Binding Site Residues Research Articles

Computational and theoretical insights into the cytotoxic prospects of compounds isolated from Elaeodendron buchananii against Leukemia

The present study investigated the cytotoxic prospects of isolated compounds from Elaeodendron buchananii against leukemia, using computational tools. Comprehensive literature searches revealed only buchaninoside, mutangin, methyl 3β-acetoxy-11α, 19α, 28-trihydroxyurs-12-en-23-oic acid, 3β, 11α, 19α-trihydroxyurs-12-en-23, 28-dioic acid, 3β-acetoxy-19α, 24, 28-trihydroxyurs-12-ene, 3-oxo-19α,28-dihydroxyurs-12-en-24-oic acid, and elabunin have been isolated from E. buchananii. The compounds were subjected to Density Functional Theory (DFT) and Molecular Dynamics (MD) analyses, with Fms-like tyrosine kinase (FLT3) and catalytic binding sites of Murine Leukemia Virus (MLV) as the target proteins in lukemia. Following DFT analysis, the structures of the compounds were optimized at the PW6B95D3/Def2-TZVP level of theory; their UV-Visible peaks were in the UV region, with mutangin, 3-oxo-19α,28-dihydroxyurs-12-en-24-oic acid and elabunin exhibiting one single peak. The potent Root-Mean-Square Deviation, Root-Mean-Square Fluctuation, solvent-accessible surface area and radius of gyration values indicated a strong and stable molecular interaction between the compounds and the proteins. These were further supported by high ∆G values, with MLV showing the best interaction. Per-residue decomposition plots also revealed high energy contributions in the interactions’ binding sites residues. These results indicate that the cytotoxic prospects of the isolated compounds against leukemia as indicated by its molecular interactions with FLT3 and MLV.

Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis

Cerebroside sulfotransferase (CST) is considered as therapeutic target for substrate reduction therapy (SRT) for metachromatic leukodystrophy (MLD). The present study evaluates the therapeutic potential of 57 phytoconstituents of Withania somnifera against CST. Using binding score cutoff ≤-7.0 kcal/mol, top 10 compounds were screened and after ADME and toxicity-based screening, Withasomidienone, 2,4-methylene-cholesterol, and 2,3-Didehydrosomnifericin were identified as safe and potent drug candidates for CST inhibition. Key substrate binding site residues involved in interaction were LYS82, LYS85, SER89, TYR176, PHE170, PHE177. Four steroidal Lactone-based withanolide backbone of these compounds played a critical role in stabilizing their position in the active site pocket. 100 ns molecular dynamics simulation and subsequent trajectory analysis through structural deviation and compactness, principal components, free energy landscape and correlation matrix confirmed the stability of CST-2,3-Didehydrosomnifericin complex throughout the simulation and therefore is considered as the most potent drug candidate for CST inhibition and Withasomidienone as the second most potent drug candidate. The reverse pharmacophore analysis further confirmed the specificity of these two compounds towards CST as no major cross targets were identified. Thus, identified compounds in this study strongly present their candidature for oral drug and provide route for further development of more specific CST inhibitors.

Investigating the Effect of GLU283 Protonation State on the Conformational Heterogeneity of CCR5 by Molecular Dynamics Simulations.

CCR5 is a class A GPCR and serves as one of the coreceptors facilitating HIV-1 entry into host cells. This receptor has vital roles in the immune system and is involved in the pathogenesis of different diseases. Various studies were conducted to understand its activation mechanism, including structural studies in which inactive and active states of the receptor were determined in complex with various binding partners. These determined structures provided opportunities to perform molecular dynamics (MD) simulations and to analyze conformational changes observed in the protein structures. The atomic-level dynamic studies allow us to explore the effects of ionizable residues on the receptor. Here, our aim was to investigate the conformational changes in CCR5 when it forms a complex with either the inhibitor maraviroc (MRV), an approved anti-HIV drug, or HIV-1 envelope protein GP120, and compare these changes to the receptor's apo form. In our simulations, we considered both ionized and protonated states of ionizable binding site residue GLU2837.39 in CCR5 as the protonation state of this residue was considered ambiguously in previous studies. Our molecular simulations results suggested that in fact, the change in the protonation state of GLU2837.39 caused interaction profiles to be different between CCR5 and its binding partners, GP120 or MRV. We observed that when the protonated state of GLU2837.39 was considered in complex with the envelope protein GP120, there were substantial structural changes in CCR5, indicating that it adopts a more active-like conformation. On the other hand, CCR5 in complex with MRV always adopted an inactive conformation regardless of the protonation state. Hence, the CCR5 coreceptor displays conformational heterogeneity not only depending on its binding partner but also influenced by the protonation state of the binding site binding site residue GLU2837.39. This outcome is also in accordance with some studies showing that GP120 binding could activate signaling pathways. This outcome could also have significant implications for discovering novel CCR5 inhibitors as anti-HIV drugs using in silico methods such as molecular docking, as it may be necessary to consider the protonated state of GLU2837.39.

Unveiling MurM inhibitors in Enterococcus faecalis V583: a promising approach to tackle antibiotic resistance

Enterococcus faecalis is commonly found in the GI tract of humans and animals. It causes various infections, especially in hospital environments, and shows growing antibiotic resistance. This study utilized a subtractive proteomics approach to find out the potential drug targets in E. faecalis. Unique metabolic pathways were analysed and compared to the host to minimize adverse effects. Among twenty nine pathogenic specific and seventy three host-pathogen common pathways identified using the KEGG database, sixty seven essential proteins were found through the DEG BLAST search. PSORTB predicted that forty cytoplasmic proteins could be suitable as druggable targets. Further analysis identified fourteen proteins with virulence properties using the VFDB BLAST. Among these, seven proteins with more than ten antigenic sites were subjected to DrugBank BLAST, identifying three novel and four existing drug targets. One of the crucial drug targets, MurM, was selected due to its critical role in peptidoglycan biosynthesis. The reason for selecting MurM is crucial for addressing antibiotic resistance, disrupting bacterial cell wall synthesis, and attaining selective antimicrobial activity. MurM belongs to the mixed αβ class with two functional domains. The possible binding site residues of MurM are Trp31, Lys35, Trp38, Arg215, and Tyr219. Virtual screening identified potential lead candidates for MurM, and four were selected based on their physiochemical, pharmacokinetic, and structural properties. This study provides valuable insights into identifying and analysing a potential drug target, the MurM protein, and its inhibitors in E. faecalis V583.

Mechanistic insights into β-glucuronidase inhibition by isoprenylated flavonoids from Centaurea scoparia: Bridging experimental and computational approaches

Exploring the intricate mechanisms underlying the inhibition of β-glucuronidase, particularly the enzyme produced by gastrointestinal bacteria, is essential for the development of novel therapeutic interventions and pharmaceutical advancements. Inhibiting bacterial β-glucuronidase can prevent the reactivation of harmful drug metabolites in the gut, thereby reducing associated toxicities. The inhibitory potential of four isoprenylated flavonoids from Centaurea scoparia against β-glucuronidase was intensively investigated by combined in vitro and in silico tools. The results of in vitro inhibitory activity showed that Compounds 1 and 3 exhibited the highest inhibitory activity, as evidenced by their low IC50 values of 3.65 ± 0.28 and 3.97 ± 0.11 μM, respectively. The enzyme kinetics analysis revealed that Compound 1 and the positive control drug (EGCG) follow a mixed inhibition mechanism. In contrast, compounds 3 and 4 exhibited a noncompetitive inhibition mode, as suggested by the intersection patterns observed in the Lineweaver-Burk plots. The docking studies corroborated the in vitro inhibitory assay results, with Compounds 1 and 3 demonstrating the lowest binding affinities and the highest extent of polar and hydrophobic interactions with residues in the enzyme's binding site. Utilizing a 200 ns molecular dynamics (MD) simulation, we examined the interaction dynamics between isolated flavonoids and β-glucuronidase. The analysis of multiple MD parameters revealed that compounds 1 and 3 maintained consistent trajectories and demonstrated significant energy stabilization when interacting with β-glucuronidase. These computational findings align with experimental results, highlighting the potential of compounds 1 and 3 as potent inhibitors for β-glucuronidase.

Identification of steroidal cardenolides from Calotropis procera as novel HIV-1 PR inhibitors: A molecular docking & molecular dynamics simulation study.

Background & objectives Despite advancements in antiretroviral therapy, drug-resistant strains of HIV (human immunodeficiency virus) remain a global health concern. Natural compounds from medicinal plants offer a promising avenue for developing new HIV-1 PR (protease) inhibitors. This study aimed to explore the potential of compounds derived from Calotropis procera, a medicinal plant, as inhibitors of HIV-1 PR. Methods This in silico study utilized natural compound information and the crystal structure of HIV-1 PR. Molecular docking of 17 steroidal cardenolides from Calotropis procera against HIV-1 PR was performed using AutoDock 4.2 to identify compounds with higher antiviral potential. A dynamic simulation study was performed to provide insights into the stability, binding dynamics, and potential efficacy of the top potential antiviral compound as an HIV-1 therapeutic. Results We found that all tested cardenolides had higher binding affinities than Amprenavir, indicating their potential as potent HIV-1 PR inhibitors. Voruscharin and uscharidin displayed the strongest interactions, forming hydrogen bonds and hydrophobic interactions with HIV-1 PR. Voruscharin showed improved stability with lower RMSD (Root Mean Square Deviation) values and reduced fluctuations in binding site residues but increased flexibility in certain regions. The radius of gyration analysis confirmed a stable binding pose between HIV-1 PR and Voruscharin. Interpretation & conclusions These findings suggest that Calotropis procera could potentially be a source of compounds for developing novel HIV-1 PR inhibitors, contributing to the efforts to combat HIV. Further studies and clinical trials are needed to evaluate the safety and efficacy of these compounds as potential drug candidates for the treatment of HIV-1 infection.

Repurposing FDA-approved drugs for combating tigecycline resistance in Acinetobacter baumannii: in silico screening against BaeR protein.

Acinetobacter baumannii is becoming a gravely threatening nosocomial infection with a higher mortality rate. The present study targets the BaeR protein that mediates resistance to tigecycline antibiotics. The BaeR protein, along with the aid of BaeS, senses the incoming antibiotics and stimulates the expression of resistance proteins. These resistance proteins efflux the antibiotics and protect the cells from its effect. The main goal of the current study is to determine potential inhibitors from already existing FDA-approved drugs that could mitigate the BaeR protein. A range of in silico approaches, including molecular dynamics, virtual screening, SIFT analysis, ADMET, DFT, MM/GBSA, MMPBSA and per residue interaction analysis, were performed to identify inhibitors against this protein. The screening of FDA-approved compounds against the BaeR protein yielded 620 compounds. These compounds were clustered by SIFT to distinguish related compounds, it resulted in 20 different clusters. The top five clusters that can accommodate the binding site with better interaction and score by fulfilling all criteria were selected. The DFT analysis showed a smaller energy gap among all the compounds, indicating the ability of the compound to form firm interactions. All the compounds showed less binding free energy in both MM/GBSA and MM/PBSA analyses. The compounds were observed to be stable throughout the simulation. The per-residue interaction analysis confirmed that interactions with binding site residues were stable throughout the simulation. As a result of the study, four compounds, namely ZINC000003801919, DB01203, DB11217 and ZINC0000000056652, were identified as efficient candidates to deal with antimicrobial resistance in A. baumannii.

Characterisation of seryl tRNA synthetase (srs-2) in Haemonchus contortus and Teladorsagia circumcincta

The aim of the study was to purify and characterise recombinant proteins with the potential as an anti-parasite vaccine. Full-length cDNAs encoding seryl-tRNA synthetase (srs-2) were cloned from Haemonchus contortus (HcSRS-2) and Teladorsagia circumcincta (TcSRS-2). TcSRS-2 and HcSRS-2 cDNA (1458bp) encoded proteins of 486 amino acids, each of which was present as a single band of about 55 kDa on SDS-PAGE. Multiple alignments of the protein sequences showed homology of 94% between TcSRS-2 and HcSRS-2, 76–93% with SRS-2s of eight nematodes and 68% with Mus musculus SRS-2. The predicted three-dimensional structures revealed an overall structural homology of TcSRS-2 and HcSRS-2, highly conserved binding and catalytic sites, and minor differences in the tautomerase binding site residues in other nematode SRS-2 homologues. A phylogenetic tree was constructed using helminth and mammalian SRS-2 sequences. Soluble C-terminal SRS-2 proteins were expressed in Escherichia coli strain AY2.4 and purified. Recombinant HcSRS-2 assay shows that the recombinant enzyme was active and stable. The Km and Vmax for ATP were 3.9 ± 1.0 μM and 2.7 ± 0.1 μmol min−1 mg−1 protein, respectively. Antibodies in serum and saliva from field-immune, but not nematode-naïve, sheep recognised recombinant HcSRS-2 and TcSRS-2 in enzyme-linked immunosorbent assays. Recognition of the recombinant proteins by antibodies generated by exposure of sheep to the native enzyme indicates similar antigenicity of the two proteins.

Irreversible Inhibition of DNMT3A by an N-Mustard Analog of S-Adenosyl-L-Methionine.

DNA methylation, an important epigenetic modification, is catalyzed by DNA methyltransferases and is essential in the regulation of gene expression. Here, the utility of an N-mustard analog designed to mimic the native methyl donor, S-adenosyl-L-methionine (SAM), was explored with the DNA methyltransferase 3A catalytic domain (DNMT3AC). In lieu of the expected analog transfer to DNA, methyltransferase activity was instead inhibited in a concentration dependent manner. Further investigation into the mechanism of analog inhibition did not reveal a typical competitive mechanism. Instead, mass spectrometry analysis provided direct evidence of two cysteine residues in the SAM binding site covalently modified by the SAM analog and confirmed its' function as an irreversible inhibitor of DNMT3AC.

Bioinformatics and computational studies of chabamide F and chabamide G for breast cancer and their probable mechanisms of action

Globally, the prevalence of breast cancer (BC) is increasing at an alarming level, despite early detection and technological improvements. Alkaloids are diverse chemical groups, and many within this class have been reported as potential anticancer compounds. Chabamide F (F) and chabamide G (G) are two dimeric amide alkaloids found in a traditional medicinal plant, Piper chaba, and possess significant cytotoxic effects. However, their scientific rationalization in BC remains unknown. Here, we aimed to investigate their potential and molecular mechanisms for BC through in silico approaches. From network pharmacology, we identified 64 BC-related genes as targets. GO and KEGG studies showed that they were involved in various biological processes and mostly expressed in BC-related pathways such as RAS, PI3K-AKT, estrogen, MAPK, and FoxO pathways. However, PPI analysis revealed SRC and AKT1 as hub genes, which play key roles in BC tumorigenesis and metastasis. Molecular docking revealed the strong binding affinity of F (− 10.7 kcal/mol) and G (− 9.4 and − 11.7 kcal/mol) for SRC and AKT1, respectively, as well as the acquisition of vital residues to inhibit them. Their long-term stability was evaluated using 200 ns molecular dynamics simulation. The RMSD, RMSF, Rg, and SASA analyses showed that the G-SRC and G-AKT1 complexes were excellently stable compared to the control, dasatinib, and capivasertib, respectively. Additionally, the PCA and DCCM analyses revealed a significant reduction in the residual correlation and motions. By contrast, the stability of the F-SRC complex was greater than that of the control, whereas it was moderately stable in complex with AKT1. The MMPBSA analysis demonstrated higher binding energies for both compounds than the controls. In particular, the binding energy of G for SRC and AKT1 was − 120.671 ± 16.997 and − 130.437 ± 19.111 kJ/mol, respectively, which was approximately twice as high as the control molecules. Van der Waal and polar solvation energies significantly contributed to this energy. Furthermore, both of them exhibited significant interactions with the binding site residues of both proteins. In summary, this study indicates that these two molecules could be a potential ATP-competitive inhibitor of SRC and an allosteric inhibitor of AKT1.

Innovative Mamba and graph transformer framework for superior protein-ligand affinity prediction

Accurate measurement of the affinity between drug targets is of great importance in the field of drug discovery, as it provides significant information about drug action. However, the diverse representations of compounds and proteins increase the difficulty of this task. Recently, numerous studies have explored the application of various deep learning methods and architectures in Drug-Target Affinity (DTA) prediction tasks, continuously improving performance. In this work, we present a multimodal late-stage fusion prediction model called MGDTA that combines the pioneering Mamba architecture with a hybrid model architecture based on graph transformers and transformers (GTT). For molecular compounds, structural characterisation is extracted using GTT layers. Additionally, a feature integration module is utilized to obtain molecular features from derived molecular fingerprints, culminating in a unified representation of drug molecules through a feature integration module. For proteins, we adopt the state-space model (SSM) module Mamba to learn feature representations from target protein sequences. This represents a preliminary exploration of the Mamba module in protein sequence feature extraction in DTA tasks. Finally, we predict the results by integrating the feature representations of both molecules and proteins. Our results indicate that the proposed model achieves superior performance on benchmark datasets, validating the feasibility of using the Mamba architecture for DTA tasks. Furthermore, sequence feature visualization demonstrates the capability of the Mamba block to focus on binding site residues within drug targets.

CC chemokine receptor 2 is allosterically modulated by sodium ions and amiloride derivatives through a distinct sodium ion binding site

CC chemokine receptor 2 and CCL2 are highly involved in cancer growth and metastasis, and immune escape. Raised sodium ion concentrations in solid tumours have also been correlated to metastasis and immune modulation. Sodium ions can modulate class A G protein-coupled receptors through the sodium ion binding site characterized by a highly conserved aspartic acid residue (D2.50), also present in CCR2. Hence, we further explored this binding site in CCR2 by radioligand binding studies and mutagenesis. Modulation of three distinctly binding radioligands by sodium ions and amiloride derivates was investigated. Sodium ions were observed to be relatively weak modulators of antagonist binding, but substantially increased 125I-CCL2 dissociation from CCR2. 6-Substituted Hexamethylene Amiloride (HMA) modulated all tested radioligands. Induced-fit docking of HMA in the presumed sodium ion binding site of CCR2 confirmed its binding site. Finally, investigation of (cancer-associated) mutations in the sodium ion binding site showed a markedly decreased expression compared to wild type. Only two mutants, G123A3.35 and G127K3.39, were able to be bound by [3H]INCB3344 and [3H]CCR2-RA-[R]. Thus, mutagenesis showed that the sodium ion binding site residues, which are distinct from other class A GPCRs and related to chemokine receptor evolution, are crucial for receptor integrity. Moreover, the tested mutations appeared to have no effect on modulation observed by HMA or a minor effect on sodium chloride modulation on the tested radioligands. All in all, these results invite further exploration of the CCR2 sodium ion binding site in (cancer) biology, and potentially as a third druggable binding site.

Phytochemical characterization, antimicrobial properties and in silico modeling perspectives of Anacyclus pyrethrum essential oil

Medicinal plants are used widely in the treatment of various infectious diseases. One of these medical plants is Moroccan plants such as Anacyclus pyrethrum. In this study, the essential oil isolated from the leaves of Anacyclus pyrethrum (APEO) by the hydrodistillation method was analyzed using (GC/MS) analysis. A total of forty-four compounds were identified form the oil and the oxygenated monoterpenes were the most abundant class of compounds. The major identified compound is santolina alcohol (40.7 %), followed by germacrene-D (8.9 %). The in-vitro assessment of the antimicrobial efficacy of APEO encompassed an investigation involving six microbial strains, including two Gram-positive bacteria, four Gram-negative bacteria, and three fungal strains. The findings revealed noteworthy antibacterial and antifungal properties against all examined microorganisms, with inhibitory zone diameters ranging from 25.67 ± 0.06 mm to 25.19 ± 0.03 mm for Gram-positive bacteria and from 22.34 ± 0.01 mm to 14.43 ± 0.02 mm for Gram-negative bacteria, as determined through the disc-diffusion assay. In the case of antifungal activity, inhibitory zones ranged from 24.57 ± 0.04 mm to 18.37 ± 0.06 mm. Further evaluation revealed that the MIC values of Gram-positive bacteria were at the concentration 0.25 % v/v, while MBC values ranged from 0.25 % to 1.0 % v/v. The Gram-negative bacteria exhibited MIC values spanning from 0.5 % to 2.0 % v/v, with MBC values in the range of 0.5 %–2.0 % v/v. For the fungal strains, MIC values ranged from 0.5 % to 1.0 % v/v, while the MFC consistently remained at 1.0 % for all tested fungal strains. The assessment of the MBC/MIC and MFC/MIC ratios collectively indicates that A. pyrethrum EO possesses bactericidal and fungicidal attributes. The in silico study of bioavailability predictions for compounds in APEO based on six physicochemical properties show optimal physiochemical properties including size, lipophilicity, solubility, flexibility, and saturation. α-Pinene, limonene, germacrene D, and (E)-β-farnesene are non-polar due to their lack of polar groups, and the ADME profile indicates desirable properties for considering these compounds in drug development. Molecular docking investigation indicates that all the compounds of APEO reside well into the binding site of the DNA gyrase B enzyme of Staphylococcus aureus by mediating a number of significant interactions with the binding site residues. The ADME analysis suggested that the major compounds APEO possess desirable properties for further consideration in drug development. In light of these findings, APEO could serve as a natural source for the elaboration of new and active antimicrobial drugs.

Direct measurements of neurosteroid binding to specific sites on GABAA receptors.

Neurosteroids are allosteric modulators of GABAA currents, acting through several functional binding sites although their affinity and specificity for each site are unknown. The goal of this study was to measure steady-state binding affinities of various neurosteroids for specific sites on the GABAA receptor. Two methods were developed to measure neurosteroid binding affinity: (1) quenching of specific tryptophan residues in neurosteroid binding sites by the neurosteroid 17-methylketone group, and (2) FRET between MQ290 (an intrinsically fluorescent neurosteroid) and tryptophan residues in the binding sites. The assays were developed using ELIC-α1GABAAR, a chimeric receptor containing transmembrane domains of the α1-GABAA receptor. Tryptophan mutagenesis was used to identify specific interactions. Allopregnanolone (3α-OH neurosteroid) was shown to bind at intersubunit and intrasubunit sites with equal affinity, whereas epi-allopregnanolone (3β-OH neurosteroid) binds at the intrasubunit site. MQ290 formed a strong FRET pair with W246, acting as a site-specific probe for the intersubunit site. The affinity and site-specificity of several neurosteroid agonists and inverse agonists was measured using the MQ290 binding assay. The FRET assay distinguishes between competitive and allosteric inhibition of MQ290 binding and demonstrated an allosteric interaction between the two neurosteroid binding sites. The affinity and specificity of neurosteroid binding to two sites in the ELIC-α1GABAAR were directly measured and an allosteric interaction between the sites was revealed. Adaptation of the MQ290 FRET assay to a plate-reader format will enable screening for high affinity agonists and antagonists for neurosteroid binding sites.

Structure modeling-based characterization of ChnD, the 6-hydroxyhexanoate dehydrogenase from Acinetobacter sp. strain NCIMB 9871

α,ω-Dicarboxylic acids, ω-aminoalkanoic acids, and α,ω-diaminoalkanes are valuable building blocks for the production of biopolyesters and biopolyamides. One of the key steps in producing these chemicals is the oxidation of ω-hydroxycarboxylic acids using alcohol dehydrogenases (e.g., ChnD of Acinetobacter sp. NCIMB 9871). However, the reaction and structural features of these enzymes remain mostly undiscovered. Thereby, we have investigated characteristics of ChnD based on enzyme kinetics, substrate-docking simulations, and mutation studies. Kinetic analysis revealed a distinct preference of ChnD for medium chain ω-hydroxycarboxylic acids, with the highest catalytic efficiency of 18.0 mM−1s−1 for 12-hydroxydodecanoic acid among C6 to C12 ω-hydroxycarboxylic acids. The high catalytic efficiency was attributed to the positive interactions between the carboxyl group of the substrates and the guanidino group of two arginine residues (i.e., Arg62 and Arg266) in the substrate binding site. The ChnD_R62L variant showed the increased efficiency and affinity, particularly for fatty alcohols (i.e., C6–C10) and branched-chain fatty alcohols, such as 3-methyl-2-buten-1-ol. Overall, this study contributes to the deeper understanding of medium-chain primary aliphatic alcohol dehydrogenases and their applications for the production of industrially relevant chemicals such as α,ω-dicarboxylic acids, ω-aminoalkanoic acids, and α,ω-diaminoalkanes from renewable biomass.

Modulation of Human Acetylthiocholine Esterase Activity by Novel Fused Pyrimidine Derivatives: In vitro, Theoretical and ADMET Studies

Pyrimidine compounds have medicinal and biological activities as previously reported. In this work, two novel fused pyrimidine compounds were synthesized, fused pyrazolo–pyrimidine compound was synthesized by cyclization of 5-amino-4-cyano-1-phenyl pyrazole with propionic acid in the presence of POCl3, and the other fused pyrrole–pyrano-pyrimidine compound was synthesized by cyclization of ethyl(E)-N-(3-cyano-4-(4-(dimethylamino)phenyl)-7-methyl-4,5,6,7-tetrahydropyrano[2,3-b] pyrrole-2-yl) formimidate with hydrazine hydrate, in methanol. These fused pyrimidine compounds were characterized by FT-IR and 1H NMR. The effect of these compounds was studied on the activity of the human neurotransmission enzyme acetylthiocholine esterase AChE. Results indicated that these compounds significantly inhibited AChE activity at concentrations of 10-11 M. Michalis-Menton showed mixed noncompetitive inhibition of AChE activity. In conclusion, newly synthesized compounds could be promising derivatives for enhancing cholinergic neurotransmission. Among the other derivatives, derivative 4 formed H-bond interactions with key amino acid residues Tyr334, and Asp72, whereas the other electrostatic interactions formed with Tyr334, Phe330, Ile287, Tyr121, Arg289, Trp279, Gly335, and Phe288. In the case of derivatives 9, similar binding interactions with active pockets of 2ACE were observed due to the high homology of the binding site residues. In addition, we examined ADMET properties with the help of online databases to search for possible drug similarity of synthesized compounds 4 and 9 and revealed that both molecules were compatible with Lipinski's five rules.

Computational Investigation of Bioactive Phytoconstituents as SarS-Cov-2 Main Protease Inhibitors Through Molecular Docking and Interaction Fingerprint Studies

Since 2019, the SARS-CoV-2 infection has continued to cause significant human suffering. Numerous investigations into the viral pathogenesis have led to converging conclusions on how the virus enters and spreads within the host. The main protease (Mpro) of coronaviruses has been considered as an attractive therapeutic target because of its important role in processing polyproteins translated from viral RNA. Many studies discovered that phytoconstituents possess potent antiviral activities. Hence, in the present work, 439 co-crystal ligands of SARS-CoV-2 Mpro were collected and docked with Mpro of SARS-CoV-2 (PDB ID:7AEH) to identify best crystal ligand. Among all the crystal ligands collected, HF0 (7-O-methyl-dihydromyricetin) showed good XP G score -7.872 Kcal/Mol and it was selected as reference to compare the docking scores of phytoconstituents. Then, molecular docking study was performed for 274 antiviral phytoconstituents from various medicinal plants against Mpro of SARS-CoV-2. Molecular docking studies found that seven phytoconstituents exhibited better docking scores than best co-crystal ligand HF0. Among the seven best docked phytoconstituents, 3,4-dicaffeoylquinic acid showed good interactions with key amino acid residues in substrate binding site of Mpro with XPG Score –9.721 Kcal/Mol. Qikprop results indicated that the most phytoconstituents have demonstrated favourable pharmacological characteristics. Interaction fingerprint analysis revealed that all the seven best docked phytoconstituents of the present study bound to Glu166, key residue situated in the centre of the substrate binding site of Mpro resulting in the reduction of the catalytic activity of main protease thus blocking the replication of SARS-CoV-2.

Molecular Mechanisms of the Impaired Heparin Pentasaccharide Interactions in 10 Antithrombin Heparin Binding Site Mutants Revealed by Enhanced Sampling Molecular Dynamics.

Antithrombin (AT) is a critical regulator of the coagulation cascade by inhibiting multiple coagulation factors including thrombin and FXa. Binding of heparinoids to this serpin enhances the inhibition considerably. Mutations located in the heparin binding site of AT result in thrombophilia in affected individuals. Our aim was to study 10 antithrombin mutations known to affect their heparin binding in a heparin pentasaccharide bound state using two molecular dynamics (MD) based methods providing enhanced sampling, GaMD and LiGaMD2. The latter provides an additional boost to the ligand and the most important binding site residues. From our GaMD simulations we were able to identify four variants (three affecting amino acid Arg47 and one affecting Lys114) that have a particularly large effect on binding. The additional acceleration provided by LiGaMD2 allowed us to study the consequences of several other mutants including those affecting Arg13 and Arg129. We were able to identify several conformational types by cluster analysis. Analysis of the simulation trajectories revealed the causes of the impaired pentasaccharide binding including pentasaccharide subunit conformational changes and altered allosteric pathways in the AT protein. Our results provide insights into the effects of AT mutations interfering with heparin binding at an atomic level and can facilitate the design or interpretation of in vitro experiments.

Two residues in the DNA binding site of Pif1 helicase are essential for nuclear functions but dispensable for mitochondrial respiratory growth.

Pif1 helicase functions in both the nucleus and mitochondria. Pif1 tightly couples ATP hydrolysis, single-stranded DNA translocation, and duplex DNA unwinding. We investigated two Pif1 variants (F723A and T464A) that have each lost one site of interaction of the protein with the DNA substrate. Both variants exhibit minor reductions in affinity for DNA and ATP hydrolysis but have impaired DNA unwinding activity. However, these variants translocate on single-stranded DNA faster than the wildtype enzyme and can slide on the DNA substrate in an ATP-independent manner. This suggests they have lost their grip on the DNA, interfering with coupling ATP hydrolysis to translocation and unwinding. Yeast expressing these variants have increased gross chromosomal rearrangements, increased telomere length, and can overcome the lethality of dna2Δ, similar to phenotypes of yeast lacking Pif1. However, unlike pif1Δ mutants, they are viable on glycerol containing media and maintain similar mitochondrial DNA copy numbers as Pif1 wildtype. Overall, our data indicate that a tight grip of the trailing edge of the Pif1 enzyme on the DNA couples ATP hydrolysis to DNA translocation and DNA unwinding. This tight grip appears to be essential for the Pif1 nuclear functions tested but is dispensable for mitochondrial respiratory growth.

Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics.

We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.