Identification of potential inhibitors for AIRS from de novo purine biosynthesis pathway through molecular modeling studies - a computational approach

Discovery of potent inhibitors targeting Glutathione S-transferase of Wuchereria bancrofti: a step toward the development of effective anti-filariasis drugs

Lymphatic filariasis (LF) is one of the major health problems for the human kind in developing countries including India. LF is caused by three major nematodes namely Wuchereria bancrofti, Brugia malayi, and Brugia timori. The recent statistics of World Health Organization (WHO) showed that 51 million people were affected and 863 million people from 47 countries around worldwide remain threatened by LF. Among them, 90% of the filarial infection was caused by the nematode W. bancrofti. Approved drugs were available for the treatment of LF but many of them developed drug resistance and no longer effective in all stages of the infection. In the current research work, we explored the Glutathione S-transferase (GST) of W. bancrofti, the key enzyme responsible for detoxification that catalyzes the conjugation of reduced GSH (glutathione) to xenobiotic compounds. Initially, we analyzed the stability of the WbGST through 200 ns MD simulation and further structure-based virtual screening approach was applied by targeting the substrate binding site to identify the potential leads from small molecule collection. The in silico ADMET profiles for the top-ranked hits were predicted and the predicted non-toxic lead molecules showed the highest docking score in the range of - 12.72 kcal/mol to - 11.97 kcal/mol. The cross docking of the identified hits with human GST revealed the potential binding specificity of the hits toward WbGST. Through WbGST-lead complex simulation, the lead molecules were observed to be stable and also intactly bound within the binding site of WbGST. Based on the computational results, the five predicted non-toxic molecules were selected for the in vitro assay. The molecules showed significant percentage of inhibition against the filarial worm Setaria digitata which is the commonly used model organism to evaluate the filarial activity. In addition, the molecules also showed better IC50 than the standard drug ivermectin. The identified lead molecules will lay a significant insight for the development of new drugs with higher specificity and lesser toxicity to control and treat filarial infections.

Integrated Functions of Cardiac Energetics, Mechanics, and Purine Nucleotide Metabolism

Purine nucleotides play central roles in energy metabolism in the heart. Most fundamentally, the free energy of hydrolysis of the adenine nucleotide adenosine triphosphate (ATP) provides the thermodynamic driving force for numerous cellular processes including the actin-myosin crossbridge cycle. Perturbations to ATP supply and/or demand in the myocardium lead to changes in the homeostatic balance between purine nucleotide synthesis, degradation, and salvage, potentially affecting myocardial energetics and, consequently, myocardial mechanics. Indeed, both acute myocardial ischemia and decompensatory remodeling of the myocardium in heart failure are associated with depletion of myocardial adenine nucleotides and with impaired myocardial mechanical function. Yet there remain gaps in the understanding of mechanistic links between adenine nucleotide degradation and contractile dysfunction in heart disease. The scope of this article is to: (i) review current knowledge of the pathways of purine nucleotide depletion and salvage in acute ischemia and in chronic heart disease; (ii) review hypothesized mechanisms linking myocardial mechanics and energetics with myocardial adenine nucleotide regulation; and (iii) highlight potential targets for treating myocardial metabolic and mechanical dysfunction associated with these pathways. It is hypothesized that an imbalance in the degradation, salvage, and synthesis of adenine nucleotides leads to a net loss of adenine nucleotides in both acute ischemia and under chronic high-demand conditions associated with the development of heart failure. This reduction in adenine nucleotide levels results in reduced myocardial ATP and increased myocardial inorganic phosphate. Both of these changes have the potential to directly impact tension development and mechanical work at the cellular level. © 2024 American Physiological Society. Compr Physiol 14:5345-5369, 2024.

Computational identification and experimental validation of anti-filarial lead molecules targeting metal binding/substrate channel residues of Cu/Zn SOD1 from Wuchereria bancrofti

Lymphatic filariasis (LF) is a neglected mosquito-borne parasitic disease, widely caused by Wuchereria bancrofti (Wb) in tropical and sub-tropical countries. During a blood meal, the filarial nematodes are transmitted to humans by the infected mosquito. To counter attack the invaded nematodes, the human immune system produces reactive oxygen species. However, the anti-oxidant enzymes of nematodes counteract the host oxidative cytotoxicity. Cu/Zn Superoxide dismutase (SOD1), a member of antioxidant enzymes and are widely used by the nematodes to sustain the host oxidative stress across its lifecycle, hence targeting SOD1 to develop suitable drug molecules would help to overcome the problems related to efficacy and activity of drugs upon different stages of nematodes. In order to find the potent inhibitors, a three-dimensional structure of Cu/Zn WbSOD1 was modelled and the structural stability was analysed through simulation studies. The structure-guided virtual screening approach has been used to identify lead molecules from the ChemBridge based on the docking score, ADMET properties and protein-ligand complex stability analysis. The identified compounds were observed to interact with the copper, metal binding residues (His48, His63, His80 and His120) and catalytically important residue Arg146, which play a crucial role in the disproportionation of incoming superoxide radicals of Cu/Zn WbSOD1. Further, in vitro validation of the selected leads in the filarial worm Setaria digitata exhibited higher inhibition and better IC50 compared to the standard drug ivermectin. Thus, the identified leads could potentially inhibit enzyme activity, which could subsequently act as drug candidates to control LF.Communicated by Ramaswamy H. Sarma.

Computational exploration of molecular flexibility and interaction of meropenem analogs with the active site of oxacillinase-23 in Acinetobacter baumannii

Background: Carbapenem-resistant Acinetobacter baumannii is an opportunistic pathogen responsible for nosocomial infections and is one of the biggest global threats according to the World Health Organization (WHO), particularly causing substantial morbidity and mortality. Objectives: This study aimed at using computational approaches to screen meropenem and its analogs against OXA-23-positive Acinetobacter baumannii, analyzing the correlations between kinetic and phenotypic characteristics. Methods: A total of 5,450 compounds were screened using virtual screening workflow (HTVS, Glide-SP, and Glide-XP) to identify the best compounds based on their binding energy and interactions against OXA-23 and OXA-27 as they had phenotypic data available. Molecular dynamics simulation and density functional theory (DFT) studies were performed from the outcome of molecular docking analysis. Results: During simulations, meropenem and its analogs exhibited high-level stable interactions with Ser79, Ser126, Thr217, Trp219, and Arg259 of OXA-23. Meropenem displayed a CovDock energy of about -3.5 and -1.9 kcal mol^-1 against OXA-23 and OXA-27, respectively. Among the 5,450 compounds, Pubchem_10645796, Pubchem_25224737, and ChEMBL_14 recorded CovDock energy between -6.0 and -9.0 kcal mol^-1. Moreover, the infra-red (IR) spectrophotometric analysis revealed C=O and C-N atoms showing bands at 1,800 and 1,125 cm^-1, respectively. These observed data are in congruence with the experimental observations. Conclusion: The identified compounds showed good agreement with the spectrophotometric analysis using DFT methods. In the earlier studies, meropenem's MIC value was 32 μg mL^-1 in OXA-23-positive isolate A2265 compared to the MIC of 1 μg mL^-1 in Δbla _OXA-23 A2265. Comparing the CovDock energy and hydrogen-bonding interactions, the predicted results are in good agreement with the experimental data reported earlier. Our results highlight the importance of OXA-23 molecular docking studies and their compliance with the phenotypic results. It will help further in developing newer antibiotics for treating severe infections associated with carbapenem-resistant A. baumannii.

Potential inhibitors for peroxiredoxin 6 of W. bancrofti: A combined study of modelling, structure-based drug design and MD simulation

Lymphatic filariasis (LF), a mosquito-borne parasitic disease caused by nematode Wuchereria bancrofti in tropical and sub-tropical countries. These nematodes are transferred into the human host when the infected mosquito carrying L3 larvae is released into the bloodstream during the blood ingestion process. The host immune system produces ROS (Reactive Oxygen Species) as a primary defence mechanism to remove the invading filarial worms. However, well-defined antioxidant enzymes of the nematodes scavenge the host-produced ROS to escape from oxidative stress. The enzyme peroxiredoxin 6 (Prx6) belongs to the peroxiredoxin family, catalyses hydrogen peroxide (H₂O₂) into water (H₂O). In order to find the inhibitors that inhibit the activity of peroxiredoxin 6 of W. bancrofti. We performed the homology modelling to predict the WbPrx6 three-dimensional structure using the Schrödinger-Prime and the dynamic stability of the modelled WbPrx6 was analyzed by carrying out the molecular dynamic (MD) simulation for the time scale of 200ns. Further, the structure-based virtual screening shortlisted the hit molecules from the ChemBridge database based on the glide score. The potential lead molecules (ID: 10239274, 11112883, 79879205, 58160895, and 42133744) that have better binding and satisfied the ADMET properties were selected for further complex simulation and DFT calculations. The identified compounds interact with the N-terminal region of the thioredoxin domain, which plays a key role in reducing phospholipase A2 activity. Interestingly, upon binding the lead molecule, the fluctuation of the loop region that connects α-IV with the β-VI plays a vital role in affecting the geometry of the active site, which in turn affects the activity WbPrx6. The outcomes of the present computational studies could help in future drug development and designing of the effective candidate to control Lymphatic filariasis.

Computational screening of potential inhibitors targeting MurF of Brugia malayi Wolbachia through multi-scale molecular docking, molecular dynamics and MM-GBSA analysis

Lymphatic filariasis is a parasitic disease caused by the worms Wuchereria bancrofti, Brugia malayi and Brugia timori. Three anti-filarial drugs namely Diethylcarbamazine, Ivermectin and Albendazole and their combinations are used as the control strategies for filariasis. The disease has received much attention in drug discovery due to the unavailability of vaccines and the toxic pharmaceutical properties of the existing drugs. In Wolbachia endosymbiont Brugia malayi, the UDP-N-acetylmuramoyl-tripeptide-d-alanyl-d-alanine ligase (MurF) plays a key role in peptidoglycan biosynthesis pathway and therefore can be considered as effective drug target against filariasis disease. Therefore, in the present study, MurF was selected as the therapeutic target to identify specific inhibitors against filariasis. Homology modeling was performed to predict the three-dimensional structure of MurF due to the absence of the experimental structure. Further molecular dynamics simulation and structure-based high throughput virtual screening with three different chemical databases (Zinc, Maybridge and Specs) were carried out to identify potent inhibitors and also to check their conformations inside the binding site of MurF, respectively. Top three compounds with high docking score and high relative binding affinity against MurF were selected. Further, validation studies, including predicted ADME (Absorption, Distribution, Metabolism, Excretion) assessment, binding free energy using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) and DFT (Density Functional Theory) calculations were performed for the top three compounds. From the results, it was observed that all the three compounds were predicted to show high reactivity, acceptable range of pharmacokinetic properties and high binding affinity with the drug target MurF. Overall, the results could provide more understanding on the inhibition of MurF enzyme and the screened compounds could lead to the development of new specific anti-filarial drugs.

Modelling studies reveal the importance of the C-terminal inter motif loop of NSP1 as a promising target site for drug discovery and screening of potential phytochemicals to combat SARS-CoV-2

COVID-19 pandemic causative SARS-CoV-2 coronavirus is still rapid in progression and transmission even after a year. Understanding the viral transmission and impeding the replication process within human cells are considered as the vital point to control and overcome COVID-19 infection. Non-structural Protein 1, one among the proteins initially produced upon viral entry into human cells, instantly binds with the human ribosome and inhibit the host translation process by preventing the mRNA attachment. However, the formation of NSP1 bound Ribosome complex does not affect the viral replication process. NSP1 plays an indispensable role in modulating the host gene expression and completely steals the host cellular machinery. The full-length structure of NSP1 is essential for the activity in the host cell and importantly the loop connecting N and C-terminal domains are reported to play a role in ribosome binding. Due to the unavailability of the experimentally determined full-length structure of NSP1, we have modelled the complete structure using comparative modelling and the stability and conformational behaviour of the modelled structure was evaluated through molecular dynamics simulation. Interestingly, the present study reveals the significance of the inter motif loop to serves as a potential binding site for drug discovery experiments. Further, we have screened the phytochemicals from medicinal plant sources since they were used for several hundred years that minimizes the traditional drug development time. Among the 5638 phytochemicals screened against the functionally associated binding site of NSP1, the best five phytochemicals shown high docking score of −9.63 to −8.75 kcal/mol were further evaluated through molecular dynamics simulations to understand the binding affinity and stability of the complex. Prime MM-GBSA analysis gave the relative binding free energies for the top five compounds (dihydromyricetin, 10-demethylcephaeline, dihydroquercetin, pseudolycorine and tricetin) in the range of −45.17 kcal/mol to −37.23 kcal/mol, indicating its binding efficacy in the predicted binding site of NSP1. The density functional theory calculations were performed for the selected five phytochemicals to determine the complex stability and chemical reactivity. Thus, the identified phytochemicals could further be used as effective anti-viral agents to overcome COVID-19 and as well as several other viral infections.

Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of Staphylococcus aureus

The bacterial DNA gyrase is an attractive target to identify the novel antibacterial agents. The flavonoid derivatives possess various biological activities such as antimicrobial, anti-inflammatory and anticancer activities. The aim of present study is to identify the potential molecule from flavonoid derivatives against Staphylococcus aureus using atomistic simulation namely Molecular Docking, Quantum Chemical and Molecular Dynamics. The molecules Cpd58, Cpd65 and Cpd70 are identified as potential molecules through molecular docking approaches by exploring through the N - H…O hydrogen bonding interactions with Asn31 and Glu35 of Gyrase B. To confirm the intramolecular charge transfer in the flavonoid derivatives, Frontier Molecular Orbital (FMO) calculation was performed at M06/6-31g(d) level in gas phase. The lowest HOMO-LUMO gap was calculated for Cpd58, Cpd65 and Cpd70 among the selected compounds used in this study. Molecular dynamics simulation were carried out for Cpd58 and Cpd70 for a time period of 50 ns and found to be stable throughout the analysis. Therefore, the identified compounds are found to be a potent inhibitor for GyrB of S. aureus that can be validated by experimental studies. Communicated by Ramaswamy H. Sarma.

Design of novel PhMTNA inhibitors, targeting neurological disorder through homology modeling, molecular docking, and dynamics approaches

Vanishing white matter (VWM) is a hereditary human disease, mostly prevalent in childhood caused by the defects in the eukaryotic initiation factor beta subunits. It is the first disease involved in the translation initiation factor, eIF2B. There is no specific treatment for VWM which mainly affect the brain and ovaries. The gray matter remains normal in all characteristics while the white matter changes texture, coming to the pathophysiology, many initiation factors are involved in the initiation of translation of mRNAs into polypeptides. In this study, the three-dimensional structure of PhMTNA protein was modeled and the stability ascertained through Molecular dynamic simulation (MDS) for 100 ns. The active site residues are conserved with the reported BsMTNA structure which is also confirmed through sitemap prediction. Through virtual screening and induced fit docking, top five leads against PhMTNA protein was identified based on their binding mode and affinity. ADME properties and DFT (Density Functional Theory) studies of these compounds were studied. In addition to that, computational mutagenesis studies were performed to identify the hotspot residues involved in the protein-ligand interactions. Overall analysis showed that the compound NCI_941 has a highest binding energy of -46.256 kcal mol^-1 in the Arg57Ala mutant. Thus, the results suggest that NCI_941 would act as a potent inhibitor against PhMTNA protein.

Conformational changes in glutaminyl-tRNA synthetases upon binding of the substrates and analogs using molecular docking and molecular dynamics approaches

Aminoacyl-tRNA synthetases (aaRSs) are considered as important components in protein translation as they facilitate the attachment of specific transfer RNA (tRNA) to form aminoacyl-tRNAs. Our study focused on understanding the crystal structure of Glutaminyl-tRNA synthetase (GlnRS) from Thermus thermophilus HB8 (PDB ID:5ZDO) and mechanism of formation of enzyme-substrate complex using substrates and its analogs by applying molecular dynamics simulation (MDS) to investigate the conformational changes. Least energy structure of TtGlnRS was considered to dock the enzyme substrates such as glutamine (Gln), glutamic acid (Glu), adenosine monophosphate (AMP), adenosine triphosphate (ATP), QSI and various substrate analogs (2MA, 4SU and 5MU) onto the active site of the enzyme. We focused on comparative analysis of binding specificity between Gln and Glu; similarly, ATP and AMP. Active site organization as observed by MDS analysis showed interactive changes associated with substrate and catalytically important loops. Study found that when tRNA^Gln specific for GlnRS was docked into the active site of the TtGlnRS enzyme it interacts with 2' OH on the ribose acceptor end of the tRNA. Upon validation with 50 ns MDS, the maximum deviations and conformational changes of secondary structural elements were observed to be high in the loop regions of enzyme-substrate complexes. Binding affinity of ATP to TtGlnRS was further proved by isothermal titration calorimetry. AbbreviationsaaRSsaminoacyl-tRNA synthetasesAMPadenosine monophosphateATPadenosine triphosphateGlideGrid-based LIgand Docking with EnergeticGlnRSglutaminyl-tRNA synthetaseGRAVYGRand AVerage of hydropathicitYGROMACSGROingen Machine for Chemical SimulationsHADDOCKHigh Ambiguity Driven protein-protein DOCKingITCisothermal titration calorimetry2MA2-methyladenosine 5'-(dihydrogen phosphate)MDSmolecular dynamics simulation5MU5-methyluridine 5'-monophosphateNPTnumber of particles, pressure and temperatureNVTnumber of particles, volume and temperatureOPLS-AAoptimized potential for liquid simulation all atomPDBBrookhaven Protein DatabankPMEParticle-Mesh EwaldQSI5'-o-[n-(l-Glutaminyl)-sulfamoyl]adenosineRgradius of gyrationRMSDroot mean square deviationRMSFroot mean square fluctuation4SU4-thiouracil 5'-monophosphateSPCsimple point chargetRNAtransfer ribo nucleic acidTtThermus thermophilusXPextra precisionCommunicated by Ramaswamy H. Sarma.

Exploration of N5-CAIR Mutase Novel Inhibitors from Pyrococcus horikoshii OT3: A Computational Study

In bacterial and archaeal purine biosynthetic pathways, sixth step involves utilization of enzyme PurE, catalyzing the translation of aminoimidazole ribonucleotide to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR) with carbon dioxide. The formation of CAIR takes place through an unstable intermediate N5-CAIR, played by two enzymes-N5-CAIR synthetase (PurK) and N5-CAIR mutase (PurE) that further catalyzes the reaction of N5-CAIR to CAIR. In this study, N5-CAIR mutase (PH0320) from Pyrococcus horikoshii OT3 (PurE) was considered. The three-dimensional structure of Pyrococcus horikoshii OT3 was modeled based on the structure of PurE from Escherichia coli. The modeled structure was subjected to molecular dynamics simulation up to 100 ns, and least energy structure from the simulation was subjected to virtual screening and induced fit docking to identify the best potent leads. A total of five best antagonists were identified based on their affinity and mode of binding leading with conserved residues Ser18, Ser20, Asp21, Ser45, Ala46, His47, Arg48, Ala72, Gly73, Ala75, and His77 promotes the activity of Ph-N5-CAIR mutase. In addition to molecular dynamics, absorption, digestion, metabolism, and excretion properties, binding free energy and density functional theory calculations of compounds were carried out. Based on analyses, compound from National Cancer Institute (NCI) database, NCI_826 was adjudged as the best potent lead molecule and could be suggested as the suitable inhibitor of N5-CAIR mutase.

Identification of anti-filarial leads against aspartate semialdehyde dehydrogenase of Wolbachia endosymbiont of Brugia malayi: combined molecular docking and molecular dynamics approaches

Lymphatic filariasis is a debilitating vector borne parasitic disease that infects human lymphatic system by nematode Brugia malayi. Currently available anti-filarial drugs are effective only on the larval stages of parasite. So far, no effective drugs are available for humans to treat filarial infections. In this regard, aspartate semialdehyde dehydrogenase (ASDase) in lysine biosynthetic pathway from Wolbachia endosymbiont Brugia malayi represents an attractive therapeutic target for the development of novel anti-filarial agents. In this present study, molecular modeling combined with molecular dynamics simulations and structure-based virtual screening were performed to identify potent lead molecules against ASDase. Based on Glide score, toxicity profile, binding affinity and mode of interactions with the ASDase, five potent lead molecules were selected. The molecular docking and dynamics results revealed that the amino acid residues Arg103, Asn133, Cys134, Gln161, Ser164, Lys218, Arg239, His246, and Asn321 plays a crucial role in effective binding of Top leads into the active site of ASDase. The stability of the ASDase-lead complexes was confirmed by running the 30 ns molecular dynamics simulations. The pharmacokinetic properties of the identified lead molecules are in the acceptable range. Furthermore, density functional theory and binding free energy calculations were performed to rank the lead molecules. Thus, the identified lead molecules can be used for the development of anti-filarial agents to combat the pathogenecity of Brugia malayi.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose.