonbinding region of proteins. Our observations indicate that the mechanical properties of protein binding sites have a decisive impact on determining the dimer stability. We introduce a new concept in analyzing protein structure by considering mechanical properties of protein structure. We conclude that the interface region between subunits of stable dimers is usually mechanically softer than the interface of unstable protein dimers. Abbreviations AAB average affinity for binding

ANM anisotropic network model

APC affinity propagation clustering

ASA accessible surface area

CCD inter residues distance

CSC complex stability code

DM distance matrix

ΔG_diss PISA-computed dissociation free energy

GNM Gaussian normal mode analysis

NMA normal mode analysis

PBP protein binding patch

PISA proteins, interfaces, structures and assemblies

rASA relative accessible area in respect to unfolded state of residues

RM recurrence matrix

rP relative protrusion

RP recurrence plot

RQA recurrence quantitative analysis

SEM standard error of mean

Communicated by Ramaswamy H. Sarma     

Evolutionary significance and functional characterization of streptomycin adenylyltransferase from Serratia marcescens

Abstract

Complete functional annotations of proteins are essential to understand the role and mechanisms in pathogenesis. Aminoglycoside nucleotidyltransferases are the subclasses of aminoglycosides modifying enzymes conferring resistance to organisms. Insight into the structural and functional understanding of nucleotidyltransferase family protein provides vital information to combat pathogenesis. Phylogenetic analysis is employed to identify the evolutionary significance and common motif’s present among the homologs of nucleotidyltransferase family protein. Structure, sequence based approaches and molecular docking were implemented to predict the exact function of the protein. Wide distribution of the nucleotidyltransferase family protein in gram-positive and gram-negative organisms are evidenced from phylogenetic analysis. Five common motifs were present in all the homolog’s of nucleotidyltransferase family protein. Sequence-structure based functional annotations predicts that the targeted protein function as ATP-Mg dependent streptomycin adenylyltransferase. Structural comparisons and docking studies correlate well with the identified function. The complete function of nucleotidyltransferase family protein was identified as Streptomycin adenylyltransferase and it could be targeted as a potential therapeutic target to overcome antibiotic resistance.

Communicated by Ramaswamy H. Sarma

Abbreviations AAC aminoglycoside acetyltransferases

AME aminoglycoside modifying enzyme

ANT aminoglycoside nucleotidyltransferases

APH aminoglycoside phosphotransferases

ATP adenosine triphosphate

CASTp computer atlas and surface topography of proteins

DUF domains of unknown function

Glide grid-based ligand docking with energetic

HMM hidden Markov model

MAST motif alignment and search tool

MEGA molecular evolutionary genetics analysis

MEME multiple Em for motif elicitation

MSA multiple sequence alignment

NMP nucleoside monophosphate

NTP nucleoside triphosphate

NT nucleotidyltransferase

OPLS optimized potential for liquid simulation

XP extra precision

     

Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR,molecule docking and molecular dynamics studies

Abstract

Peroxisome proliferator-activated receptors (PPARs) are considered important targets for the treatment of Type 2 diabetes (T2DM). To accelerate the discovery of PPAR α/γ dual agonists, the comparative molecular field analysis (CoMFA) were performed for PPARα and PPARγ, respectively. Based on the molecular alignment, highly predictive CoMFA model for PPARα was obtained with a cross-validated q² value of 0.741 and a conventional r² of 0.975 in the non-cross-validated partial least-squares (PLS) analysis, while the CoMFA model for PPARγ with a better predictive ability was shown with q² and r² values of 0.557 and 0.996, respectively. Contour maps derived from the 3D-QSAR models provided information on main factors towards the activity. Then, we carried out structural optimization and designed several new compounds to improve the predicted biological activity. To investigate the binding modes of the predicted compounds in the active site of PPARα/γ, a molecular docking simulation was carried out. Molecular dynamic (MD) simulations indicated that the predicted ligands were stable in the active site of PPARα/γ. Therefore, combination of the CoMFA and structure-based drug design results could be used for further structural alteration and synthesis and development of novel and potent dual agonists. Abbreviations DM diabetes mellitus

T2DM type 2 diabetes

PPARs peroxisome proliferator-activated receptors

LBDD ligand based drug design

3D-QSAR three-dimensional quantitative structure activity relationship

CoMFA comparative molecular field analysis

PLS partial least square

LOO leave-one-out

q² cross-validated correlation coefficient

ONC optimal number of principal components

r² non-cross-validated correlation coefficient

SEE standard error of estimate

F the Fischer ratio

r²_pred predictive correlation coefficient

DBD DNA binding domain

MD molecular dynamics

RMSD root-mean-square deviation

RMSF root mean square fluctuations

Communicated by Ramaswamy H. Sarma     

Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation

Abstract

Phosphorylation of protein is critical for various cell processes, which preferentially happens in intrinsically disordered proteins (IDPs). How phosphorylation modulates structural ensemble of disordered peptide remains largely unexplored. Here, using replica exchange molecular dynamics (REMD) and Markov state model (MSM), the conformational distribution and kinetics of p53 N-terminal transactivation domain (TAD) 2 as well as its dual-site phosphorylated form (pSer46, pThr55) were simulated. It reveals that the dual phosphorylation does not change overall size and secondary structure element fraction, while a change in the distribution of hydrogen bonds induces slightly more pre-existing bound helical conformations. MSM analysis indicates that the dual phosphorylation accelerates conformation exchange between disordered and order-like states in target-binding region. It suggests that p53 TAD2 after phosphorylation would be more apt to bind to both the human p62 pleckstrin homology (PH) domain and the yeast tfb1?PH domain through different binding mechanism, where experimentally it exhibits an extended and α-helix conformation, respectively, with increased binding strength in both complexes. Our study implies except binding interface, both conformation ensemble and kinetics should be considered for the effects of phosphorylation on IDPs. Abbreviations IDPs intrinsically disordered proteins

REMD replica exchange molecular dynamics

MSM Markov state model

TAD transactivation domain

PH pleckstrin homology

PRR proline-rich region

DBD DNA-binding domain

TET Tetramerization domain

REG regulatory domain

MD molecular dynamics

PME particle-mesh Ewald

TICA time-lagged independent component analysis

CK Chapman–Kolmogorov

GMRQ generalized matrix Rayleigh quotient

SARW self-avoiding random walk

KID kinase-inducible domain

MFPT mean first passage time

DSSP definition of secondary structure of proteins

RMSD root mean square deviation

R_g radius of gyration

R_ee end to end distance

Communicated by Ramaswamy H. Sarma     

Autophagy and inflammation in chronic respiratory disease

Persistent inflammation within the respiratory tract underlies the pathogenesis of numerous chronic pulmonary diseases including chronic obstructive pulmonary disease, asthma and pulmonary fibrosis. Chronic inflammation in the lung may arise from a combination of genetic susceptibility and environmental influences, including exposure to microbes, particles from the atmosphere, irritants, pollutants, allergens, and toxic molecules. To this end, an immediate, strong, and highly regulated inflammatory defense mechanism is needed for the successful maintenance of homeostasis within the respiratory system. Macroautophagy/autophagy plays an essential role in the inflammatory response of the lung to infection and stress. At baseline, autophagy may be critical for inhibiting spontaneous pulmonary inflammation and fundamental for the response of pulmonary leukocytes to infection; however, when not regulated, persistent or inefficient autophagy may be detrimental to lung epithelial cells, promoting lung injury. This perspective will discuss the role of autophagy in driving and regulating inflammatory responses of the lung in chronic lung diseases with a focus on potential avenues for therapeutic targeting.

Abbreviations AR allergic rhinitis

AM alveolar macrophage

ATG autophagy-related

CF cystic fibrosis

CFTR cystic fibrosis transmembrane conductance regulator

COPD chronic obstructive pulmonary disease

CS cigarette smoke

CSE cigarette smoke extract

DC dendritic cell

IH intermittent hypoxia

IPF idiopathic pulmonary fibrosis

ILD interstitial lung disease

MAP1LC3B microtubule associated protein 1 light chain 3 beta

MTB Mycobacterium tuberculosis

MTOR mechanistic target of rapamycin kinase

NET neutrophil extracellular traps

OSA obstructive sleep apnea

PAH pulmonary arterial hypertension

PH pulmonary hypertension

ROS reactive oxygen species

TGFB1 transforming growth factor beta 1

TNF tumor necrosis factor

     

A systematic computational analysis of human matrix metalloproteinase 13 (MMP-13) crystal structures and structure-based identification of prospective drug candidates as MMP-13 inhibitors repurposable for osteoarthritis

Abstract

Osteoarthritis (OA) is the most common form of arthritis with no available disease-modifying treatments, and is a major cause of disability. Matrix metalloproteinase 13 (MMP-13) is vital for OA progression and thus, inhibition of MMP-13 is an effective strategy to treat OA. Since the past few decades, drug repurposing has gained substantial popularity worldwide as a time- and cost-effective approach to find new indications for the existing drugs. Therefore, more than 40 X-ray co-crystal structures of the human MMP-13 with bound inhibitors are investigated to gain the structural insights such as conserved direct interactions with binding site residues, namely Ala-238, Thr-245 and Thr-247. Afterwards, enrichment study using active and decoy set of ligands revealed three MMP-13 structures (PDB-IDs: 1XUC, 3WV1 and 5BPA) with optimal enrichment performance. Docking-based screening of existing drugs against the three crystal structures followed by binding free-energy calculation suggested drugs namely eltrombopag, cilostazol and domperidone as potential MMP-13 inhibitors that need further experimental validation. These insights may serve as a potential starting point of further experimental validation and structure-based drug design/repurposing of MMP-13 inhibitors for the treatment of OA. Abbreviations 2D two-dimensional

3D three-dimensional

FDA Food and Drug Administration

MM-GBSA Molecular Mechanics Generalized Born Surface Area

MMPs matrix metalloproteinases

MMP-13 matrix metalloproteinase 13

NMR nuclear magnetic resonance

OA osteoarthritis

PDB Protein Data Bank

PDB-ID Protein Data Bank ID

PLIP protein–ligand interaction profiler

ROC receiver operating characteristic,

RMSD root mean square deviation

Communicated by Ramaswamy H. Sarma     

Chromosomes of African Hepatics—Jubulae

Abstract

The chromosome numbers of five species belonging to the Jubulae have been described, and are as follows:

Lejeuneaceae

Cololejeunea cf. dissita, n = 9.

Arehilejeunea autoiea Vanden Berghen, n=9.

Caudalejeunea hanningtonii (Mitt.) Schiffn., n =9.

Mastigolejeunea florea (Mitt.) Steph., n=9.

Frullaniaceae

Frullania spongiosa Steph., female, n = 9.

F. spongiosa Steph., male, n=8.

The author wishes to thank Dr E. W. Jones for assistance in identifications, especially with Cololejeunea cf. dissita.     

Inhibitory effects of persistent apoptotic cells on monoclonal antibody production in vitro

Cells undergoing apoptosis in vivo are rapidly detected and cleared by phagocytes. Swift

recognition and removal of apoptotic cells is important for normal tissue homeostasis

and failure in the underlying clearance mechanisms has pathological consequences

associated with inflammatory and auto-immune diseases. Cell cultures in vitro usually

lack the capacity for removal of non-viable cells because of the absence of phagocytes

and, as such, fail to emulate the healthy in vivo micro-environment from which dead cells

are absent. While a key objective in cell culture is to maintain viability at maximal levels,

cell death is unavoidable and non-viable cells frequently contaminate cultures in

significant numbers. Here we show that the presence of apoptotic cells in monoclonal

antibody-producing hybridoma cultures has markedly detrimental effects on antibody

productivity. Removal of apoptotic hybridoma cells by macrophages at the time of

seeding resulted in 100% improved antibody productivity that was, surprisingly to us,

most pronounced late on in the cultures. Furthermore, we were able to recapitulate this

effect using novel super-paramagnetic Dead-Cert?Nanoparticles to remove non-viable

cells simply and effectively at culture seeding. These results (1) provide direct evidence

that apoptotic cells have a profound influence on their non-phagocytic neighbours in

culture and (2) demonstrate the effectiveness of a simple dead-cell removal strategy for

improving antibody manufacture in vitro.     

Metabolic phenotyping to monitor chronic enteritis canceration

Introduction

Untargeted metabolomics intends to objectively analyze a wide variety of compounds. Their diverse physicochemical properties make it difficult to choose an appropriate reconstitution solvent after sample evaporation without influencing the chromatography or hamper column sorbent integrity.

Objectives

The study aimed to identify the most appropriate reconstitution solvent for blood plasma samples in terms of feature recovery, four endogenous compounds, and one selected internal standard.

Methods

We investigated several reconstitution solvent mixtures containing acetonitrile and methanol to resolve human plasma extract and evaluated them concerning the peak areas of tryptophan-d₅, glucose, creatinine, palmitic acid, and the phophatidylcholine PC(P-16:0/P-16:0), as well as the total feature count

Results

Results indicated that acetonitrile containing 30% methanol was best suited to match all tested criteria at least for human blood plasma samples.

Conclusion

Despite identifying the mixture of acetonitrile and methanol being suitable as solvent for human blood plasma extracts, we recommend to systematically test for an appropriate reconstitution solvent for each analyzed biomatrix.

     

Role of prions in neuroprotection and neurodegeneration

There is increasing evidence that cellular prion protein plays important roles in

neurodegeneration and neuroprotection. One of the possible mechanism by which this may occur

is a functional inhibition of ionotropic glutamate receptors, including N-Methyl-D-Aspartate

(NMDA) receptors. Here we review recent evidence implicating a possible interplay between

NMDA receptors and prions in the context of neurodegenerative disorders. Such a functional

link between NMDA receptors and normal prion protein, and therefore possibly between these

receptors and pathological prion isoforms, raises interesting therapeutic possibilities for prion

diseases.     

An amicable separation: Chick’s way of doing EMT

Epithelial to mesenchymal transition (EMT) is a morphogenetic process in which cells lose their

epithelial characteristics and gain mesenchymal properties, and is fundamental for many tissue

remodeling events in developmental and pathological conditions. Although general cell biology of

EMT has been well-described, how it is executed in diverse biological settings depends largely on

individual context, and as a consequence, regulatory points for each EMT may vary. Here we discuss

developmental and cellular events involved in chick gastrulation EMT. Regulated disruption of

epithelial cell/basement membrane (BM) interaction is a critical early step. This takes place after

molecular specification of mesoderm cell fate, but before the disruption of tight junctions. The

epithelial cell/BM interaction is mediated by small GTPase RhoA and through the regulation of basal

microtubule dynamics. We propose that EMT is not regulated as a single morphogenetic event.

Components of EMT in different settings may share similar regulatory mechanisms, but the sequence

of their execution and critical regulatory points vary for each EMT.     

Structure based docking and molecular dynamics studies: Peroxisome proliferator-activated receptors –α/γ dual agonists for treatment of metabolic disorders

Abstract

Diabetes is a foremost health problem globally susceptible to increased mortality and morbidity. The present therapies in the antidiabetic class have sound adverse effects and thus, emphasis on the further need to develop effective medication therapy. Peroxisome proliferator-activated receptor alpha-gamma dual approach represents an interesting target for developing novel anti-diabetic drug along with potential anti-hyperlipidimic activity. In the current study, the peroxisome proliferator-activated receptor alpha-gamma agonistic hits were screened by hierarchical virtual screening of drug like compounds followed by molecular dynamics simulation and knowledge-based structure-activity relation analysis. The key amino acid residues of binding pockets of both target proteins were acknowledged as essential and were found to be associated in the key interactions with the most potential dual hit. This dual targeted approach of structure based computational technique was undertaken to identify prevalent promising hits for both targets with binding energy and absorption distribution metabolism excretion prediction supported the analysis of their pharmacokinetic potential. In addition, stability analysis using molecular dynamics simulation of the target protein complexes was performed with the most promising dual targeted hit found in this study. Further, comparative analysis of binding site of both targets was done for the development of knowledge-based structure-activity relationship, which may useful for successful designing of dual agonistic candidates. Abbreviations ADME absorption distribution metabolism excretion

HTVS highthroughput virtual screening

MD molecular dynamics

MMGBSA molecular mechanics generalized bonn solvation accessible

PDB protein data bank

PPAR peroxisome proliferator-activated receptor

RMSD Root mean square deviation

RMSF Root mean square fluctuation

SAR structural activity relationship

SP simple precision

T2DM TypeII diabetes mellitus

XP Extra precision

Communicated by Ramaswamy H. Sarma     

How plants make light work of growth

Entry to medical schools; Harry Grenville

Nuffleld Advanced Biology

Environmental politics and policy

Grants for school nature areas

Biology in TVEI/CPVE courses - new handbook

New AV catalogue     

Vorinostat,a possible alternative to metronidazole for the treatment of amebiasis caused by Entamoeba histolytica

Abbreviations SAHA suberoylanilide hydroxamic acid

EhHDAC Histone Deacetylase from Entamoeba histolytica

Rg Radius of gyration

RMSD root-mean-square deviation

RMSF root-mean-square fluctuation

MDS molecular dynamics simulation

VMD Visual Molecular Dynamics

NAMD Nanoscale Molecular Dynamics

PBC periodic boundary conditions

PME Particle Mesh Ewald

3D three-dimensional

Cα alpha carbon

FDA Food and Drug Administration

ns nanoseconds

GPU CUDA Graphics Processing Unit Compute Unified Device Architecture

Communicated by Ramaswamy H. Sarma     

Recent activities of the Microbiology in Schools Advisory Committee

Ecology and evolution

Agricultural education

Evolution and education

Education division elections

ISII in Europe

Tree project

Science teaching scholarship

Biology of terrestrial arthropods

A microscopied museum     

Dodecamers derived from the crystal structure were found in the pre-crystallization solution of the transaminase from the thermophilic bacterium Thermobaculum terrenum by small-angle X-ray scattering

Abstract

The pre-crystallization solution of the transaminase from Thermobaculum terrenum (TaTT) has been studied by small-angle X-ray scattering (SAXS). Regular changes in the oligomeric composition of the protein were observed after the addition of the precipitant. Comparison of the observed oligomers with the crystal structure of TaTT (PDB ID 6GKR) shows that dodecamers may act as building blocks in the growth of transaminase single crystals. Correlating of these results to the similar X-ray studies of other proteins suggests that SAXS may be a valuable tool for searching optimum crystallization conditions. Abbreviation SAXS small-angle X-ray scattering

Ta transaminase

TaTT transaminase from Thermobaculum terrenum

PLP pyridoxal-5’-phosphate

R-PEA R-(þ)-1-phenylethylamine

BCAT branched-chain amino acid aminotransferase

DAAT D-aminoacid aminotransferase

R-TA R-amine:pyruvate transaminase

Communicated by Ramaswamy H. Sarma     

Effect of tea catechins on tRNA structure and dynamics

Abbreviations C catechin

ECG epicatechin gallate

EGCG Epigallocatechin gallate

A Adenine

C cytosine

G Guanine

U uracil

FTIR Fourier transform infrared

Communicated by Ramaswamy H. Sarma