Search

Clamp loaders ensure processive DNA replication by loading the toroidal shaped sliding clamps onto the DNA. The sliding clamps serve as a platform for the attachment of polymerases and several other proteins associated with the regulation of various cellular processes. Clamp loaders are fascinating as nanomachines that engage in protein-protein and protein-DNA interactions. The loading mechanism of the clamp around dsDNA at the atomic level has not yet been fully explored. We performed microsecond timescale molecular dynamics simulations to reveal the dynamics of two different intermediate complexes involved in loading of the clamps around DNA. We conducted various time-dependent MD-driven analyses including the highly robust Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) calculations to observe changes in the structural elements of the clamp loader-clamp-DNA complexes in open and closed states. Our studies revealed the structural consequences of ATP hydrolysis events at different subunits of the clamp loader. This study would help in a better understanding of the clamp loading mechanism and would allow tackling various complications that might arise due to irregularities in this process.

BRD3-BD2 protein belongs to the bromodomain and extra-terminal domain (BET) protein family.

Superoxide dismutases (SODs) protect the cells by catalyzing the dismutation of harmful superoxide radicals (O2•-) into molecular oxygen (O2) and hydrogen peroxide (H2O2). Here, a Cu, Zn SOD (WT) from a high altitude plant (Potentilla atrosanguinea) was engineered by substituting a conserved residue proline to glycine at position 61 (P61G). The computational analysis showed higher structural flexibility and clusters in P61G than WT. The P61G exhibited moderately higher catalytic efficiency (Km = 0.029 μM, Vmax = 1488) than WT protein (Km = 0.038 μM, Vmax = 1290.11). P61G showed higher thermostability as revealed from residual activity (72.25% for P61G than 59.31% for WT after heating at 80 °C for 60 min), differential calorimetry scanning and CD-spectroscopic analysis. Interestingly, the P61G mutation also resulted in enhanced tolerance to H2O2 inactivation than WT protein. The finding on enhancing the biophysico-chemical properties by mutating conserved residue could stand as an example to engineer other enzymes. Also, the reported mutant can be exploited in food and pharmaceutical industries.

An ecdysone receptor (EcR) is a nuclear receptor protein, a prime target for pesticide development processes due to its involvement in the growth and development of insects. The activation of EcRs leads to hasty and premature development of insects, thereby preventing them from destroying the crops. The high cost, environmental toxicity, and resistance towards the currently available insecticides have resulted in a growing demand for the development of economical and environment-friendly pesticides with unique insecticidal activity. Several reports on resistance towards conventional pesticides like ponasterone A and RH-5849 were reported in recent years. In this study, the plant derived (C. deodara), in-house synthesized molecules with benzosuberene scaffolds were screened for their ability to interact with the EcRs of both Hemiptera and Coleoptera. The preliminary analysis by molecular docking showed that some of our molecules exhibited excellent binding with the target protein. Moreover, molecular dynamics simulations, binding free energy estimations, and umbrella sampling simulations were conducted to validate the docking results. Our analysis revealed Com-7 and Com-3 as potential EcR agonists to target Hemiptera and Coleoptera, respectively. Also, Com-8 and Com-12 could be used as lead compounds against the EcR of Coleoptera.

Aminoarylbenzosuberene (AAB) molecules were chosen for in silico analysis to develop effective and more competent 11β-hydroxysteroid dehydrogenase (11β-HSD1) protein inhibitors.

The proliferating cell nuclear antigen (PCNA) has emerged as a promising candidate for the development of novel cancer therapeutics. PCNA is a nononcogenic mediator of DNA replication that regulates a diverse range of cellular functions and pathways through a comprehensive list of protein-protein interactions. The hydrophobic binding pocket on PCNA offers an opportunity for the development of inhibitors to target various types of cancers and modulate protein-protein interactions. In the present study, we explored the binding modes and affinity of molecule I1 (standard molecule) with the previously suggested dimer interface pocket and the hydrophobic pocket present on the frontal side of the PCNA monomer. We also identified potential lead molecules from the library of in-house synthesized 3-methylenisoindolin-1-one based molecules to inhibit the protein-protein interactions of PCNA. Our results were based on robust computational methods, including molecular docking, conventional, steered, and umbrella sampling molecular dynamics simulations. Our results suggested that the standard inhibitor I1 interacts with the hydrophobic pocket of PCNA with a higher affinity than the previously suggested binding site. Also, the proposed molecules showed better or comparable binding free energies as calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach and further validated by enhanced umbrella sampling simulations. In vitro and in vivo methods could test the computationally suggested molecules for advancement in the drug discovery pipeline.

Abscisic acid (ABA) although complicated and expensive to produce, plays an important role in signalling responsible for regulation of developmental manifestations such as seed maturation and surviving through stress conditions. Hence, development of cost effective molecules with minimal side effects that mimic the functions of ABA is the need of the hour. In this agreement, we screened a series of 27 in-house synthesized 3-methyleneisoindolin-1-one molecules over three ABA receptors (PYR1, PYL1, and PYL3). The commercial ABA agonist Pyrabactin was taken as a standard ligand in this study. The top three molecules for each receptor were selected and further evaluated to estimate the dynamical contribution and complex stability via Molecular Mechanics-Poisson Boltzmann surface area calculations. Two molecules (Mol26 and Mol25) showed higher binding free energy and stable complex conformation for PYL3 in comparison to Pyrabactin. This study revealed the structural basis of the binding mechanism of 3-methyleneisoindolin-1-one molecules with ABA receptors. Mol26 and Mol25 were identified for the development of specific PYL3 agonists with a vast potential in agriculture to accentuate the ABA like action in plants.

Malaria remains a deadliest disease brought about by Plasmodium species, among one of these species, disease due to Plasmodium falciparum (Pf) is life-threatening. The structures of PfLDH and human LDH are very similar in terms of L-LDH activity, and their biological functions are also equivalent. Therefore, any treatment aiming blocking the functions of PfLDH can affect human LDH. Thus, the main objective of this study is to identify the molecule that exhibits selectivity towards PfLDH without a profound effect on human LDH. In this research, a set of 68 quinolines based molecules were used for molecular docking. From molecular docking, we selected molecules 3j, 4b, 4h, 4m based on their binding affinity, ligand efficiency, lipophilic ligand efficiency, and torsion with selectivity towards PfLDH. The stability of the docked molecules was compared to Chloroquine (reference inhibitor) by applying molecular dynamics simulations and molecular mechanics poisson boltzmann surface area calculations. All the selected molecules showed selectivity for PfLDH with stable dynamic behavior and high binding free energy in comparison to Chloroquine. After examining the molecular mechanics poisson boltzmann surface area ratio results, molecule 3j was reported as a potential and specific inhibitor for PfLDH with a novel mechanism of binding to PfLDH while the remaining molecules 4b, 4h, 4m could further be modified to be used as potent inhibitors against malarial infection.

Cyclin-dependent kinases (CDKs) are known for their vital role in regulating cell cycle progression through protein-kinase interactions. CDKs also help in regulating transcription and development of the central nervous system. Inhibition of CDKs is a very fundamental approach for drug discovery in areas of different types of cancers, Alzheimer's, and HIV infections. The present research focuses on finding a novel, potent, and specific natural inhibitors of CDK isoforms (CDK2, CDK5, CDK7, CDK9). Molecular docking, molecular dynamics (MD) simulations, and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) were carried out to get an in-depth understanding of protein-ligand interactions. Based on our molecular docking results, Ligands-3, 5, 14, and 16 were screened among 17 different Pyrrolone-fused benzosuberene compounds as potent and specific inhibitors without any cross-reactivity against different CDK isoforms. Analysis of MD simulations and MM-PBSA studies, revealed the binding energy profiles of all the selected complexes. Our selected ligands performed better than the standard inhibitor (Roscovitine). Ligands-3 and 14 show specificity for CDK7 and Ligands-5 and 16 were specific against CDK9. These ligands are expected to possess lower risk of side effects due to their natural origin. Moreover, the backbone structure of these ligands could also be exploited to develop specific inhibitors against other CDK isoforms.Communicated by Ramaswamy H. Sarma.

Superoxide dismutases (SODs) protect the cells by catalyzing the dismutation of harmful superoxide radicals (O

Graphical abstract, Highlights • Nsp15 is involved in viral replication and suppression of host immune response. • Three bioactive molecules of tea showed high binding affinity with Nsp15. • The molecules selected on basis of robust MD simulations and MMPBSA calculations. • Tea bioactive molecules could be developed as inhibitors of Nsp15 to fight the virus., Immensely aggravated situation of COVID-19 has pushed the scientific community towards developing novel therapeutics to fight the pandemic. Small molecules can possibly prevent the spreading infection by targeting specific vital components of the viral genome. Non-structural protein 15 (Nsp15) has emerged as a promising target for such inhibitor molecules. In this investigation, we docked bioactive molecules of tea onto the active site of Nsp15. Based on their docking scores, top three molecules (Barrigenol, Kaempferol, and Myricetin) were selected and their conformational behavior was analyzed via molecular dynamics simulations and MMPBSA calculations. The results indicated that the protein had well adapted the ligands in the binding pocket thereby forming stable complexes. These molecules displayed low binding energy during MMPBSA calculations, substantiating their strong association with Nsp15. The inhibitory potential of these molecules could further be examined by in-vivo and in-vitro investigations to validate their use as inhibitors against Nsp15 of SARS-CoV2.

Background and Aim A novel coronavirus, called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some other mammals. The nonstructural protein 16 (NSP16) of SARS-CoV-2 plays a significant part in the replication of viruses and suppresses the ability of innate immune system to detect the virus. Therefore, inhibiting NSP16 can be a secure path towards identifying a potent medication against SARS-CoV-2. Tea (Camellia sinensis) polyphenols have been reported to exhibit potential treatment options against various viral diseases. Methods We conducted molecular docking and structural dynamics studies with a set of 65 Tea bioactive compounds to illustrate their ability to inhibit NSP16 of SARS-CoV-2. Moreover, post-simulations end state thermodynamic free energy calculations were estimated to strengthen our results. Results and Conclusion Six bioactive tea molecules showed better docking scores than the standard molecule sinefungin. These results were further validated by MD simulations, where Theaflavin compound demonstrated lower binding free energy in comparison to the standard molecule sinefungin. The compound theaflavin could be considered as a novel lead compound for further evaluation by in-vitro and in-vivo studies., Graphical abstract Image 1

Pyrrolone-fused benzosuberene (PBS) compounds were semi-synthesized from α,β,γ-Himachalenes extracted from the essential oil of Cedrus deodara following amino-vinyl-bromide substituted benzosuberenes as intermediates. These PBSs compounds classified as an attractive source of therapeutics. The α-isoform of PI3K which is a pivotal modulator of PI3K/AKT/mTOR signaling pathway, responsible for neurological disorders like epilepsy, found as a potential target molecule against these 17 semi-synthesized PBS compounds using in silico ligand-based pharmacophore mapping and target screening. The compounds screened using binding affinities, ADMET properties, and toxicity that were accessed by in silico docking simulations and pharmacokinetics profiling. Ultimately two compounds viz., PBS-8 and PBS-9 were selected for further in vivo evaluation using a zebrafish (Danio rerio) model of pentylenetetrazol (PTZ)-induced clonic convulsions. Additionally, gene expression studies performed for the genes of the PI3K/AKT/mTOR pathway which further validated our results. In conclusion, these findings suggested that PBS-8 is a promising candidate that could bedeveloped as a potential antiepileptic.

Background: The SARS-CoV-2 main protease (Mpro) is an attractive target in the COVID-19 drug development process. It catalyzes the polyprotein's translation from viral RNA and specifies a particular cleavage site. Due to the absence of identical cleavage specificity in human cell proteases, targeting Mpro with chemical compounds can obstruct the replication of the virus. Methods: To explore the potential binding mechanisms of 1,2,3-triazole scaffolds in comparison to co-crystallized inhibitors 11a and 11b towards Mpro, we herein utilized molecular dynamics and enhanced sampling simulation studies. Results and conclusion: All the 1,2,3-triazole scaffolds interacted with catalytic residues (Cys145 and His41) and binding pocket residues of Mpro involving Met165, Glu166, Ser144, Gln189, His163, and Met49. Furthermore, the adequate binding free energy and potential mean force of the topmost compound 3h was comparable to the experimental inhibitors 11a and 11b of Mpro. Overall, the current analysis could be beneficial in developing the SARS-CoV-2 Mpro potential inhibitors. © 2022 Elsevier Ltd 5058; Department of Biotechnology, Ministry of Science and Technology, India, DBT; Indian Council of Medical Research, ICMR; Council of Scientific and Industrial Research, India, CSIR; Ministry of Education and Science of the Russian Federation, Minobrnauka: 075-15-2020-777 We gratefully acknowledge to the Director, CSIR-Institute of Himalayan Bioresource Technology, Palampur for providing the facilities to carry out this work. This research received no specific grant from any funding agency. The work was carried out under the aegis of the Himalayan Centre for High-throughput Computational Biology (HiCHiCoB), a BIC supported by DBT. The CSIR support in the form of projects MLP:0201 and OLP:0043 for bioinformatics studies is highly acknowledged. R. S. expresses gratitude to the Indian Council of Medical Research, New Delhi, India for providing Senior Research Fellowship. G.V.Z. acknowledge the Ministry of Science and Higher Education of the Russian Federation within the framework of the grant agreement as government subsidies from the Federal budget in accordance with paragraph 4 of article 78.1 of the Budget Code of the Russian Federation (Moscow, October 1, 2020, No. 075-15-2020-777). This manuscript represents CSIR-IHBT communication no. 5058. We gratefully acknowledge to the Director, CSIR-Institute of Himalayan Bioresource Technology, Palampur for providing the facilities to carry out this work. This research received no specific grant from any funding agency. The work was carried out under the aegis of the Himalayan Centre for High-throughput Computational Biology (HiCHiCoB), a BIC supported by DBT. The CSIR support in the form of projects MLP:0201 and OLP:0043 for bioinformatics studies is highly acknowledged. R. S. expresses gratitude to the Indian Council of Medical Research, New Delhi, India for providing Senior Research Fellowship. G.V.Z. acknowledge the Ministry of Science and Higher Education of the Russian Federation within the framework of the grant agreement as government subsidies from the Federal budget in accordance with paragraph 4 of article 78.1 of the Budget Code of the Russian Federation (Moscow, October 1, 2020, No. 075-15-2020-777). This manuscript represents CSIR-IHBT communication no. 5058.

Superoxide dismutase (SOD) leads the front line of defense against injuries mediated by the reactive oxygen species (ROS). The SOD from a high-altitude plant Potentilla atrosanguinea is a unique thermostable enzyme. In this study, we applied a structure-guided consensus approach on Cu,Zn SOD from Potentilla atrosanguinea plant, to improve its enzymatic properties. The polar uncharged amino acid (threonine) at position 97 of wild-type (WT) SOD was selected as a target residue for substitution by aspartate (T97D) through site-directed mutagenesis. The WT and T97D were examined by a combinative approach consisting of robust computational and experimental tools. The in-silico analysis indicated improved dimeric stability in T97D as compared to the WT. The strong interactions between the monomers were related to improved dimerization and enhanced catalytic efficiency of T97D. These results were validated by in-vitro assays showing improved dimer stability and catalytic efficiency in T97D than WT. Moreover, the mutation also improved the thermostability of the enzyme. The combined structural and functional data described the basis for improved specific activity and thermostability. This study could expand the scope of interface residue to be explored as targets for designing of SODs with improved kinetics.

Benzosuberene compounds with a pyrrolone group adhered to it are compounds extracted from the oils of Cedrus deodara plant, that bear inhibitory capabilities. Tobacco mosaic virus is known to affect crop production every year. The currently known inhibitors against TMV have a weak inhibition effect and also tend to be toxic towards non-target living organisms as well as the environment. Thus, the requirement of non-toxic potent inhibitors is the need of the hour, which led us to test our benzosuberene molecules on the binding site of TMV and check their affinity as well as stability. The non-toxic nature of these molecules has already been experimentally established. Through in-silico analysis involving docking and simulation experiments, we compared the interaction pattern of these ligand molecules with the already present inhibitors. Our investigation proved that the reported ligands (ligands 3, 7, 9, and 17 obtained −177.103, −228.632, −184.134, and − 188.075 kJ/mol binding energies, respectively) interacted with the binding site of TMV much efficiently than the known inhibitors (Ribavirin and Zhao et al. 2020 obtained 121.561 and − 221.393 kJ/mol binding energies, respectively). Moreover, they acquired a stable conformation inside the binding pocket, where a higher number of binding site residues contributed towards interaction. Thus, their structural framework can be optimized for the exploration of their antiviral properties to develop potent botanical viricides against plant virus infection.

The human immunodeficiency virus interacts with the cluster of differentiation 4 receptors and one of the two chemokine receptors (CCR5 and CXCR4) to gain entry in human cells. Both the co-receptors are essential for viral entry, replication, and are considered critical targets for antiviral drugs. In this study, bioactive molecules from different Himalayan plants were screened considering their potential to bind with the CCR5 and CXCR4 co-receptors. We utilized computational and thermodynamic parameters to validate the binding of the selected biomolecules to the active site of the co-receptors. The molecules Butyl 2-ethylhexyl phthalate and Dactylorhin-A showed a higher binding affinity with CCR5 co-receptor than the standard antagonist Maraviroc. Moreover, Pseudohypericin, Amarogentin, and Dactylorhin-E exhibited stronger interactions with CXCR4 than the co-crystallized inhibitor Isothiourea-1 t. Hence, we suggest that these molecules could be developed as potential inhibitors of the CCR5 and CXCR4 co-receptors. However, this require further in-vitro and in-vivo validation.

Benzosuberene-sulfone (BSS) analogues have been semi-synthesized following green approaches from himachalenes, which has been extracted from essential oil of Cedrus deodara. In this process, benzosuberene in presence of different aryl or alkyl sodium sulfinates, I2 and potassium persulfate (K2S2O8) in acetonitrile–water solvent conditions gave BSS-analogues at room temperature. Under this reaction, a facile endocyclic β-H elimination has been noticed for BSS-analogues synthesis instead of vinyl sulfones and the reason may be due to its specific structure and electronic environment. The BSS-compounds were obtained with moderate to excellent yields under mild conditions. All the compounds were computationally subjected to drug likeliness and toxicity prediction studies. Further, the synthesized molecules were evaluated under in-silico studies for their binding affinity towards the native Peroxisome Proliferator-Activated Receptor Gamma (PPARG), and two PPARG mutants (R357A and V290M). Both the mutant forms of PPARG are deficient in eliciting a response to treatment with full and partial agonists. Our computational studies suggested that the molecule 3q performed better than the standard drug (Rosiglitazone) in all three protein structures. This implies that our suggested molecule could act as a more potent antagonist to native PPARG and could also be developed to treat type-2 diabetes patients with R357A and V290M mutations, which didn’t elicit any response to currently available drugs in the market.

Checkpoint kinase 1 (CHK1) is an essential kinase with a critical function in cell cycle arrest. Several potent inhibitors targeting CHK1 have been published, but most of them have failed in clinical trials. Acknowledging the emerging consequence of CHK1 inhibitors in medication of cancer, there is a demand for widening the chemical range of CHK1 inhibitors. In this research, we considered a set of in-house plant based semi-synthetic aminoarylbenzosuberene molecules as potential CHK1 inhibitors. Based on a combined computational research that consolidates molecular docking and binding free energy computations we recognized the crucial determinants for their receptor binding. The drug likeness of these molecules were also scrutinized based on their toxicity and bioavailibilty profile. The computational strategy indicates that the Bch10 could be regarded as a potential CHK1 inhibitor in comparison with top five co-crystallize molecules. Bch10 signifies a promising outlet for the development of potent inhibitors for CHK1.

Aurora-A is a novel therapeutic target that belongs to the serine/threonine kinase family of proteins. Several cancers are associated with gene amplification or over-expression of Aurora-A. The somatic mutation (S155R) in Aurora-A results in a loss of interaction with its binding partner TPX2. The S155R mutation thus leads to ectopic expression of Aurora-A, resulting in centrosome amplification, chromosomal instability, aneuploidy, and oncogenic transformations. In order to restore the interaction between mutant Aurora-A and TPX2, we predicted a binding pocket in the interface of the Aurora-A-TPX2 complex. We performed molecular docking of potential bioactive molecules of the Himalayan region at the predicted site. Alantolactone and Dactylose-A were selected as potential molecules that could bind to the interface pocket and restore the lost interaction between mutant Aurora-A and TPX2. The molecular docking results were validated by performing explicit long term molecular dynamics simulations (4.0 μs) and MM-PBSA analysis. The molecular dynamics results confirmed that both the selected molecules could act as potent drugs to tackle the abnormal expression of Aurora-A manifested due to the somatic mutation (S155R). [Formula: see text] Communicated by Ramaswamy H. Sarma.

Cucumber mosaic virus infection leads to mosaic symptoms on a broad range of crop plants. Mutation at positions 129 in the coat protein of virus causes alterations in the severity of symptoms caused by the viral infection. In our investigation, we performed long term molecular dynamics simulations to elucidate the effect of different amino acid substitutes (infectious and non-infectious) at position 129 in the coat protein of Cucumber mosaic virus using various structural parameters. We found that the contagious mutants displayed more flexibility at loops βE-αEF (129–136) and βF-βG loop (155–163) as compared to the non-infectious and native structures. This specific study at the atomic level yields innovative ideas for designing new therapeutic agents against the pathogen, which would further pave the path for researchers to control this devastating plant virus.

γ-aminobutyric acid, being a principle neuromediator in humans controlling the inhibition signals, acts on the ligand-gated pentameric type A receptors to transmit their response. Any dysfunction of these receptors leads to neurological disorders and mental illness. Benzodiazepine has been used extensively for the treatment of these disorders, which shows its effect by reducing the threshold concentration of γ-aminobutyric acid required to activate the receptor. Being a central nervous system depressant, benzodiazepine is also a common substance of abuse along with other recreational drugs that show affinity towards the benzodiazepine binding site. Flumazenil is considered the first line of treatment for the overdose of these substances, which competes with them to bind with the receptor having a higher binding affinity towards the receptor. Like most of the synthetic drugs, Flumazenil also has some side-effects associated with it. Here we focus our work towards finding specific naturally originated antagonist of the benzodiazepine binding site to suggest an alternative for Flumazenil by performing various computational analysis like docking experiments followed by simulations and molecular mechanics poisson-boltzmann surface area analysis. Molecular docking experiments filtered out four ligand molecules specific for the benzodiazepine binding site, namely, ligand-1,7,9 and 17. Further, molecular dynamics simulations showed ligand-17 to have stable conformation in the binding site as well as a lower binding free energy as compared to Flumazenil. Due to its natural origin, ligand-17 is supposed to have lower side effects; therefore, its backbone can be further explored to develop specific antagonists of benzodiazepines. Communicated by Ramaswamy H. Sarma.

The cyclin-dependent kinase 5 (CDK5) is an unusual member of the CDKs family due to its role in the central nervous system. The specific inhibition of cyclin-dependent kinase 5 (CDK5) is highly desirable in combating a wide range of conditions including, neurodegeneration, cancer, and diabetes. In this study, we elucidated the potential of in-house developed plant-derived semi-synthetic (AAB) analogues to act as ATP competitive inhibitors to selectively inhibit CDK5. We integrated high-end computational approaches including, explicit-solvent molecular dynamics (MD) simulations, steered MD simulations, and enhanced umbrella sampling simulations to rank and compare the AAB molecules with two selective CDK5 inhibitors (4a and Indolinone-A). Our results suggested the high affinity of AAB scaffolds (AAB-6 and AAB-8) to selectively interact with the active site of CDK5. Simultaneously, both these molecules showed unfavorable binding free energies for CDK2, manifesting selectivity for CDK5 over CDK2. Moreover, we demonstrated the possible unbinding pathways of the top AAB analogues from the catalytic pocket of CDK5 and compared them with the standard molecules. The present computational approach could also be used to target critical proteins involved in various diseases.

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Currently, there are no particular antivirals available to battle with COVID-19. The RNA-dependent RNA polymerase (RdRp) has emerged as a novel drug target due to its essential role in virus replication. In this study, turmeric-derived compounds were chosen and subjected to in-silico analysis to evaluate their binding affinity against the RdRp-RNA complex of SARS-CoV-2. Our in-silico approach included the analysis of protein-ligand interactions by molecular docking and molecular dynamics simulations, followed by free energy calculations by molecular mechanics Poisson-Boltzmann surface area analysis. Curcumin and diacetylcurcumin showed stability and good binding affinity at the active site of the SARS-CoV-2 RdRp-RNA complex. Furthermore, to validate the potency of selected compounds, we compared them with Favipiravir and Remdesivir antiviral drugs from our previous analysis on targeting tea bioactive molecules to inhibit RdRp-RNA complex. The comparative analysis revealed that the selected compounds showed higher potential to be developed as RdRp-RNA inhibitors than antiviral medicines Remdesivir and Favipiravir. However, these compounds need to be further validated by in-vitro and in-vivo investigations., Graphical abstract Image 1

KIT is involved in signal transduction activities of many pathways regulating bodily functions by providing docking sites for downstream signaling proteins. Mutations in this receptor leads to its independent ligand activation, which develops cancer conditions. Sunitinib has already been used for inhibition of the mutant KIT receptor for suppression of cancer but the mutation at residue D816 show resistance towards it. So, there is an immediate need of finding new potent inhibitors for mutant KIT, therefore we performed the current study. Here we filtered a library of isoindolin moiety molecules to find a potent inhibitor for KIT and docked them onto the sunitinib binding site in native and mutant KIT (D816H, D816V, and D816Y) receptors. This filtration left us with ligands which showed a better affinity towards the receptor as compared to sunitinib. Further, we also validated the affinity of the selected ligands via molecular dynamics simulation as well as MMPBSA calculations, where they attained better binding energy values than sunitinib. It implied that they had stronger binding with the receptors. We also compared our ligand molecules with dasatinib, which is an inhibitor developed for the resistant D816V mutant KIT. One of our ligands also performed better than dasatinib. Drug likeliness of the ligand molecules was verified via ADMET, Lipinski and TOPKAT profiling. Backbone architecture of these ligands can be modified to develop more potent inhibitors against resistant mutant KIT receptors.

The accumulation of aberrant superoxide dismutase (SOD1) protein causes a neurodegenerative disease known as amyotrophic lateral sclerosis (ALS). A mutation in SOD1 that changed Isoleucine to Threonine at position 113 (I113T) was found to be a leading cause of protein aggregation and development of ALS. The most affected regions of I113T were 2-β, 3-β, 6-β-sheet, loop-IV, and loop-VII. It also has an abnormally solvent-exposed tryptophan residue (Trp32) on the surface of 3-β-sheet, responsible for initiation of aggregation. Molecular docking and molecular dynamic simulations were carried out to investigate the binding mechanism and structural impact of Himalayan bioactive molecules (Epigallocatechin-gallate, Isorhamnetin, and Kaempferol) on I113T. This investigation revealed that bioactive molecules reverted the structural changes, including hydrogen bonding pattern, flexibility, and conformational stability of I113T to a substantially similar level as that of WT SOD1. Moreover, these molecules could prevent the abnormal oligomerization of I113T monomers by interacting with Trp32 on 3-β-sheet. Therefore, we intend to suggest that the Himalayan bioactive molecules could effectively revert the structural changes and prevent aggregate formation due to I113T, and could act as potential molecules for ALS therapy. However, these finding would required further validations by in-vitro and in-vivo studies.

The proliferating cell nuclear antigen (PCNA) is a multipurpose nuclear protein in almost every form of life. It plays a significant role as a part of the mechanism for DNA replication and DNA repair process. Owing to its multi-functional role inside the cell, PCNA is often referred as the ringmaster of the genome or the maestro of the replication fork. PCNA was suggested for anticancer therapy as a potential non-oncogenic target. In this study, a set of bioactive molecules was screened to identify molecules that could effectively bind to the target site on PCNA and alter its protein–protein interactions. A combined computational approach consisting of molecular interactions, thermodynamics free energy estimations by the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations, conventional and steered MD simulations were utilized to identify potential inhibitors of PCNA. Our robust computational approach suggested two bioactive molecules, Hypericin and Pseudohypericin, from plant Hypericum perforatum as more potent inhibitors of PCNA than the standard co-crystallized inhibitor. These molecules could be developed as modulators of PCNA protein–protein interactions and effective anticancer drugs. These results, however, require validation by appropriate experimental studies.

Background Non-structural protein 1 (Nsp1), a virulence agent of SARS-CoV-2, has emerged as an important target for drug discovery. Nsp1 shuts down the host gene function by associating with the 40S ribosomal subunit. Methods Molecular interactions, drug-likeness, physiochemical property predictions, and robust molecular dynamics (MD) simulations were employed to discover novel Nsp1 inhibitors. In this study, we evaluated a series of molecules based on the plant (Cedrus deodara) derived α,β,γ-Himachalenes scaffolds. Results The results obtained from estimated affinity and ligand efficiency suggested that BCH10, BCH15, BCH16, and BCH17 could act as potential inhibitors of Nsp1. Moreover, MD simulations comprising various MD driven time-dependent analyses and thermodynamic free energy calculations also suggested stable protein-ligand complexes and strong interactions with the binding site. Furthermore, the selected molecules passed drug likeliness parameters and the physiochemical property analysis showed acceptable bioactivity scores. Conclusion The structural parameters of dynamic simulations revealed that the reported molecules could act as lead compounds against SARS-CoV-2 Nsp1 protein., Graphical abstract Image 1

Stevioside is a natural non-caloric sweetener obtained from Stevia rebaudiana Bertoni plant. The major challenge in the commercialization of stevioside as a natural sweetener is its bitter-off taste. In this study, we prepared molecular models of potential taste receptors of stevioside, both sweet and bitter. With appropriate modifications on the stevioside backbone, we performed molecular docking of prepared ligands with both sweet and bitter taste receptors. Based on binding energy, we found that one of the potential substituents, Kamiya-8, shows a good affinity towards sweet taste and a weak affinity for bitter receptors. Further, we selected Kamiya-8 for molecular dynamics simulations to improve the prediction of binding energy and to check the binding strength of Kamiya-8 with taste receptors. Moreover, we also performed MM-PBSA calculation for calculating the end state free energies of molecules in solvent and found that Kamiya-8 gives a 2-fold effect as it interacts with sweet receptors (T1R2, T1R3) with lowest binding energy conformation (−285.265 kcal/mol, −571.481 kcal/mol). Secondly, it gives high binding energy (–273.319 kcal/mol, −355.500 kcal/mol) with bitter taste receptors (T2R4, T2R14) as compared to stevioside. Based on this study, we found that Kamiya-8 can be the potential substituent that can improve the palatability of stevioside.

From bacteria to mammals, DNA mismatch repair (MMR) pathway plays an essential role in eliminating mismatched nucleotides and insertion-deletion mismatches during the process of DNA replication. Among many of the proteins which participate in the mismatch repair process, proliferating cell nuclear antigen (PCNA) remains the principal conductor at the replication fork. The pol30-201 and pol30-204 are the two mutated alleles which encode for C22Y and C81R mutant forms of PCNA proteins. We performed long term molecular dynamics (MD) simulations analysis (0.8 μs) to understand the dynamic behavior and alterations in the structure of wild type and mutated forms of PCNA at the atomic level. We observed changes in the structural characteristics like length, radius, rise per residue of alpha helices in both the mutated forms of PCNA. Apart from it, disfigurement of the charge distribution which effects binding with the dsDNA due to mutant C22Y and other structural perturbations were also seen in regions significant for the formation of a biologically active trimeric form of PCNA due to mutant C81R. Our analysis of native and mutated forms of PCNA provides an insight into the essential structural and functional features required for proper and well-coordinated DNA mismatch repair process and consequences of the mutation leading to an impaired process of MMR. These structural characteristics are fundamental for the MMR process and hence our analysis likely contributes to or presents the novel mechanism involved in the process of MMR.Communicated by Ramaswamy H. Sarma.

PI3Kα is a heterodimer protein consisting of two subunits (p110α and p85α) which promotes various signaling pathways. Oncogenic mutation in the catalytic subunit p110α of PI3Kα at the 1047 position in the kinase domain substitutes the histidine with arginine. This mutation brings about conformational transitions in the protein complex. These transitions expose the membrane binding region of PI3Kα, and then it independently binds to the cell membrane through its kinase domain without the involvement of the membrane-bound protein RAS. We observed notable changes between the protein complexes (p110α-p85α) of native and mutant structures at the atomic level using molecular dynamics simulations. Simulation results revealed formation of a less number of hydrogen bonds between the two subunits in the mutant protein complex which led the two subunits to move away from each other. This increase in distance between the subunits led to an expanded structure, thereby increasing the flexibility of the protein complex. Furthermore, a study of secondary structure elements and the electrostatic potential of the protein also gave a molecular insight into the change in interaction patterns of the protein with the plasma membrane. Our finding clearly indicates the role of mutation in oncogenesis and provides an insight into considering the structural aspects to handle this mutation.

Phosphodiesterases (PDEs) play an important function in transduction of cellular signals by modulating the activation of G-proteins by hydrolyzing cAMP and cGMP. PDE10A has emerged as an inhibitory target for development of effective therapeutics against various disorders such as schizophrenia, psychosis, Huntington disease, and other disorders related to the central nervous system. We utilized various computational methods such as molecular docking, molecular dynamic simulations, and MM-PBSA to find a more potent and selective PDE10A inhibitor compared to papaverine, which is a known standard inhibitor of PDE10A. Molecular docking of papaverine and twenty-eight in house synthesized 3-Methylenisoindolin-1-one based molecules provided two potential lead molecules (molecule #3 and molecule #28), which could be developed as potent PDE10A inhibitors. However, molecule #28 was excluded from further studies due to its cross reactivity with other PDE isoforms. Molecular dynamics and MM-PBSA techniques were used to further analyze the molecular docking results. Molecule #3 binds to the conserved substrate recognizing residue (Gln726) and also fits into the selectivity pocket by anchoring to the hydrophobic residue Tyr693. This study provides a promising candidate molecule that could be developed as a more potent and selective inhibitor of PDE10A.

Background The main protease (Mpro) of SARS-CoV-2 is involved in the processing of vital polypeptides required for viral genome replication and transcription and is one of the best-characterized targets to inhibit the progression of SARS-CoV-2 in infected individuals. Methods We screened a set of novel classes of acridinediones molecules to efficiently bind and inhibit the activity of the SARS-CoV-2 by targeting the Mpro. The repurposed FDA-approved antivirals were taken as standard molecules for this study. Long term (1.1 μs) MD simulations were performed to analyze the conformational space of the binding pocket of Mpro bound to the selected molecules. Results The molecules DSPD-2 and DSPD-6 showed more favorable MM-PBSA interaction energies and were seated more deeply inside the binding pocket of Mpro than the topmost antiviral drug (Saquinavir). Moreover, DSPD-5 also exhibited comparable binding energy to Saquinavir. The analysis of per residue contribution energy and SASA studies indicated that the molecules showed efficient binding by targeting the S1 subsite of the Mpro binding pocket. Conclusion The DSPD-2, DSPD-6, and DSPD-5 could be developed as potential inhibitors of SARS-CoV-2. Moreover, we suggest that targeting molecules to bind effectively to the S1 subsite could potentially increase the binding of molecules to the SARS-CoV-2 Mpro., Graphical abstract Image 1, Highlights • A robust computational strategy applied to identify the potential lead for COVID-19. • Repurposed FDA approved antiviral drugs were compared with a set of acridinedione analogs against Mpro of SARS-CoV-2. • The acridinedione analogs have acceptable ADMET values and low toxicity profile. • In-house synthesized acridinedione analogs showed good amount of interaction with Mpro of SARS-CoV-2.

Background and Objectives The Dual-specificity tyrosine-phosphorylation regulated kinase-1A (DYRK1A) a serine/threonine kinase that has freshly gained recognition as an essential drug target due to the discovery of its involvement in pathological diseases. The development of new potent inhibitors of DYRK1A would contribute to clarify the molecular mechanisms of associated diseases. It would administer a new lead compound for molecular-targeted protein, which was the primary focus of our study. Methods The library of in-house synthesized pyrrolone-fused benzosuberene (PBS) compounds was docked with DYRK1A receptor. Further, molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) estimations were conducted to confirm our docking outcomes and compared the stability of chosen complexes with the 2C3 (standard molecule) complex. Results This study reports Ligand15, Ligand14, and Ligand11 as potent inhibitors which showed higher ligand efficiency, binding affinity, lipophilic ligand efficiency, and favorable torsion values as compared to 2C3. Conclusion The stated methodologies revealed a unique mechanism of active site binding. The binding interactions within the active site showed that the chosen molecules had notable interactions than the standard molecule, which led to the generation of potential compounds to inhibit DYRK1A.