Identifying discriminative features of brain network for prediction of Alzheimer's disease using graph theory and machine learning.

Alzheimer's disease (AD) is a challenging neurodegenerative condition, necessitating early diagnosis and intervention. This research leverages machine learning (ML) and graph theory metrics, derived from resting-state functional magnetic resonance imaging (rs-fMRI) data to predict AD. Using Southwest University Adult Lifespan Dataset (SALD, age 21-76 years) and the Open Access Series of Imaging Studies (OASIS, age 64-95 years) dataset, containing 112 participants, various ML models were developed for the purpose of AD prediction. The study identifies key features for a comprehensive understanding of brain network topology and functional connectivity in AD. Through a 5-fold cross-validation, all models demonstrate substantial predictive capabilities (accuracy in 82-92% range), with the support vector machine model standing out as the best having an accuracy of 92%. Present study suggests that top 13 regions, identified based on most important discriminating features, have lost significant connections with thalamus. The functional connection strengths were consistently declined for substantia nigra, pars reticulata, substantia nigra, pars compacta, and nucleus accumbens among AD subjects as compared to healthy adults and aging individuals. The present finding corroborate with the earlier studies, employing various neuroimagining techniques. This research signifies the translational potential of a comprehensive approach integrating ML, graph theory and rs-fMRI analysis in AD prediction, offering potential biomarker for more accurate diagnostics and early prediction of AD.

Disallowed spots in protein structures.

Ramachandran (ϕ, ψ) steric map was introduced in 1963 to describe available conformation space for protein structures. Subsequently, residues were observed in high-energy disallowed regions of the map. To unequivocally identify the locations of disallowed conformations of residues, we got 36 noise-free protein structures (resolution ≤1 Å, Rwork/Rfree ≤ 0.10). These stringent criteria were applied to rule out data or model errors or any crystallographic disorders. No disallowed conformation was found in the dataset. Further, we also examined disallowed conformations in a larger dataset (resolution ≤1.5 Å, devoid of any model errors, or disorders). The observed locations of disallowed residues are referred as disallowed spots. These spots include short loops of 3-5 residues, and locations where residues participate in disulfide bonding or intramolecular interactions or inter-molecular interactions with neighboring water, metals or ligands. Conformational sampling revealed that short loops in between secondary structures hardly have any opportunity to relieve from conformational strain. Residues involved in interactions, which provide energetic compensation for high-energy conformational states, were relieved from strain once the causative interaction was removed. The present study aims to identify disallowed spots in the native state of proteins, wherein residues are forced to be trapped in high-energy disallowed conformations. Moreover, it was also observed that pre-Pro, Ser, Asp, trans-Pro, Val, Asn & Gly have higher tendency to occur in disallowed conformation, which could be attributed to factors such as conformational restrictions, residue propensity of secondary structures and compensating sidechain and mainchain interactions, stabilizing turn-mimics.

Categorization of hotspots into three types - weak, moderate and strong to distinguish protein-protein versus protein-peptide interactions.

Protein-protein and protein-peptide interactions (PPI and PPepI) belong to a similar category of interactions, yet seemingly subtle differences exist among them. To characterize differences between protein-protein (PP) and protein-peptide (PPep) interactions, we have focussed on two important classes of residues-hotspot and anchor residues. Using implicit solvation-based free energy calculations, a very large-scale alanine scanning has been performed on benchmark datasets, consisting of over 5700 interface residues. The differences in the two categories are more pronounced, if the data were divided into three distinct types, namely - weak hotspots (having binding free energy loss upon Ala mutation, ΔΔG, ∼2-10 kcal/mol), moderate hotspots (ΔΔG, ∼10-20 kcal/mol) and strong hotspots (ΔΔG ≥ ∼20 kcal/mol). The analysis suggests that for PPI, weak hotspots are predominantly populated by polar and hydrophobic residues. The distribution shifts towards charged and polar residues for moderate hotspot and charged residues (principally Arg) are overwhelmingly present in the strong hotspot. On the other hand, in the PPepI dataset, the distribution shifts from predominantly hydrophobic and polar (in the weak type) to almost similar preference for polar, hydrophobic and charged residues (in moderate type) and finally the charged residue (Arg) and Trp are mostly occupied in the strong type. The preferred anchor residues in both categories are Arg, Tyr and Leu, possessing bulky side chain and which also strike a delicate balance between side chain flexibility and rigidity. The present knowledge should aid in effective design of biologics, by augmentation or disruption of PPIs with peptides or peptidomimetics.Communicated by Ramaswamy H. Sarma.

1-Meth-oxy-4-({[(4-meth-oxy-phen-yl)-sulfan-yl](phen-yl)meth-yl}sulfan-yl)benzene.

The title compound, C(21)H(20)O(2)S(2), forms a propeller-shaped structure with the tetra-hedral C atom as the central hub and meth-oxy-benzene and phenyl residues as radiating blades. Short C-H⋯π contacts are observed.

1,1'-[(2-Bromo-phen-yl)-methyl-ene]-dipyrrolidin-2-one.

In the title compound, C(15)H(17)BrN(2)O(2), both pyrrolidinone rings adopt envelope conformations. The crystal packing is characterized by short C-Br⋯O=C inter-actions [Br⋯O = 3.1730 (13) Å], leading to supra-molecular dimers. Inter-molecular C-H⋯O and C-H⋯π inter-actions are also observed.

Minimum MD simulation length required to achieve reliable results in free energy perturbation calculations: case study of relative binding free energies of fructose-1,6-bisphosphatase inhibitors.

In an attempt to establish the criteria for the length of simulation to achieve the desired convergence of free energy calculations, two studies were carried out on chosen complexes of FBPase-AMP mimics. Calculations were performed for varied length of simulations and for different starting configurations using both conventional- and QM/MM-FEP methods. The results demonstrate that for small perturbations, 1248 ps simulation time could be regarded a reasonable yardstick to achieve convergence of the results. As the simulation time is extended, the errors associated with free energy calculations also gradually tapers off. Moreover, when starting the simulation from different initial configurations of the systems, the results are not changed significantly, when performed for 1248 ps. This study carried on FBPase-AMP mimics corroborates well with our previous successful demonstration of requirement of simulation time for solvation studies, both by conventional and ab initio FEP. The establishment of aforementioned criteria of simulation length serves a useful benchmark in drug design efforts using FEP methodologies, to draw a meaningful and unequivocal conclusion.

4-(4-Chloro-phen-yl)-N-[(E)-4-(dimethyl-amino)-benzyl-idene]-1,3-thia-zol-2-amine.

The title compound, C(18)H(16)ClN(3)S, adopts an extended mol-ecular structure. The thia-zole ring is inclined by 9.2 (1) and 15.3 (1)° with respect to the chloro-phenyl and 4-(dimethyl-amino)-phenyl rings, respectively, while the benzene ring planes make an angle of 19.0 (1)°. A weak inter-molecular C-H⋯π contact is observed in the crystal structure.

Bis(acetyl-acetonato-κO,O')(pyridine-κN)zinc(II).

In the title compound, [Zn(C(5)H(7)O(2))(2)(C(5)H(5)N)], the metal atom has square-pyramidal coordination geometry with the basal plane defined by the four O atoms of the chelating acetyl-acetonate ligands and with the axial position occupied by the pyridine N atom. The crystal packing is characterized by a C-H⋯O hydrogen-bonded ribbon structure approximately parallel to [10[Formula: see text]].

3-Ethyl-4-methyl-1H-pyrazol-2-ium-5-olate.

The title compound, C(6)H(10)N(2)O, is a zwitterionic pyrazole derivative. The crystal packing is predominantly governed by a three-center iminium-amine N(+)-H⋯O(-)⋯H-N inter-action, leading to an undulating sheet-like structure lying parallel to (100).

Comparative analysis of cultural isolation and PCR based assay for detection of campylobacter jejuni in food and faecal samples.

In the present study, the efficacy of polymerase chain reaction (PCR) based on mapA gene of C. jejuni was tested for detection of Campylobacter jejuni in naturally infected as well as spiked faecal and food samples of human and animal origin. Simultaneously, all the samples were subjected to the cultural isolation of organism and biochemical characterization. The positive samples resulted in the amplification of a DNA fragment of size ~589 bp in PCR assay whereas the absence of such amplicon in DNA extracted from E. coli, Listeria, Salmonella and Staphylococcus confirmed the specificity of the primers. Of randomly collected 143 faecal samples comprising human diarrheic stools (43), cattle diarrheic faeces (48) and poultry faecal swabs (52) only 4, 3 and 8, respectively, could be detected by isolation whereas 6, 3 and 10, respectively, were found positive by PCR. However, among food samples viz. beef (30), milk (35), cheese (30), only one beef sample was detected both by culture as well as PCR. Additionally, PCR was found to be more sensitive for C. jejuni detection in spiked faecal and food samples (96.1% each) as relative to culture isolation which could detect the organism in 86.7% and 80% samples, respectively. The results depicted the superior efficacy of PCR for rapid screening of samples owing to its high sensitivity, specificity and automation potential.

Phenylbenzopyrone of Flavonoids as a Potential Scaffold to Prevent SARSCoV-2 Replication by Inhibiting its MPRO Main Protease.

BACKGROUND: In December 2019, an outbreak of a pneumonia-like illness, Corona virus disease 2019 (COVID-19), originating from Wuhan, China, was linked to novel coronavirus, now termed SARS-CoV-2. Unfortunately, no effective drugs or vaccines have been reported yet. The main protease (MPRO) remains the most validated pharmacological target for the design and discovery of inhibitors. OBJECTIVE: The purpose of the study was to find a prospective natural scaffold as an inhibitor for MPRO main protease in SARS-CoV-2 and compare it with repurposed antiviral drugs lopinavir and nelfinavir. METHODS: Natural compound libraries were screened for potential scaffold against MPRO main protease. Molecular dynamics simulation, MM-GBSA and principal component analyses of enzyme- ligand complexes were carried out with the top-ranking hits and compared with the repurposed antiviral drugs lopinavir and nelfinavir. RESULTS: The structure-based virtual screening indicated phenylbenzopyrone of flavonoids as one of the top-ranking scaffolds that have the potential to inhibit the main protease with the Oglycosidic form, performing better than the corresponding aglyconic form. Simulation studies indicated that glycosidic form of flavonoid is a more suitable inhibitor with compounds rutin, procyanidin B6, baicalin and galloylquercetin, demonstrating high affinity and stability, and rutin, emerging as one of the best candidate compounds. Interestingly, rutin was reported to have inhibitory activity against similar protease (3Cprotease of enterovirus A71) and implicated in lung fibrosis. CONCLUSION: The present study on flavonoids, possessing a potential scaffold for inhibiting main protease activity for all betacoronavirus is an attempt to provide new and safe drug leads within a reasonably short period.

(2E)-1-(1,3-Benzodioxol-5-yl)-3-(2-bromo-phen-yl)prop-2-en-1-one.

The mol-ecule of the title compound, C(16)H(11)BrO(3), is essentially planar with a maximum deviation of 0.178 (4) Šand the configuration of the keto group with respect to the olefinic double bond is typically s-cis. In the crystal structure, inter-molecular Br⋯O inter-actions [3.187 (3)Å] give rise to chains parallel to the b axis. Adjacent chains are further linked along the a axis by C-H⋯π inter-actions. The crystal studied was a racemic twin with a 0.595 (13):0.405 (13) ratio.

(7E)-5-Benzyl-7-(2-chloro-benzyl-idene)-3-(2-chloro-phen-yl)-2-phenyl-3,3a,4,5,6,7-hexa-hydro-2H-pyrazolo-[4,3-c]pyridine.

In the title 2H-pyrazolo-[4,3-c]pyridine derivative, C(32)H(27)Cl(2)N(3), the dihydro-pyrazole ring adopts an envelope conformation and the piperidine fused ring a twisted-chair conformation. Two short intra-molecular C-H⋯Cl contacts are observed. The crystal packing is characterized by dimeric C-Cl⋯π inter-actions involving the 5-benzyl ring, with Cl⋯centroid and closest atomic Cl⋯π distances of 3.778 (2) and 3.366 (4) Å, respectively.

3-(7,8,13,14-Tetra-hydrodi-benzo-[a,i]phen-an-thridin-5-yl)benzene-1,2-diol.

In the title compound, C(27)H(21)NO(2), the half-chair conformation of the alicyclic rings gives rise to a slightly folded structure of the central tricyclic tetra-hydrophenanthridine unit. Tandem intra-molecular O-H⋯N and O-H⋯O hydrogen bonds give rise to adjacent S(6) and S(5) rings, respectively, which dictate the conformation of the 5-aryl substituent. In the crystal structure, an inter-molecular C-H⋯O contact generates chains parallel to [101]. Short O-H⋯π and C-H⋯π contacts are also observed.

Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs.

BACKGROUND: The accurate ranking of analogs of lead molecules with respect to their estimated binding free energies to drug targets remains highly challenging in molecular docking due to small relative differences in their free energy values. METHODS: Free energy perturbation (FEP) method, which provides the most accurate relative binding free energy values were earlier used to calculate free energies of many ligands for several important drug targets including Fructose-1,6-BisphosPhatase (FBPase). The availability of abundant structural and experimental binding affinity data for FBPase inhibitors provided an ideal system to evaluate four widely used docking programs, AutoDock, Glide, GOLD and SurflexDock, distinct from earlier comparative evaluation studies. RESULTS: The analyses suggested that, considering various parameters such as docking pose, scoring and ranking accuracy, sensitivity analysis and newly introduced relative ranking score, Glide provided reasonably consistent results in all respects for the system studied in the present work. Whereas GOLD and AutoDock also demonstrated better performance, AutoDock results were found to be significantly superior in terms of scoring accuracy compared to the rest. CONCLUSION: Present analysis serves as a useful guide for researchers working in the field of lead optimization and for developers in upgradation of the docking programs.

Starch phosphorylase: role in starch metabolism and biotechnological applications.

The alpha-glucan phosphorylases of the glycosyltransferase family are important enzymes of carbohydrate metabolism in prokaryotes and eukaryotes. The plant alpha-glucan phosphorylase, commonly called starch phosphorylase (EC 2.4.1.1), is largely known for the phosphorolytic degradation of starch. Starch phosphorylase catalyzes the reversible transfer of glucosyl units from glucose-1-phosphate to the nonreducing end of alpha-1,4-D-glucan chains with the release of phosphate. Two distinct forms of starch phosphorylase, plastidic phosphorylase and cytosolic phosphorylase, have been consistently observed in higher plants. Starch phosphorylase is industrially useful and a preferred enzyme among all glucan phosphorylases for phosphorolytic reactions for the production of glucose-1-phosphate and for the development of engineered varieties of glucans and starch. Despite several investigations, the precise functional mechanisms of its characteristic multiple forms and the structural details are still eluding us. Recent discoveries have shed some light on their physiological substrates, precise biological functions, and regulatory aspects. In this review, we have highlighted important developments in understanding the role of starch phosphorylases and their emerging applications in industry.

Hantzsch 1,4-dihydropyridine esters and analogs: candidates for generating reproducible one-dimensional packing motifs.

Examination of the symmetric Hantzsch 1,4-dihydropyridine ester derivatives of the prototypical nifedipine molecule indicates the tendency of this class of molecule to form a common packing motif. Crystal structure analysis of 2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylic diesters and analogs reveals that they form extended chains, characterized as the C(6) packing motif, via intermolecular (amine) N-H...O=C (C3,C5 carbonyl) hydrogen bonds. In addition, all the prepared derivatives also satisfy the basic structural requirements for their high binding efficiency to the receptor. The reproducible C(6) packing motif observed among these compounds has a use in the design of solid-state materials.

(3E,5E)-1-Benzyl-3,5-bis-(2-fluoro-benzyl-idene)piperidin-4-one.

The inversion-related mol-ecules of the title compound, C(26)H(21)F(2)NO, associate into closed dimeric subunits via co-operative C-H⋯π inter-actions. Two non-classical C-H⋯O and one C-H⋯N intra-molecular hydrogen bonds are also found in the crystal structure. The piperidin-4-one ring adopts a sofa conforamtion with the 1-benzyl group in the equatorial position, and the equiplanar fluoro-phenyl substituents in the 3- and 5-positions stretched out on either side. The 1-benzyl group is disposed towards the substituent in the 6th position of the piperidin-4-one ring. The 3,5-diene units possess E configurations.

(3E,5E)-1-Benzyl-3,5-dibenzyl-idenepiperidin-4-one.

In the title compound, C(26)H(23)NO, C-H⋯O hydrogen bonds generate a ribbon structure along the a axis. These ribbons further assemble into a one-dimensional sheet parallel to the ac plane via C-H⋯π inter-actions. The piperidin-4-one ring adopts a sofa conformation with the 1-benzyl group in the equatorial position, and the 3- and 5-phenyl substituents stretched out on either side. The benzyl-idene units adopt E configurations and the 1-benzyl group is disposed towards the 3- substituent of the piperidin-4-one ring.

(3E,5E)-3,5-Bis(4-allyl-oxybenzyl-idene)-1-benzyl-piperidin-4-one.

In the title compound C(32)H(31)NO(3), the all-yloxy groups on either side of the piperidin-4-one ring are conformationally disordered. The contribution of major and minor components of the allyloxy group at the 3rd position of the ring are 0.576 (4) and 0.424 (4), respectively, and those at the 5th position are 0.885 (3) and 0.115 (3), respectively. The six-membered piperidin-4-one ring adopts a sofa conformation with the benzyl group occupying an equatorial position and the olefinic double bonds possessing an E configuration. Flanking phenyl substituents are stretched out on either side of the six-membered ring. π-π inter-actions with a centroid-centroid distance of 3.885 (1) Šgive rise to mol-ecular dimers and short C-H⋯π contacts lead to chains along the c axis.