Mohd Hassan Baig

Antioxidant and α -amylase inhibitory property of phyllanthus virgatus L.: an in vitro and molecular interaction study.

The present study on Phyllanthus virgatus, known traditionally for its remedial potential, for the first time provides descriptions of the antioxidant and inhibition of α-amylase enzyme activity first by in vitro analyses, followed by a confirmatory in silico study to create a stronger biochemical rationale. Our results illustrated that P. virgatus methanol extract exhibited strong antioxidant and oxidative DNA damage protective activity than other extracts, which was well correlated with its total phenolic content. In addition, P. virgatus methanol extract strongly inhibited the α-amylase activity (IC50 33.20 ± 0.556 μg/mL), in a noncompetitive manner, than acarbose (IC50 76.88 ± 0.277 μg/mL), which showed competitive inhibition. Moreover, this extract stimulated the glucose uptake activity in 3T3-L1 cells and also showed a good correlation between antioxidant and α-amylase activities. The molecular docking studies of the major bioactive compounds (9,12-octadecadienoic acid, asarone, 11-octadecenoic acid, and acrylic acid) revealed via GC-MS analysis from this extract mechanistically suggested that the inhibitory property may be due to the synergistic effect of these bioactive compounds. These results provide substantial basis for the future use of P. virgatus methanol extract and its bioactive compound in in vivo system for the treatment and management of diabetes as well as in the related condition of oxidative stress.

Implication of Caspase-3 as a Common Therapeutic Target for Multineurodegenerative Disorders and Its Inhibition Using Nonpeptidyl Natural Compounds

Caspase-3 has been identified as a key mediator of neuronal apoptosis. The present study identifies caspase-3 as a common player involved in the regulation of multineurodegenerative disorders, namely, Alzheimers disease (AD), Parkinsons disease (PD), Huntingtons disease (HD), and amyotrophic lateral sclerosis (ALS). The protein interaction network prepared using STRING database provides a strong evidence of caspase-3 interactions with the metabolic cascade of the said multineurodegenerative disorders, thus characterizing it as a potential therapeutic target for multiple neurodegenerative disorders. In silico molecular docking of selected nonpeptidyl natural compounds against caspase-3 exposed potent leads against this common therapeutic target. Rosmarinic acid and curcumin proved to be the most promising ligands (leads) mimicking the inhibitory action of peptidyl inhibitors with the highest Gold fitness scores 57.38 and 53.51, respectively. These results were in close agreement with the fitness score predicted using X-score, a consensus based scoring function to calculate the binding affinity. Nonpeptidyl inhibitors of caspase-3 identified in the present study expeditiously mimic the inhibitory action of the previously identified peptidyl inhibitors. Since, nonpeptidyl inhibitors are preferred drug candidates, hence, discovery of natural compounds as nonpeptidyl inhibitors is a significant transition towards feasible drug development for neurodegenerative disorders.

Structure-based screening of inhibitors against KPC-2: designing potential drug candidates against multidrug-resistant bacteria.

KPC-2 β-lactamase demonstrates a wide substrate spectrum that includes carbapenamases, oxyimino-cephalosporins, and cephamycins. In addition, strains harboring KPC-type β-lactamases are often identified as resistant to standard β-lactamase inhibitors. Thus, KPC-2 carbapenems present a significant clinical challenge, as the mechanistic bases for KPC-2-associated phenotypes remain mysterious. Inhibiting the function of these resistance enzymes could control the hydrolysis of antibiotics. In the present study, we have reported two novel (non-β-lactatam) compounds that inhibit the activity of the KPC-2 enzyme. These compounds were identified by structure-based virtual screening using computational docking programs and molecular dynamics simulations with the solved crystal structure. Two compounds (ZINC01807204 and ZINC02318494) were selected on the basis of fitness scores from docking program and 5 ns molecular dynamics simulations. These commercially available compounds have been procured and their biological activity was experimentally evaluated on the E. coli strain carrying recombinant KPC-2. These new compounds in combination with ceftazidime and cefoxitin exhibited the Minimum Inhibitory Concentration (MIC) values of 2 and 8 μg/ml respectively, which were found to be lower as compared to known β-lactamase inhibitors. Moreover, these compounds were also found to have comparable MICs values being 64 μg/ml in combination with ceftriaxone. This study explored novel inhibitors against KPC-2, a class A β-lactamase, which may be putative drug candidates against KPC-2 producing bacterial infection.

AMDD: Antimicrobial Drug Database

Drug resistance is one of the major concerns for antimicrobial chemotherapy against any particular target. Knowledge of the primary structure of antimicrobial agents and their activities is essential for rational drug design. Thus, we developed a comprehensive database, anti microbial drug database (AMDD), of known synthetic antibacterial and antifungal compounds that were extracted from the available literature and other chemical databases, e.g., PubChem, PubChem BioAssay and ZINC, etc. The current version of AMDD contains ∼2900 antibacterial and ∼1200 antifungal compounds. The molecules are annotated with properties such as description, target, format, bioassay, molecular weight, hydrogen bond donor, hydrogen bond acceptor and rotatable bond. The availability of these antimicrobial agents on common platform not only provides useful information but also facilitate the virtual screening process, thus saving time and overcoming difficulties in selecting specific type of inhibitors for the specific targets. AMDD may provide a more effective and efficient way of accessing antimicrobial compounds based on their properties along with the links to their structure and bioassay. All the compounds are freely available at the advanced web-based search interface http://www.amddatabase.info.

Virtual screening, ADMET profiling, molecular docking and dynamics approaches to search for potent selective natural molecules based inhibitors against metallothionein-III to study Alzheimer's disease.

MOTIVATION Metallothionein-III (MT-III) displays neuro-inhibitory activity and is involved in the repair of neuronal damage. An altered expression level of MT-III suggests that it could be a mitigating factor in Alzheimers disease (AD) neuronal dysfunction. Currently there are limited marketed drugs available against MT-III. The inhibitors are mostly pseudo-peptide based with limited ADMET. In our present study, available database InterBioScreen (natural compounds) was screened out for MT-III. Pharmacodynamics and pharmacokinetic studies were performed. Molecular docking and simulations of top hit molecules were performed to study complex stability. RESULTS Study reveals potent selective molecules that interact and form hydrogen bonds with amino acids Ser-6 and Lys-22 are common to established melatonin inhibitors for MT-III. These include DMHMIO, MCA B and s27533 derivatives. The ADMET profiling was better with comparable interaction energy values. It includes properties like blood brain barrier, hepatotoxicity, druggability, mutagenicity and carcinogenicity. Molecular dynamics studies were performed to validate our findings.

Insight into the Effect of Inhibitor Resistant S130G Mutant on Physico-Chemical Properties of SHV Type Beta-Lactamase: A Molecular Dynamics Study

Bacterial resistance is a serious threat to human health. The production of β-lactamase, which inactivates β-lactams is most common cause of resistance to the β-lactam antibiotics. The Class A enzymes are most frequently encountered among the four β-lactamases in the clinic isolates. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. SHV and TEM type are known to be most common class A β-lactamases. In the present study, we have analyzed the effect of inhibitor resistant S130G point mutation of SHV type Class-A β-lactamase using molecular dynamics and other in silico approaches. Our study involved the use of different in silico methods to investigate the affect of S130G point mutation on the major physico-chemical properties of SHV type class A β-lactamase. We have used molecular dynamics approach to compare the dynamic behaviour of native and S130G mutant form of SHV β-lactamase by analyzing different properties like root mean square deviation (RMSD), H-bond, Radius of gyration (Rg) and RMS fluctuation of mutation. The results clearly suggest notable loss in the stability of S130G mutant that may further lead to decrease in substrate specificity of SHV. Molecular docking further indicates that S130G mutation decreases the binding affinity of all the three inhibitors in clinical practice.

BLAD: A comprehensive database of widely circulated beta-lactamases

MOTIVATION Beta-lactamases confer resistance to a broad range of antibiotics and inhibitors by accumulating mutations. The number of beta-lactamases and their variants is steadily increasing. The horizontal gene transfer likely plays a major role in dissemination of these markers to new environments and hosts. Moreover, information about the beta-lactamase classes and their variants was scattered. Categorizing all these classes and their associated variants along with their epidemiology and resistance pattern information on one platform could be helpful to the researcher working on multidrug-resistant bacteria. Thus, the beta-lactamase database (BLAD) has been developed to provide comprehensive information (epidemiology and resistance pattern) on beta-lactamases. Beta-lactamase gene sequences in BLAD are linked with structural data, phenotypic data (i.e. antibiotic resistance) and literature references to experimental studies. In summary, BLAD integrates information that may provide insight into the epidemiology of multidrug resistance and enable the designing of novel drug candidates. AVAILABILITY The database can be accessed from the website www.blad.co.in.

Molecular docking analysis of new generation cephalosporins interactions with recently known SHV-variants.

Extended-spectrum-β-lactamases (ESBLs), constitutes the growing class of betalactamses, these are enzymes produced by bacteria which impart resistance against advanced-generation-cephalosporins. SHV enzymes are among the most prevalent ESBLs. The mode of molecular interactions of recent SHV-variants to advanced generation cephalosporins has not been reported yet. This is the first time we are reporting the insilico study of these recent variants with new generation cephaosporins. Homology models for SHV-105, SHV-95, SHV-89, SHV-61 and SHV-48 were generated using MODELLER9v3. New generation Cephalosporins were selected to target the active site amino acid residues of these modeled SHV enzymes for predicting comparative efficacies of these inhibitors against the said enzymes on the basis of interaction energies of docking. The docked complexes were analyzed by using DISCOVERY STUDIO 2.5. In this study A237, S70, K234, R275, N132, R244 and S130 were found crucial to the correct positioning of drugs within the binding site of SHV enzymes in 11, 6, 6, 6, 5, 5 and 5 instances, respectively. On the basis of interaction energy and Ki calculations cefatoxime emerged as the most efficient among the other advanced cephalosporins against all the studied SHV variants, excluding SHV-48 where ceftazidime was found to be most effective drug. Furthermore, this study identified amino acid residues crucial to ‘SHV-Cephalosporins’ interactions and this information will be useful in designing effective and versatile drug candidates.

Identification of common therapeutic targets for selected neurodegenerative disorders: An in silico approach

Abstract Neurodegenerative disorders (NDs) are a heterogeneous group of disorders generally characterized by a profound decrease in the size and volume of the human brain due to death of neurons. These disorders include a variety of progressive disorders that result in cognitive and/or motor degradation. The present study was conducted to identify common potential targets for multi-neurodegenerative diseases. To accomplish this, we have selected six common neurodegenerative diseases, Alzheimer’s disease (AD), Parkinson’s disease (PD), Amyotrophic lateral sclerosis (ALS), Huntington’s disease (HD), Prion disease and Dentatorubral-pallidoluysian atrophy (DRPLA) for identification of common regulatory target proteins. A total of sixteen common proteins were identified as target proteins by disease pathway analysis and previous studies based on their association with more than two NDs, including AD. An interaction network of each of the sixteen target proteins was then constructed against causative proteins selected from all six NDs by using the STRING 9.1 program. Pathway analysis and the protein–protein interaction network suggested that CASP-3 and CASP-8 were associated with the maximum number of selected NDs and may therefore be the most potent target proteins for treatment of multi-neurodegenerative diseases.

The effect of Benzothiazolone-2 on the expression of Metallothionein-3 in modulating Alzheimer's disease

Metallothioneins (MTs) are a class of ubiquitously occurring low‐molecular‐weight cysteine‐ and metal‐rich proteins containing sulfur‐based metal clusters. MT‐3 exhibits neuro‐inhibitory activity. The possibility to enhance the expression of MT‐3 or protect it from degradation is an attractive therapeutic target, because low levels of MT‐3 were found in brains of Alzheimers disease (AD) patients.