Three-state dynamics of zinc(II) complexes yielding significant antidiabetic targets.

Protein Tyrosine Phosphatase 1B (PTP1B), being negative regulator of insulin signaling pathways is considered as potential medicinal target. Selective and targeted inhibitors for PTP1B can impact the therapeutic options available to cure chronic illness such as diabetes. Significant research evidence including computational studies on the role of Zn2+ in binding and inhibiting the catalytic pocket have been reported along with experimental exploration of zinc(II) complexes as potent inhibitors of the enzyme. The current study has employed advanced computational methods to explore the binding and conformational orientation of zinc(II) complexes in the active site of apoenzyme, phosphoenzyme, and TSA 2 of PTP1B. Metal ion modeling was performed for zinc metal center (Zn-OOOO) utilizing a Python based Metal Center Parameter Builder (MCPB.py). The findings of the study suggest that zinc(II) complex binds to structurally and functionally important residues in open and closed conformation as well as in the phosphorylated state of the enzyme. It was observed that when the catalytic cysteine is phosphorylated in a closed conformation, the zinc(II) complex forms significant interactions with PHE182, VAL184, GLY183, and PRO180 while pushing away Q-loop GLN262 which is crucial for the hydrolysis of phosphoenzyme. Subsequently, the reported inhibitor has also demonstrated its potential to function as allosteric modulator of the enzyme occupying catalytic WPD loop residues. The study uncovers putative binding sites of zinc-containing drugs and gives insight into the size and design of such compounds which keeps them accessible and anchored in the vicinity of active site residues. Reported inhibitor offers enhanced selectivity and inhibition in all three states of the enzyme in contrast to zinc ions which can only impede enzyme in the phosphorylated state. In addition to this, investigation of ASP265→GLU265 mutation reveals the role of GLU265 in affecting the flexibility of WPD loop residues highlighting it as loss-of-function mutation. Our results hints towards a metallodrug approach that builds on the research evidence of inhibition effects of Zn2+ in the binding pocket of PTP1B. The findings presented are noteworthy, not just due to their significant relevance for clinical application, but also for the design and synthesis of novel zinc(II) complexes.

Dynamics of water-mediated interaction effects on the stability and transmission of Omicron.

SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.

Non-ß Lactam Inhibitors of the Serine ß-Lactamase blaCTX-M15 in Drug-Resistant Salmonella typhi.

Antibiotic resistance by bacterial pathogens against widely used ß-lactam drugs is a major concern to public health worldwide, resulting in high healthcare cost. The present study aimed to extend previous research by investigating the potential activity of reported compounds against the S. typhi ß-lactamase protein. 74 compounds from computational screening reported in our previous study against ß-lactamase CMY-10 were subjected to docking studies against blaCTX-M15. Site-Identification by Ligand Competitive Saturation (SILCS)-Monte Carlo (SILCS-MC) was applied to the top two ligands selected from molecular docking studies to predict and refine their conformations for binding conformations against blaCTX-M15. The SILCS-MC method predicted affinities of -8.6 and -10.7 kcal/mol for Top1 and Top2, respectively, indicating low micromolar binding to the blaCTX-M15 active site. MD simulations initiated from SILCS-MC docked orientations were carried out to better characterize the dynamics and stability of the complexes. Important interactions anchoring the ligand within the active site include pi-pi stacked, amide-pi, and pi-alkyl interactions. Simulations of the Top2-blaCTX-M15 complex exhibited stability associated with a wide range of hydrogen-bond and aromatic interactions between the protein and the ligand. Experimental ß-lactamase (BL) activity assays showed that Top1 has 0.1 u/mg BL activity, and Top2 has a BL activity of 0.038 u/mg with a minimum inhibitory concentration of 1 mg/mL. The inhibitors proposed in this study are non-ß-lactam-based ß-lactamase inhibitors that exhibit the potential to be used in combination with ß-lactam antibiotics against multidrug-resistant clinical isolates. Thus, Top1 and Top2 represent lead compounds that increase the efficacy of ß-lactam antibiotics with a low dose concentration.

Deciphering the relational dynamics of AF-2 domain of PAN PPAR through drug repurposing and comparative simulations.

Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors, and their activation has been proven to treat mild liver fibrosis, reduce steatosis, inflammation, and the extrahepatic effects of chronic liver disease. Considering the significance of the PPARs, it is targeted for the treatment of Non-Alcoholic Steatohepatitis (NASH), for which currently there is no FDA-approved drug. Lanifibranor is a next-generation highly potential indole sulfonamide derivative that is presently in clinical trial phase III as an anti-NASH drug which fully activates PPARα and PPARδ and partially activates PPARγ. In the current study, a comprehensive computational investigation including 3D-QSAR pharmacophore modeling, MD simulations and binding free energy calculations is performed to get insights into the activation mechanism of the Lanifibranor. Furthermore, FDA-approved drugs were explored for repurposing through virtual screening against each PPAR pharmacophore to identify potential drug candidates. Forasartan, Raltitrexed, and Lifitegrast stood out as potential agonists for PPARα (full agonist), PPARγ (partial agonist), and PPARδ (full agonist), respectively. The findings of the study highlighted a lack of hydrogen bond acceptor feature in Raltitrexed and Lanifibranor which is responsible for partial activation of PPARγ that plays a critical role in preventing lipid accumulation. In addition to this, the significant role of AF2 domain in full and partial activation of PPARs through electrostatic interactions was also revealed, that facilitates the anchoring of ligand within the binding cavity. Moreover, common chemical scaffolds (methyl sulfonyl benzene, butyric acid, and chlorobenzene) identified using Fingerprinting technique were presented in this study which hold the potential to aid in the design and development of target specific novel Pan PPAR medications in future.

Role of hinge motion and ATP dynamics in factors for inversion stimulation FIS protein deduced while targeting drug resistant Orientia tsutsugamushi.

Orientia tsutsugamushi, the causative agent of scrub typhus has been found resistant to various classes of antibiotics such as penicillins, gentamycin and cephalosporins. Review of current literature suggests that the prevalence of scrub typhus has increased globally. Therefore, the current study has aimed at exploring the genome of O. tsutsugamushi to identify potential drug target proteins that can be used for developing novel antibiotics against the pathogen. Subtractive proteomics approach has revealed FIS as a potential drug target protein involved in two component system (TCS), a signaling pathway crucial for bacteria to survive and adjust in changing environmental conditions. Molecular docking studies have revealed compound-356 (CHEMBRIDGE-10040641-3710.356) as a potential inhibitor in both chains A and B of the FIS protein. Simulation results suggest that the docked complex has remained stable and compact throughout the 200 ns run. Significant conformational changes including the hinge motion was observed in the DNA binding domain. Furthermore, the presence of salt bridge between GLU910 and ARG417, rearrangement of interaction residues and displacement of ATP in the central AAA + domain upon binding to the inhibitor were also observed playing a role in stabilizing the protein structure.

Senna makki and other active phytochemicals: Myths and realities behind covid19 therapeutic interventions.

This study aims to investigate the binding potential of chemical compounds of Senna in comparison with the experimentally tested active phytochemicals against SARS-CoV-2 protein targets to assist in prevention of infection by exploring multiple treatment options. The entire set of phytochemicals from both the groups were subjected to advanced computational analysis that explored functional molecular descriptors from a set of known medicinal-based active therapeutics followed by MD simulations on multiple SARS-CoV-2 target proteins. Our findings manifest the importance of hydrophobic substituents in chemical structures of potential inhibitors through cross-validation with the FDA-approved anti-3CLpro drugs. Noteworthy improvement in end-point binding free energies and pharmacokinetic profiles of the proposed compounds was perceived in comparison to the control drug, vizimpro. Moreover, the identification of common drug targets namely; AKT1, PTGS1, TNF, and DPP4 between proposed active phytochemicals and Covid19 using network pharmacological analysis further substantiate the importance of medicinal scaffolds. The structural dynamics and binding affinities of phytochemical compounds xanthoangelol_E, hesperetin, and beta-sitosterol reported as highly potential against 3CLpro in cell-based and cell-free assays are consistent with the computational analysis. Whereas, the secondary metabolites such as sennosides A, B, C, D present in higher amount in Senna exhibited weak binding affinity and instability against the spike protein, helicase nsp13, RdRp nsp12, and 3CLpro. In conclusion, the results contravene fallacious efficacy claims of Senna tea interventions circulating on electronic/social media as Covid19 cure; thus emphasizing the importance of well-examined standardized data of the natural products in hand; thereby preventing unnecessary deaths under pandemic hit situations worldwide.

Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae.

ß-lactam antibiotics are the most widely used antimicrobial agents since the discovery of benzylpenicillin in the 1920s. Unfortunately, these life-saving antibiotics are vulnerable to inactivation by continuously evolving ß-lactamase enzymes that are primary resistance determinants in multi-drug resistant pathogens. The current study exploits the strategy of combination therapeutics and aims at identifying novel ß-lactamase inhibitors that can inactivate the ß-lactamase enzyme of the pathogen while allowing the ß-lactam antibiotic to act against its penicillin-binding protein target. Inhibitor discovery applied the Site-Identification by Ligand Competitive Saturation (SILCS) technology to map the functional group requirements of the ß-lactamase CMY-10 and generate pharmacophore models of active site. SILCS-MC, Ligand-grid Free Energy (LGFE) analysis and Machine-learning based random-forest (RF) scoring methods were then used to screen and filter a library of 700,000 compounds. From the computational screens 74 compounds were subjected to experimental validation in which ß-lactamase activity assay, in vitro susceptibility testing, and Scanning Electron Microscope (SEM) analysis were conducted to explore their antibacterial potential. Eleven compounds were identified as enhancers while 7 compounds were recognized as inhibitors of CMY-10. Of these, compound 11 showed promising activity in ß-lactamase activity assay, in vitro susceptibility testing against ATCC strains (E. coli, E. cloacae, E. agglomerans, E. alvei) and MDR clinical isolates (E. cloacae, E. alvei and E. agglomerans), with synergistic assay indicating its potential as a ß-lactam enhancer and ß-lactamase inhibitor. Structural similarity search against the active compound 11 yielded 28 more compounds. The majority of these compounds also exhibited ß-lactamase inhibition potential and antibacterial activity. The non-ß-lactam-based ß-lactamase inhibitors identified in the current study have the potential to be used in combination therapy with lactam-based antibiotics against MDR clinical isolates that have been found resistant against last-line antibiotics.

Design of a Novel Multi Epitope-Based Vaccine for Pandemic Coronavirus Disease (COVID-19) by Vaccinomics and Probable Prevention Strategy against Avenging Zoonotics.

The emergence and rapid expansion of the coronavirus disease (COVID-19) require the development of effective countermeasures especially a vaccine to provide active acquired immunity against the virus. This study presented a comprehensive vaccinomics approach applied to the complete protein data published so far in the National Center for Biotechnological Information (NCBI) coronavirus data hub. We identified non-structural protein 8 (Nsp8), 3C-like proteinase, and spike glycoprotein as potential targets for immune responses to COVID-19. Epitopes prediction illustrated both B-cell and T-cell epitopes associated with the mentioned proteins. The shared B and T-cell epitopes: DRDAAMQRK and QARSEDKRA of Nsp8, EDMLNPNYEDL and EFTPFDVVR of 3C-like proteinase, and VNNSYECDIPI of the spike glycoprotein are regions of high potential interest and have a high likelihood of being recognized by the human immune system. The vaccine construct of the epitopes shows stimulation of robust primary immune responses and high level of interferon gamma. Also, the construct has the best conformation with respect to the tested innate immune receptors involving vigorous molecular mechanics and solvation energy. Designing of vaccination strategies that target immune response focusing on these conserved epitopes could generate immunity that not only provide cross protection across Betacoronaviruses but additionally resistant to virus evolution.