MM-PBSA and per-residue decomposition energy studies on 7-Phenyl-imidazoquinolin-4(5H)-one derivatives: Identification of crucial site points at microsomal prostaglandin E synthase-1 (mPGES-1) active site

Molecular dynamics simulations to decipher the hotspots at the allosteric site of human 5-lipoxygenase

Human 5-lipoxygenase (LOX) is a non-heme, Fe-containing LOX which catalyses the conversion of arachidonic acid (AA) to leukotriene A4 (LTA4). LTA4 is subsequently converted to cysteinyl-LTs and LTB4 that cause bronchoconstriction and act as chemotactic and chemokinetic agent on human leukocytes, respectively. Leukotrienes play significant roles in inflammation in asthma, cardiovascular diseases, allergic rhinitis, atopic dermatitis, inflammatory bowel disease, rheumatoid arthritis, psoriasis and many more. Thus, in order to suppress LT formation for the management of such diseases, the intrinsic details of the structure of 5-LOX are crucial for the design/development of 5-LOX inhibitors. Here, we deciphered the role of various amino acids at the allosteric site of 5-LOX through molecular dynamics simulations. 3-O-Acetyl-11-keto-beta-boswellic acid (AKBA), a well-recognized allosteric inhibitor of 5-LOX, was used as reference compound. The consequences of amino acid mutations (R101, E108, H130, E134) on AKBA binding have been studied in silico. The changes were characterized at the interaction level. Our observations provide structural insights into crucial residues which are important for stabilizing the ligand at the allosteric site. Principal component analysis (PCA) was applied to the molecular dynamics simulation data to identify the structural fluctuations in the 5-LOX structure. The derived mechanistic details of allosteric 5-LOX inhibition may facilitate the development of novel therapeutics targeting 5-LOX.

Exploring the anti-diabetic potential of the Vigna sesquipedalis using in vitro, in vivo and computational models

Vigna sesquipedalis is traditionally used for the treatment of various disorders including diabetes but without scientific rational. Therefore, the current study was designed to evaluate its anti-diabetic potential. Antioxidant activity was assessed through DPPH and ABTS radical scavenging assays, while α-glucosidase and α-amylase inhibitory activities for anti-diabetic potential. Based on in vitro results, acute toxicity tests were performed, followed by in vivo studies using streptozotocin-induced diabetic model in mice. The ethyl acetate fraction exhibited the highest antioxidant potential, followed by crude extract. The methanolic crude extract showed the strongest in vitro antidiabetic activity. It was also found to be non-toxic up to 2000 mg/kg body weight. In vivo, the crude extract significantly (P < 0.05) improved body weight and displayed significant anti-diabetic effects. Further analysis of liver glycogen, serum insulin, glycosylated hemoglobin, and histopathology supported the extract overall performance. The virtual screening results showed highest binding energy of the Cyanidin-3-0-G (Cyanidin) with the amylase, Daucosterol with the GLP1, and Psoralidin with the Glucosidase. Similarly, MD simulation of the top hits was performed to investigate the dynamic stability and results showed that the ligand-protein system remains stable for during the simulation. The thermodynamic stability of the system was assessed by performing the binding free energy calculation using MM-PBSA/GBSA. The results of the binding free energy calculations showed favorable binding energies ligand-protein system. In short, the results illustrated potential as a pharmaceutical drug for insulin-dependent diabetes mellitus.

Machine learning and molecular docking prediction of potential inhibitors against dengue virus

Introduction

Dengue Fever continues to pose a global threat due to the widespread distribution of its vector mosquitoes, Aedes aegypti and Aedes albopictus. While the WHO-approved vaccine, Dengvaxia, and antiviral treatments like Balapiravir and Celgosivir are available, challenges such as drug resistance, reduced efficacy, and high treatment costs persist. This study aims to identify novel potential inhibitors of the Dengue virus (DENV) using an integrative drug discovery approach encompassing machine learning and molecular docking techniques.

Method

Utilizing a dataset of 21,250 bioactive compounds from PubChem (AID: 651640), alongside a total of 1,444 descriptors generated using PaDEL, we trained various models such as Support Vector Machine, Random Forest, k-nearest neighbors, Logistic Regression, and Gaussian Naïve Bayes. The top-performing model was used to predict active compounds, followed by molecular docking performed using AutoDock Vina. The detailed interactions, toxicity, stability, and conformational changes of selected compounds were assessed through protein-ligand interaction studies, molecular dynamics (MD) simulations, and binding free energy calculations.

Results

We implemented a robust three-dataset splitting strategy, employing the Logistic Regression algorithm, which achieved an accuracy of 94%. The model successfully predicted 18 known DENV inhibitors, with 11 identified as active, paving the way for further exploration of 2683 new compounds from the ZINC and EANPDB databases. Subsequent molecular docking studies were performed on the NS2B/NS3 protease, an enzyme essential in viral replication. ZINC95485940, ZINC38628344, 2',4'-dihydroxychalcone and ZINC14441502 demonstrated a high binding affinity of -8.1, -8.5, -8.6, and -8.0 kcal/mol, respectively, exhibiting stable interactions with His51, Ser135, Leu128, Pro132, Ser131, Tyr161, and Asp75 within the active site, which are critical residues involved in inhibition. Molecular dynamics simulations coupled with MMPBSA further elucidated the stability, making it a promising candidate for drug development.

Conclusion

Overall, this integrative approach, combining machine learning, molecular docking, and dynamics simulations, highlights the strength and utility of computational tools in drug discovery. It suggests a promising pathway for the rapid identification and development of novel antiviral drugs against DENV. These in silico findings provide a strong foundation for future experimental validations and in-vitro studies aimed at fighting DENV.

PCSK9 inhibitors as safer therapeutics for atherosclerotic cardiovascular disease (ASCVD): Pharmacophore design and molecular dynamics analysis

Cardiovascular disorders are still challenging and are among the deadly diseases. As a major risk factor for atherosclerotic cardiovascular disease, dyslipidemia, and high low-density lipoprotein cholesterol in particular, can be prevented primary and secondary by lipid-lowering medications. Therefore, insights are still needed into designing new drugs with minimal side effects. Proprotein convertase subtilisin/kexin 9 (PCSK9) enzyme catalyses protein-protein interactions with low-density lipoprotein, making it a critical target for designing promising inhibitors compared to statins. Therefore, we screened for potential compounds using a redesigned PCSK9 conformational behaviour to search for a significantly extensive chemical library and investigated the inhibitory mechanisms of the final compounds using integrated computational methods, from ligand essential functional group screening to all-atoms MD simulations and MMGBSA-based binding free energy. The inhibitory mechanisms of the screened compounds compared with the standard inhibitor. K31 and K34 molecules showed stronger interactions for PCSK9, having binding energy (kcal/mol) of -33.39 and -63.51, respectively, against -27.97 of control. The final molecules showed suitable drug-likeness, non-mutagenesis, permeability, and high solubility values. The C-α atoms root mean square deviation and root mean square fluctuation of the bound-PCSK9 complexes showed stable and lower fluctuations compared to apo PCSK9. The findings present a model that unravels the mechanism by which the final molecules proposedly inhibit the PCSK9 function and could further improve the design of novel drugs against cardiovascular diseases.

In silico identification of cyclosporin derivatives as potential inhibitors for RdRp of rotavirus by molecular docking and molecular dynamic studies

Rotavirus is one of the most common gastrointestinal viral diseases. Till date, there are only two vaccines available in the markets, which are specifically to be administered to young babies. In this study, VP1 RdRp is selected as potential target to carry out inhibitory activities. Cyclosporin A (Cys A) derivatives were designed via FBDD, pharmacokinetics, molecular docking, molecular dynamics (MD) simulation and molecular mechanics generalized born surface area was applied on these compounds. The results from these investigations were analyzed and it was found that the considered derivatives in this study were nontoxic and docking results revealed that the derivatives made some important bonds inside the active site of the receptors within a catalytic triad (Serine-Histidine-Aspartate). After analyzing the mean values of root mean square density (RMSD), root mean square fluctuation (RMSF), radius of gyration (RoG) and solvent accessible surface area (SASA) at 100 ns MD simulation of the selected compounds, it was found that compound 1 exhibits RMSD of 0.74 ± 0.10 Å, RMSF of 0.85 ± 0.15 Å, RoG of 16.45 ± 0.40 Å, SASA of 66.55 ± 0.35 nm2 and ΔGbind of -32.76 ± 0.02 kcal/mol. Therefore, the study revealed that amongst the designed and reported compounds, compound 1 was more stable within the active region of the RdRp and also this compound possesses lower binding free energy as compared to other selected compounds and Cys A as well.Communicated by Ramaswamy H. Sarma.

Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning

The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, and pY137 leads to more disordered states of the switch domains than the wild-type (WT) KRAS and induces conformational transformations between the closed and open states. The results from principal component analysis (PCA) indicate that principal motions PC1 and PC2 are responsible for the closed and open states of the phosphorylated KRAS. Interaction networks were analyzed and the results verify that the phosphorylation alters interactions of GTP and magnesium ion Mg2+ with the switch domains. It is concluded that the phosphorylation pY32, pY64, and pY137 tune the activity of KRAS through changing conformational dynamics and interactions of the switch domains. We anticipated that this work could provide theoretical aids for deeply understanding the function of KRAS.

Identification of potent BRD4-BD1 inhibitors using classical and steered molecular dynamics based free energy analysis

In the present work a combination of traditional and steered molecular dynamics based techniques were employed to identify potential inhibitors against the human BRD4 protein (BRD4- BD1); an established drug target for multiple illnesses including various malignancies. Quinoline derivatives that were synthesized in-house were tested for their potential as new BRD4-BD1 inhibitors. Initially molecular docking experiments were performed to determine the binding poses of BRD4-BD1 inhibitors. To learn more about the thermodynamics of inhibitor binding to the BRD4-BD1 active site, the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) free energy calculations were conducted afterwards. The findings of the MM-PBSA analysis were further reinforced by performing steered umbrella sampling simulations which revealed crucial details about the binding/unbinding process of the most potent quinoline derivatives at the BRD4-BD1 active site. We report a novel quinoline derivative which can be developed into a fully functional BRD4-BD1 inhibitor after experimental validation. The identified compound (4 g) shows better properties than the standard BRD4-BD1 inhibitors considered in the study. The study also highlights the crucial role of Gln78, Phe79, Trp81, Pro82, Phe83, Gln84, Gln85, Val87, Leu92, Leu94, Tyr97, Met105, Cys136, Asn140, Ile146 and Met149 in inhibitor binding. The study provides a possible lead candidate and key amino acids involved in inhibitor recognition and binding at the active site of BRD4-BD1 protein. The findings might be of significance to medicinal chemists involved in the development of potent BRD4-BD1 inhibitors.

In silico investigation of cholesterol-lowering drugs to find potential inhibitors of dehydrosqualene synthase in Staphylococcus aureus

Staphylococcus aureus is a lethal pathogen that can cause various bacterial infections. This study targets the CrtM enzyme of S. aureus, which is crucial for synthesizing golden carotenoid pigment: staphyloxanthin, which provides anti-oxidant activity to this bacterium for combating antimicrobial resistance inside the host cell. The present investigation quests for human SQS inhibitors against the CrtM enzyme by employing structure-based drug design approaches including induced fit docking (IFD), molecular dynamic (MD) simulations, and binding free energy calculations. Depending upon the docking scores, two compounds, lapaquistat acetate and squalestatin analog 20, were identified as the lead molecules exhibit higher affinity toward the CrtM enzyme. These docked complexes were further subjected to 100 ns MD simulation and several thermodynamics parameters were analyzed. Further, the binding free energies (ΔG) were calculated for each simulated protein-ligand complex to study the stability of molecular contacts using the MM-GBSA approach. Pre-ADMET analysis was conducted for systematic evaluation of physicochemical and medicinal chemistry properties of these compounds. The above study suggested that lapaquistat acetate and squalestatin analog 20 can be selected as potential lead candidates with promising binding affinity for the S. aureus CrtM enzyme. This study might provide insights into the discovery of potential drug candidates for S. aureus with a high therapeutic index.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03862-y.

Molecular docking, molecular dynamics and binding free energy based identification of novel potential multitarget inhibitors of Nipah virus

Nipah virus (NiV) is one of the most common viral diseases affecting the brain and nervous system of the body. To date, there is no significant antiviral drug specifically designed to inhibit NiV. In the last ten years, there has been a significant increase in interest in multitarget drug development. Therefore, the reported work focuses on designing a multitarget inhibitor for NiV. Among the twelve designed compounds, five exhibited better drug-likeness and ADMET properties, hence being selected for further analysis. In a molecular docking study, these compounds possessed better binding affinity as compared to Favipiravir. The RMSD of these compounds was ≤2Å and the number of H-bonds signified the better stability of the complexes formed. The ΔGbind of C4, C6 and C7 was found to be comparatively higher than the other screened compounds, revealing their greater ability to bind efficiently with NiV-G, NiV-F and NiV-N receptors, respectively. Therefore, based on molecular docking, molecular dynamics, and MM/PBSA analysis, these compounds can act as potential inhibitors of multitargets of NiV.Communicated by Ramaswamy H. Sarma.

Sesquiterpenes from two Compositae plants as promising inhibitors to nuclear hormone receptor 3 of Tribolium castaneum

Essential oils (EOs) and their volatile secondary metabolites have been proved to be effective on storage pests control, while restricted on the application due to unclear mechanism. Molecular dynamics (MD) simulations and binding free energies analysis provided an effective approach to reveal mechanism on conformational calculation. In this work, the insecticidal and repellent capacities of Praxelis clematidea and Ageratum houstonianum oils and their main components identified by gas chromatography-mass spectrometry (GC-MS) were scientifically measured. Interestingly, P. clematidea oil exhibited strong fumigant toxicity against Tribolium castaneum (LC50 = 7.07 mg/L air). Moreover, two EOs exhibited over 80% repellent rate against T. castaneum at the highest concentration of 78.63 nL/cm2. Furthermore, hundreds of enzymes related to the regulation of biological processes of T. castaneum were screened to explore the underlying molecular mechanism and develop promising insecticides. Besides, top hits were subjected to MD simulations and binding free energies analysis to elucidate complex inter-molecular stability and affinity over simulated time. The results demonstrated that isolongifolene, δ-cadinene, β-caryophyllene and caryophyllene oxide were prioritized as they were establishing conserved and stable interactions with residues of nuclear hormone receptor 3 (TcHR3) of T. castaneum, which suggested that the four sesquiterpenes have potential to be promising insecticides on storage pests control.

Large scale peptide screening against main protease of SARS CoV-2

The COVID-19 pandemic has been a public health emergency, with deadly forms constantly emerging around the world, highlighting the dire need for highly effective antiviral therapeutics. Peptide therapeutics show significant potential for this viral disease due to their efficiency, safety, and specificity. Here, two thousand seven hundred eight antibacterial peptides were screened computationally targeting the Main protease (Mpro) of SARS CoV-2. Six top-ranked peptides according to their binding scores, binding pose were investigated by molecular dynamics to explore the interaction and binding behavior of peptide-Mpro complexes. The structural and energetic characteristics of Mpro-DRAMP01760 and Mpro-DRAMP01808 complexes fluctuated less during a 250 ns MD simulation. In addition, three peptides (DRAMP01760, DRAMP01808, and DRAMP01342) bind strongly to Mpro protein, according to the free energy landscape and principal component analysis. Peptide helicity and secondary structure analysis are in agreement with our findings. Interaction analysis of protein-peptide complexes demonstrated that Mpro's residue CYS145, HIS41, PRO168, GLU166, GLN189, ASN142, MET49, and THR26 play significant contributions in peptide-protein attachment. Binding free energy analysis (MM-PBSA) demonstrated the energy profile of interacting residues of Mpro in peptide-Mpro complexes. To summarize, the peptides DRAMP01808 and DRAMP01760 may be highly Mpro specific, resulting disruption in a viral replication and transcription. The results of this research are expected to assist future research toward the development of antiviral peptide-based therapeutics for Covid-19 treatment.

Identification of common genes in obesity and cancer through network interaction and targeting those genes by virtual screening approach

Obesity may have an effect on cancer outcomes, resulting in global inequalities in cancer survival and death. Microarray data analysis was done to identify differentially expressed genes (DEGs) in obese and cancer patients. Total 1977 differentially expressed genes among obesity and gastric cancer, breast cancer, pancreatic cancer, and colorectal cancer were used to build a gene interaction network, which was then analyzed by using Cytoscape software. It has been identified that JUN, CXCL12, and LEP genes show a higher degree and stress, and play an important role in obesity and cancer progression. Further, CXCL12 and LEP were taken for virtual screening study with coumarin and its derivatives to develop a drug against obesity and cancer. The interactions of CXCL12 and LEP with coumarins were studied by molecular docking and it shows good interaction as well as docking score as compared to the standard one. The ADME properties were predicted to check the drug-likeness activity of coumarins and the most of the drug-likeness activities are in admire range. The Binding free energy of the docked complex was calculated by performing MM-GBSA. The molecular docking, ADME properties prediction, and MM-GBSA was performed on Maestro 12.6. The top docked score compounds were further subjected to molecular dynamic simulation to check the stability by using GROMACS. The MM-PBSA study was performed to calculate the binding energy components as well as the energy contributions of specific amino acids. The resultant compounds could be a potent anti-obesity and anti-cancer drug.Communicated by Ramaswamy H. Sarma.

Energy decomposition and waterswapping analysis to investigate the SNP associated DPD mediated 5-FU resistance

5-fluorouracil is an essential component of systemic chemotherapy for colon, breast, head, and neck cancer patients. However, tumoral overexpression of the dihydropyrimidine dehydrogenase has rendered 5-FU clinically ineffective by inactivating it to 5'-6'-dihydro fluorouracil. The responses to 5-FU in terms of efficacy and toxicity greatly differ depending upon the population group, because of variability in the DPD activity levels. In the current study, key active site amino acids involved in the 5-FU inactivation were investigated by modelling the 3D structure of human DPD in a complex with 5-FU. The identified amino acids were analyzed for their possible missense mutations available in dbSNP database. Out of 12 missense SNPs, four were validated either by sequencing in the 1000 Genomes project or frequency/genotype data. The recorded validated missense SNPs were further considered to analyze the effect of their respective alterations on 5-FU binding. Overall findings suggested that population bearing the Glu611Val DPD mutation (rs762523739) is highly vulnerable to 5-FU resistance. From the docking, electrostatic complementarity, dynamics, and energy decomposition analyses it was found that the above mutation showed superior scores than the wild DPD -5FU complex. Therefore, prescribing prodrug NUC-3373 or DPD inhibitors (Gimeracil/3-Cyano-2,6-Dihydroxypyridines) as adjuvant therapy may overcome the 5-FU resistance.

Relaxed complex scheme and molecular dynamics simulation suggests small molecule inhibitor of human TMPRSS2 for combating COVID-19

As the coronavirus disease 19 (COVID-19) pandemic continues to pose a health and economic crisis worldwide, the quest for drugs and/or vaccines against the virus continues. The human transmembrane protease serine 2 (TMPRSS2) has attracted attention as a target for drug discovery, as inhibition of its catalytic reaction would result in the inactivation of the proteolytic cleavage of the SARS-CoV-2 S protein. As a result, the inactivation prevents viral cell entry to the host's cell. In this work, we screened and identified two potent molecules that interact and inhibit the catalytic reaction by using computational approaches. Two docking screening experiments were performed utilizing the crystal structure and holo ensemble structure obtained from molecular dynamics in bound form. There is enhancement and sensitivity of docking results to the holo ensemble as compared to the crystal structure. Compound 1 demonstrated a similar inhibition value to nafamostat by interacting with catalytic triad residues His296 and Ser441, thereby disrupting the already established hydrogen bond interaction. The stability of the ligand-TMPRSS2 complexes was studied by molecular dynamics simulation, and the binding energy was re-scored by using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy. The obtained compounds may serve as an initial point toward the discovery of potent TMPRSS2 inhibitors upon further in vivo validation.Communicated by Ramaswamy H. Sarma.

"Mango in all her majesty"-the potential of mangiferin and its analogues in the inhibition of Eimeria tenella hexokinase-a computational approach

The potential of natural products in mitigating infections and diseases are being considered lately. Herein, via in silico methods, we report the possible molecular mechanism of mangiferin (isolated from the fruit, peel, bark and leaves of mango tree) and its derivatives in inhibiting Eimeria tenella hexokinase. We evaluated the binding affinity of these inhibitors to the glucose binding site of EtHK and thereafter proceeded to molecular dynamics simulation. The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) reveals that three of the derivatives (CPAMM, MxPAMM and NAMM) had better total binding free energy than mangiferin. The ADMET and physicochemical properties assessed shows that inhibitors also hold a potential to be drug-likely. Finally, in mediating their inhibitory potentials, the ligands stabilize both the global and local structures of the protein. This study provides a theoretical premise on which the anti-coccidial propensities of mangiferin most especially its derivatives can be investigate in vitro and in vivo.Communicated by Ramaswamy H. Sarma.

Computer-Aided Drug Design of Anti-inflammatory Agents Targeting Microsomal Prostaglandin E2 Synthase-1 (mPGES-1)

Inflammation is a natural process in response to external stimuli associated with organism protection. However, this reaction could be exaggerated, leading to severe damages related to physiopathological processes, such as rheumatoid arthritis, cancer, diabetes, allergies, infections, among others. Inflammation is mainly characterized by pain, increased temperature, flushing, and edema, which can be controlled using anti-inflammatory drugs. In this context, prostaglandin E2 (PGE2) inhibition has been targeted for designing new compounds with anti-inflammatory properties. It is a bioactive lipid overproduced during an inflammatory process, in which its increased production is carried out mainly by COX-1, COX-2, and microsomal prostaglandin E2 synthase-1 (mPGES-1). Recently, studies have demonstrated that mPGES-1 inhibition is a safe strategy to develop anti-inflammatory agents, which could protect against pain, acute inflammation, arthritis, autoimmune diseases, and different types of cancers. To decrease production costs and increase the probability of discovering active substances, computer-aided drug design (CADD) approaches have been increasingly used for designing new inhibitors. Thus, this review will cover all aspects involving high-throughput virtual screening, molecular docking, dynamics, fragment-based drug design, quantitative structure-activity relationship in seeking new promising mPGES-1 inhibitors.

Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase

Diabetes mellitus is a disorder characterized by higher levels of blood glucose due to impaired insulin mechanisms. Alpha glucosidase is a critical drug target implicated in the mechanisms of diabetes mellitus and its inhibition controls hyperglycemia. Since the existing standard synthetic drugs have therapeutic limitations, it is imperative to identify new potent inhibitors of natural product origin which may slow carbohydrate digestion and absorption via alpha glucosidase. Since plant extracts from Calotropis procera have been extensively used in the treatment of diabetes mellitus, the present study used molecular docking and dynamics simulation techniques to screen its constituents against the receptor alpha glucosidase. Taraxasterol, syriogenin, isorhamnetin-3-O-robinobioside and calotoxin were identified as potential novel lead compounds with plausible binding energies of −40.2, −35.1, −34.3 and −34.3 kJ/mol against alpha glucosidase, respectively. The residues Trp⁴⁸¹, Asp⁵¹⁸, Leu⁶⁷⁷, Leu⁶⁷⁸ and Leu⁶⁸⁰ were identified as critical for binding and the compounds were predicted as alpha glucosidase inhibitors. Structurally similar compounds with Tanimoto coefficients greater than 0.7 were reported experimentally to be inhibitors of alpha glucosidase or antidiabetic. The structures of the molecules may serve as templates for the design of novel inhibitors and warrant in vitro assaying to corroborate their antidiabetic potential.

Importance of protein intrinsic conformational dynamics and transient nature of non-covalent interactions in ligand binding affinity

We have recently identified BEN1 as a protein interactor of seryl-tRNA synthetase (SerRS) from model plant Arabidopsis thaliana. BEN1 contains an NADP⁺ binding domain and possesses acidic N-terminal extension essential for interaction with A. thaliana SerRS. This extension, specific for BEN1 homologues from Brassicaceae family, is solvent-exposed and distant to the nucleotide-binding site. We prepared a truncated BEN1 variant ΔN17BEN1 lacking the first 17 amino acid of this N-terminal extension as well as full-length BEN1 to investigate how the truncation affects the binding affinity towards coenzyme NADP⁺. By performing microscale thermophoresis (MST) experiments we have shown that both BEN1 variants bind the NADP⁺ cofactor, however, truncated BEN1 showed 34-fold higher affinity towards NADP⁺ indicating that its core protein structure is not just preserved but it binds NADP⁺ even stronger. To further corroborate the obtained results, we opted for a computational approach based on classical molecular dynamics simulations of both complexes. Our results have shown that both truncated and intact BEN1 variants form the same number of interactions with the NADP⁺ cofactor; however, it was the interaction occupancy that was affected. Namely, three independent MD simulations showed that the ΔN17BEN1 variant in complex with NADP⁺ has significantly higher interaction occupancy thus binds NADP⁺ with more than one order of magnitude higher affinity. Contrary to our expectations, the truncation of this distant region that does not communicate with the nucleotide-binding site didn't result in the gain of interaction but affected the intrinsic conformational dynamics which in turn fine-tuned the binding affinity by increasing the interaction occupancy and strength of the key conserved cation-π interaction between Arg69 and adenine of NADP⁺ and hydrogen bond between Ser244 and phosphate of NADP⁺.

Structural basis of UDP-N-acetylglucosamine pyrophosphorylase and identification of promising terpenes to control Aedes aegypti

According to the world health organization (WHO) 2020 report, vector borne diseases account for 17 % of all infections with reported 700 thousand death each year. They are of considerable importance to health professionals as they are posing a serious health threat and include dengue fever, Zika fever, chikungunya, yellow fever, and other disease agents. Aedes aegypti serve as a vector for transmitting several of these tropical fevers. In the present study, UDP-N-acetylglucosamine pyrophosphorylase enzyme (Aa-UAP) of A. aegypti which plays a significant contribution in chitin metabolism is targeted with natural terpenes to propose an eco-friendly and novel candidates for the development of new insecticides. The three dimensional Aa-UAP structure was constructed via a comparative homology approach and validated, followed by structure-based virtual screening against 1000 terpenes collected from natural MDP3 and NPACT databases. Top hits were subjected to molecular dynamics (MD) simulations and binding free energies analysis to elucidate complex intermolecular stability and affinity over simulated time. The results demonstrated that Aa-UAP possesses a homodimer state and its active site residues are well conserved. Three compounds (NPACT00138, NPACT00452, and NPACT00839) were prioritized as they are establishing conserved and stable interactions with the active binding-site residues of Aa-UAP. Conclusively, the reported Aa-UAP specific terpenes could serve as promising leads in order to develop potential insecticides. Importantly, the FDA approved drug NPACT00839 (Paclitaxel) could be used further in the fast-track experimental testing pipeline for biological optimization.

Luteolin: a blocker of SARS-CoV-2 cell entry based on relaxed complex scheme, molecular dynamics simulation, and metadynamics

Natural products have served human life as medications for centuries. During the outbreak of COVID-19, a number of naturally derived compounds and extracts have been tested or used as potential remedies against COVID-19. Tetradenia riparia extract is one of the plant extracts that have been deployed and claimed to manage and control COVID-19 by some communities in Tanzania and other African countries. The active compounds isolated from T. riparia are known to possess various biological properties including antimalarial and antiviral. However, the underlying mechanism of the active compounds against SARS-CoV-2 remains unknown. Results in the present work have been interpreted from the view point of computational methods including molecular dynamics, free energy methods, and metadynamics to establish the related mechanism of action. Among the constituents of T. riparia studied, luteolin inhibited viral cell entry and was thermodynamically stable. The title compound exhibit residence time and unbinding kinetics of 68.86 ms and 0.014 /ms, respectively. The findings suggest that luteolin could be potent blocker of SARS-CoV-2 cell entry. The study shades lights towards identification of bioactive constituents from T. riparia against COVID-19, and thus bioassay can be carried out to further validate such observations.

A Molecular Modeling Approach to Identify Potential Antileishmanial Compounds Against the Cell Division Cycle (cdc)-2-Related Kinase 12 (CRK12) Receptor of Leishmania donovani

The huge burden of leishmaniasis caused by the trypanosomatid protozoan parasite Leishmania is well known. This illness was included in the list of neglected tropical diseases targeted for elimination by the World Health Organization. However, the increasing evidence of resistance to existing antimonial drugs has made the eradication of the disease difficult to achieve, thus warranting the search for new drug targets. We report here studies that used computational methods to identify inhibitors of receptors from natural products. The cell division cycle-2-related kinase 12 (CRK12) receptor is a plausible drug target against Leishmania donovani. This study modelled the 3D molecular structure of the L. donovani CRK12 (LdCRK12) and screened for small molecules with potential inhibitory activity from African flora. An integrated library of 7722 African natural product-derived compounds and known inhibitors were screened against the LdCRK12 using AutoDock Vina after performing energy minimization with GROMACS 2018. Four natural products, namely sesamin (NANPDB1649), methyl ellagic acid (NANPDB1406), stylopine (NANPDB2581), and sennecicannabine (NANPDB6446) were found to be potential LdCRK12 inhibitory molecules. The molecular docking studies revealed two compounds NANPDB1406 and NANPDB2581 with binding affinities of -9.5 and -9.2 kcal/mol, respectively, against LdCRK12 which were higher than those of the known inhibitors and drugs, including GSK3186899, amphotericin B, miltefosine, and paromomycin. All the four compounds were predicted to have inhibitory constant (Ki) values ranging from 0.108 to 0.587 μM. NANPDB2581, NANPDB1649 and NANPDB1406 were also predicted as antileishmanial with Pa and Pi values of 0.415 and 0.043, 0.391 and 0.052, and 0.351 and 0.071, respectively. Molecular dynamics simulations coupled with molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations reinforced their good binding mechanisms. Most compounds were observed to bind in the ATP binding pocket of the kinase domain. Lys488 was predicted as a key residue critical for ligand binding in the ATP binding pocket of the LdCRK12. The molecules were pharmacologically profiled as druglike with inconsequential toxicity. The identified molecules have scaffolds that could form the backbone for fragment-based drug design of novel leishmanicides but warrant further studies to evaluate their therapeutic potential.

A Mechanistic Probe into the Dual Inhibition of T. cruzi Glucokinase and Hexokinase in Chagas Disease Treatment - A Stone Killing Two Birds?

Glucokinase (GLK) and Hexokinase (HK) have been characterized as essential targets in Trypanosoma cruzi (Tc)-mediated infection. A recent study reported the propensity of the concomitant inhibition of TcGLK and TcHK by compounds GLK2-003 and GLK2-004, thereby presenting an efficient approach in Chagas disease treatment. We investigated this possibility using atomic and molecular scaling methods. Sequence alignment of TcGLK and TcHK revealed that both proteins shared approximately 33.3 % homology in their glucose/inhibitor binding sites. The total binding free energies of GLK2-003 and GLK2-004 were favorable in both proteins. PRO92 and THR185 were pivotal to the binding and stabilization of the ligands in TcGLK, likewise their conserved counterparts, PRO163 and THR237 in TcHK. Both compounds also induced a similar pattern of perturbations in both TcGLK and TcHK secondary structure. Findings from this study therefore provide insights into the underlying mechanisms of dual inhibition exhibited by the compounds. These results can pave way to discover and optimize novel dual Tc inhibitors with favorable pharmacokinetics properties eventuating in the mitigation of Chagas disease.

Cheminformatics-Based Identification of Potential Novel Anti-SARS-CoV-2 Natural Compounds of African Origin

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome virus 2 (SARS-CoV-2) has impacted negatively on public health and socioeconomic status, globally. Although, there are currently no specific drugs approved, several existing drugs are being repurposed, but their successful outcomes are not guaranteed. Therefore, the search for novel therapeutics remains a priority. We screened for inhibitors of the SARS-CoV-2 main protease and the receptor-binding domain of the spike protein from an integrated library of African natural products, compounds generated from machine learning studies and antiviral drugs using AutoDock Vina. The binding mechanisms between the compounds and the proteins were characterized using LigPlot+ and molecular dynamics simulations techniques. The biological activities of the hit compounds were also predicted using a Bayesian-based approach. Six potential bioactive molecules NANPDB2245, NANPDB2403, fusidic acid, ZINC000095486008, ZINC0000556656943 and ZINC001645993538 were identified, all of which had plausible binding mechanisms with both viral receptors. Molecular dynamics simulations, including molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) computations revealed stable protein-ligand complexes with all the compounds having acceptable free binding energies <-15 kJ/mol with each receptor. NANPDB2245, NANPDB2403 and ZINC000095486008 were predicted as antivirals; ZINC000095486008 as a membrane permeability inhibitor; NANPDB2403 as a cell adhesion inhibitor and RNA-directed RNA polymerase inhibitor; and NANPDB2245 as a membrane integrity antagonist. Therefore, they have the potential to inhibit viral entry and replication. These drug-like molecules were predicted to possess attractive pharmacological profiles with negligible toxicity. Novel critical residues identified for both targets could aid in a better understanding of the binding mechanisms and design of fragment-based de novo inhibitors. The compounds are proposed as worthy of further in vitro assaying and as scaffolds for the development of novel SARS-CoV-2 therapeutic molecules.

A probable means to an end: exploring P131 pharmacophoric scaffold to identify potential inhibitors of Cryptosporidium parvum inosine monophosphate dehydrogenase

Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were identified and subsequently adopted to create a pharmacophore model for virtual screening in the ZINC database. This search generated eight ADMET-compliant hits that were examined thoroughly to fit into the active site of CpIMPDH via molecular docking. Three compounds ZINC46542062, ZINC58646829, and ZINC89780094, with favorable docking scores of - 8.3 kcal/mol, - 8.2 kcal/mol, and - 7.5 kcal/mol, were selected. The potential inhibitory mechanism of these compounds was probed using molecular dynamics simulation and Molecular Mechanics Generalized Poisson Boltzmann Surface Area (MM/PBSA) analyses. Results revealed that one of the hits (ZINC46542062) exhibited a lower binding free energy of - 39.52 kcal/mol than P131, which had - 34.6 kcal/mol. Conformational perturbation induced by the binding of the identified hits to CpIMPDH was similar to P131, suggesting a similarity in inhibitory mechanisms. Also, in silico investigation of the properties of the hit compounds implied superior physicochemical properties with regards to their synthetic accessibility, lipophilicity, and number of hydrogen bond donors and acceptors in comparison with P131. ZINC46542062 was identified as a promising hit compound with the highest binding affinity to the target protein and favorable physicochemical and pharmacokinetic properties relative to P131. The identified compounds can serve as a basis for conducting further experimental investigations toward the development of anticryptosporidials, which can overcome the challenges of existing therapeutic options. Graphical abstract P131 and the identified compounds docked in the NAD⁺ binding site of Cryptosporidium parvum IMPDH.

Molecular Basis of P131 Cryptosporidial-IMPDH Selectivity-A Structural, Dynamical and Mechanistic Stance

Cryptosporidiosis accounts for a surge in infant (<5 years) mortality and morbidity. To date, several drug discovery efforts have been put in place to develop effective therapeutic options against the causative parasite. Based on a recent report, P131 spares inosine monophosphate dehydrogenase (IMPDH) in a eukaryotic model (mouse IMPDH (mIMPDH)) while binding selectively to the NAD⁺ site in Cryptosporidium parvum (CpIMPDH). However, no structural detail exists on the underlining mechanisms of P131-CpIMPDH selective targeting till date. To this effect, we investigate the selective inhibitory dynamics of P131 in CpIMPDH relative to mIMPDH via molecular biocomputation methods. Pairwise sequence alignment revealed prominent variations at the NAD⁺ binding regions of both proteins that accounted for disparate P131 binding activities. The influence of these variations was further revealed by the MM/PBSA energy estimations coupled with per-residue energy decomposition which monitored the systematic binding of the compound. Furthermore, relative high-affinity interactions occurred at the CpIMPDH NAD⁺ site which were majorly mediated by SER22, VAL24, PRO26, SER354, GLY357, and TYR358 located on chain D. These residues are unique to the parasite IMPDH form and not in the eukaryotic protein, highlighting variations that account for preferential P131 binding. Molecular insights provided herein corroborate previous experimental reports and further underpin the basis of CpIMPDH inhibitor selectivity. Findings from this study could present attractive prospects toward the design of novel anticryptosporidials with improved selectivity and binding affinity against parasitic targets.

Pharmacoinformatics-based identification of potential bioactive compounds against Ebola virus protein VP24

BACKGROUND

The impact of Ebola virus disease (EVD) is devastating with concomitant high fatalities. Currently, various drugs and vaccines are at different stages of development, corroborating the need to identify new therapeutic molecules. The VP24 protein of the Ebola virus (EBOV) plays a key role in the pathology and replication of the EVD. The VP24 protein interferes with the host immune response to viral infections and promotes nucleocapsid formation, thus making it a viable drug target. This study sought to identify putative lead compounds from the African flora with potential to inhibit the activity of the EBOV VP24 protein using pharmacoinformatics and molecular docking.

METHODS

An integrated library of 7675 natural products originating from Africa obtained from the AfroDB and NANPDB databases, as well as known inhibitors were screened against VP24 (PDB ID: 4M0Q) utilising AutoDock Vina after energy minimization using GROMACS. The top 19 compounds were physicochemically and pharmacologically profiled using ADMET Predictor™, SwissADME and DataWarrior. The mechanisms of binding between the molecules and EBOV VP24 were characterised using LigPlot+. The performance of the molecular docking was evaluated by generating a receiver operating characteristic (ROC) by screening known inhibitors and decoys against EBOV VP24. The prediction of activity spectra for substances (PASS) and machine learning-based Open Bayesian models were used to predict the anti-viral and anti-Ebola activity of the molecules, respectively.

RESULTS

Four natural products, namely, ZINC000095486070, ZINC000003594643, ZINC000095486008 and sarcophine were found to be potential EBOV VP24-inhibitiory molecules. The molecular docking results showed that ZINC000095486070 had high binding affinity of -9.7 kcal/mol with EBOV VP24, which was greater than those of the known VP24-inhibitors used as standards in the study including Ouabain, Nilotinib, Clomiphene, Torimefene, Miglustat and BCX4430. The area under the curve of the generated ROC for evaluating the performance of the molecular docking was 0.77, which was considered acceptable. The predicted promising molecules were also validated using induced-fit docking with the receptor using Schrödinger and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The molecules had better binding mechanisms and were pharmacologically profiled to have plausible efficacies, negligible toxicity as well as suitable for designing anti-Ebola scaffolds. ZINC000095486008 and sarcophine (NANPDB135) were predicted to possess anti-viral activity, while ZINC000095486070 and ZINC000003594643 to be anti-Ebola compounds.

CONCLUSION

The identified compounds are potential inhibitors worthy of further development as EBOV biotherapeutic agents. The scaffolds of the compounds could also serve as building blocks for designing novel Ebola inhibitors.

Does Size Really Matter? Probing the Efficacy of Structural Reduction in the Optimization of Bioderived Compounds - A Computational "Proof-of-Concept"

Over the years, numerous synthetic approaches have been utilized in drug design to improve the pharmacological properties of naturally derived compounds and most importantly, minimize toxic effects associated with their transition to drugs. The reduction of complex bioderived compounds to simpler bioactive fragments has been identified as a viable strategy to develop lead compounds with improved activities and minimal toxicities. Although this ‘reductive’ strategy has been widely exemplified, underlying biological events remain unresolved, hence the unanswered question remains how does the fragmentation of a natural compound improve its bioactivity and reduce toxicities? Herein, using a combinatorial approach, we initialize a computational “proof-of- concept” to expound the differential pharmacological and antagonistic activities of a natural compound, Anguinomycin D, and its synthetic fragment, SB640 towards Exportin Chromosome Region Maintenance 1 (CRM1). Interestingly, our findings revealed that in comparison with the parent compound, SB640 exhibited improved pharmacological attributes, while toxicities and off-target activities were relatively minimal. Moreover, we observed that the reduced size of SB640 allowed ‘deep access’ at the Nuclear Export Signals (NES) binding groove of CRM1, which favored optimal and proximal positioning towards crucial residues while the presence of the long polyketide tail in Anguinomycin D constrained its burial at the hydrophobic groove. Furthermore, with regards to their antagonistic functions, structural inactivation (rigidity) was more pronounced in CRM1 when bound by SB640 as compared to Anguinomycin D. These findings provide essential insights that portray synthetic fragmentation of natural compounds as a feasible approach towards the discovery of potential leads in disease treatment.