RESUMO
The FMN riboswitch is a novel drug target for the design of new antibiotics, and efforts have been made to design new charged and uncharged ligands. Uncharged ligands have shown advantages of not requiring any transporter for intracellular transport or proteins for their phosphorylation. 5FDQD (5-(3-(4-fluorophenyl)butyl)-7,8-dimethylpyrido(3,4-b)quinoxaline-1,3(2H,5H)-dione) is a recently reported neutral ligand for the FMN riboswitch active against Clostridium difficile infection in mice. However, the crystal structure of the 5FDQD bound FMN riboswitch is not available, and the mechanism of ligand binding and triggering the function of the riboswitch is not well understood. We have examined 5FDQD for its binding affinity with the FMN riboswitch using the well-tempered metadynamics (WT-MtD) simulation technique. The crystal structure of the FMN riboswitch shows that the FMN interacts with the J4/5 region through the phosphate group with G62; however, the uncharged ligands take advantage of π-π stacking interactions with the same residue of the riboswitch observed from the WT-MtD simulation results. The simulation results show that the presence of fluorine on the phenyl ring in 5FDQD is important to enhance the binding affinity of the neutral ligands with the FMN riboswitch. The WT-MtD results showed that the 1,2-difluoro substitution on the phenyl ring in 5FDQD (FMN-difluoro2) and the 1,3 positions in the phenyl ring (FMN-difluoro1) showed weaker binding energy with the FMN riboswitch compared to 5FDQD. The substitution of another fluorine atom at the 5-position of the phenyl ring (FMN-trifluoro) showed a comparable binding affinity (â¼-31.4 kcal mol-1) to 5FDQD. Electron-donating substitution on the phenyl ring such as the amino group also lowered the binding affinity (-28.8 kcal mol-1) with the riboswitch compared to 5FDQD. The computed results suggest that the position and nature of substitution in the phenyl ring of the uncharged ligands affect the overall binding and such a delicate balance is important to achieve superior binding affinity with the FMN riboswitch.
RESUMO
Synthesis of linearly fused aromatic systems using a glycal-based diene with an aryne is a long-standing topic of interest in glycal chemistry. We have examined the mechanistic pathways for the transformation of substituted glycals to chiral fused aromatic cores via Diels-Alder (DA) reaction using the SMDACN-M06-2X/6-31G(d) level of theory. The DA reactions of E (1a) and Z (1a') forms of C-2 alkenyl glycal and an aryl glycal (1b) as a diene were examined with a benzyne intermediate generated as a dienophile. The computational results reveal that 1a and 1b can only be transformed into the fused aromatic cores by the base-catalyzed reaction because a [1,5] sigmatropic hydrogen shift is not feasible. The activation free energy barrier for the base-catalyzed proton abstraction process is 4.2 kcal mol-1 and there is almost no barrier for stereoisomeric 1a DA-complexes. The activation free energy barrier values for stereoisomeric 1b DA-complexes for the base-catalyzed proton abstraction process are 10.8 and 12.4 kcal mol-1. The appropriate orientation of glycal-ring-oxygen and hydrogen at the 5th position of Z (1a') forms of C-2 alkenyl glycal facilitates the [1,5] sigmatropic hydrogen shift; however, the base-catalyzed reaction is energetically more favored than the former case. The rate-determining step for 1a and 1a' is the ring-opening step (18.2 and 19.5 kcal mol-1 for the S-stereoisomer), whereas the DA adduct formation step is the rate-determining step for 1b (16.1 kcal mol-1 for the S-stereoisomer). The structural analysis reveals the formation of the preferred S-stereoisomer over the R-stereoisomer with the respective dienes.
RESUMO
The hydrogen, carbon dioxide, and carbon monoxide gas adsorption and storage capacity of lithium-decorated cyclopropane ring systems were examined with quantum chemical calculations at density functional theory, DFT M06-2X functional using 6-31G(d) and cc-pVDZ basis sets. To examine the reliability of M06-2X DFT functional, a few representative systems are also examined with complete basis set CBS-QB3 method and CCSD-aug-cc-pVTZ level of theory. The cyclopropane systems can bind to one Li+ ion; however, the corresponding the methylated systems can bind with two Li+ ions. The cyclopropane systems can adsorb six hydrogen molecules with an average binding energy of 3.8 kcal/mol. The binding free energy (ΔG) values suggest that the hydrogen adsorption process is feasible at 273.15 K. The calculation of desorption energies indicates the recyclable property of gas adsorbed complexes. The same number of CO2 and CO gas molecules can also be adsorbed with an average binding energy of -14.4 kcal/mol and -10.7 kcal/mol, respectively. The carbon dioxide showed ~3-4 kcal/mol better binding energy as compared to carbon monoxide and hence such designed systems can function as a potential candidate for the separation of these flue gas molecules. The nature of interactions in complexes was examined with atoms in molecules analysis revealed the electrostatic nature for the interaction of Li+ ion with cyclopropane rings. The chemical hardness and electrophilicity calculations showed that the gas adsorbed complexes are rigid and therefore robust as gas storage materials.
RESUMO
The electronic structure of hexasilaprismane (HSP) was examined with different computational techniques to elucidate the bonding features and the electrostatic surface potential of HSP. The carbon dioxide adsorption and separation capacities of metal-ion-decorated hexasilaprismane (HSP) were examined with DFT and CBS-QB3. Furthermore, the 1,2,3,4,5,6-hexaphenylprismasilane (HPPS) molecule was examined for its binding with metal ions and gas adsorption capacity. The Mg2+ ion complexed HPPS molecule adsorbs 15CO2 molecules with an average binding free energy of -0.98 eV per molecule. The calculated gravimetric densities of 45.1 and 48.4 wt% show that these systems can be employed for CO2 capture. The substantial difference in the affinity of the designed systems for CO2 gas molecules compared to N2 and CH4 molecules show the potential of the systems for CO2 separation from N2 and CH4 gas molecules.
RESUMO
During the last decade, riboswitches emerged as new small-molecule sensing RNA in bacteria. Thiamine pyrophosphate (TPP) riboswitch is widely distributed and occurs in plants, bacteria, fungi, and archaea. Extensive biochemical, structural, and genetic studies have been carried out to elucidate the recognition mechanism of TPP riboswitches. However, a comprehensive report summarizing all information on recognition principles and newly designed ligands for TPP riboswitch is scarce in the literature. This review gives a comprehensive understanding of the TPP riboswitch's structure, mechanism, and methods applied to design ligands for the TPP riboswitch. The ligand-bound TPP riboswitch was studied with various experimental and theoretical techniques to elucidate the conformational dynamics. The mutation studies shed light on the significance of pyrimidine sensing helix for the binding of ligands. Further, the structure-activity relationship study and fragment-based approach lead to the development of ligands with Kd values at the sub-micromolar level. However, there is a need to design more potent inhibitors for TPP riboswitch for therapeutic applications. The recent advancements in ligand design highlight the TPP riboswitch as a promising target for developing new antibiotics. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Riboswitches Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
Assuntos
Riboswitch , Tiamina Pirofosfato , Tiamina Pirofosfato/química , Tiamina Pirofosfato/genética , Tiamina Pirofosfato/metabolismo , Ligantes , RNA , Conformação de Ácido Nucleico , Antibacterianos/farmacologiaRESUMO
Three new 22-membered polyol macrolides, dactylides A-C (1-3), were isolated from Dactylosporangium aurantiacum ATCC 23491 employing repeated chromatographic separations, and their structures were established based on detailed analysis of NMR and MS data. The relative configurations at the stereocenters were established via vicinal 1H-1H coupling constants, NOE correlations, and by application of Kishi's universal NMR database. In order to get insights into the biosynthetic pathway of 1-3, the genome sequence of the producer strain D. aurantiacum was obtained and the putative biosynthetic gene cluster encoding their biosynthesis was identified through bioinformatic analysis using antiSMASH. Compounds 1-3 showed significant in-vitro antimycobacterial and cytotoxic activity.
Assuntos
Macrolídeos , Micromonosporaceae , Macrolídeos/química , Antibacterianos/química , Espectroscopia de Ressonância MagnéticaRESUMO
The thiamine pyrophosphate (TPP) riboswitch has emerged as the new target for designing new ligands for antibiotic purpose. Binding of the natural ligand TPP to the TPP riboswitch causes downregulation of the genes responsible for its biosynthesis. We have reported the role of π-stacking energy contributions to ligand binding with a TPP riboswitch. In conjunction with the docking study, the higher-level quantum chemical calculations performed with the wB97XD and Def2TZVPP basis set in the aqueous phase revealed that the optimum ring size is crucial to attain the effective binding efficiency of ligands with a TPP riboswitch. The π-stacking energy contributions observed for the ligands studied are largely similar; however, the cases studied with higher π-stacking energies with larger rings have a weaker ability to displace the radiolabeled thiamine from the riboswitch. The EDA and NCI analyses suggest the role of larger dispersive interactions in stabilizing the π-stacking rings. The contribution from hydrogen-bonding interactions of the hydrogen-bond donor groups on the A ring augments the binding affinity of the ligand. This study sheds light on various factors that contribute to the design of new ligands for efficient binding with a TPP riboswitch and inhibition of gene expression.
Assuntos
Riboswitch , Ligantes , Conformação de Ácido Nucleico , Tiamina , Tiamina Pirofosfato/genética , Tiamina Pirofosfato/metabolismo , Tiamina Pirofosfato/farmacologiaRESUMO
Galantamine is one of the approved drugs based on the cholinergic hypothesis for the symptomatic treatment of mild to moderate Alzheimer's disease (AD). The etiology of AD is not fully known; however, the reported cholinergic hypothesis suggests the inadequate synthesis of the neurotransmitter acetylcholine (ACh) is responsible for this disease. The crystal structure of galantamine bound human acetylcholinesterase (hAChE) has been reported; however, the inhibition mechanism of hAChE by galantamine is not well understood. A Well-tempered metadynamics (WTMtD) simulation study has been performed with the crystal structure of galantamine bound hAChE. The reported mechanism for the degradation of ACh is suggested through a proton transfer process from a carboxylic group of Glu334 to the hydroxyl group of Ser203, which attacks ACh for the degradation to acetic acid and choline. Such proton transfer process is lowered in the presence of galantamine due to the separation of catalytic triad inside the gorge of AChE as observed with WTMtD. A docking study has been performed to examine the ACh's binding with the catalytic triad of galantamine bound hAChE. The docking results reveal that the approach of ACh to the catalytic triad is interrupted due to the galantamine's presence in the gorge of the enzyme.
Assuntos
Doença de Alzheimer , Inibidores da Colinesterase , Galantamina , Acetilcolinesterase/metabolismo , Doença de Alzheimer/tratamento farmacológico , Inibidores da Colinesterase/química , Inibidores da Colinesterase/farmacologia , Galantamina/química , Galantamina/farmacologia , Humanos , PrótonsRESUMO
Riboswitches are metabolite sensing aptamer domains present in non-coding regions in RNA and act as gene-regulating elements. Thiamine pyrophosphate (TPP) riboswitch is evolved as a new target for developing antibiotics against many pathogenic bacteria. The earlier reports suggest that the modification of the pyrophosphate group in the ligand molecule can enhance gene expression. In this work, we have examined the binding affinity and efficacy of TPP and two recently reported ligands, CH2-TPP, and CF2-TPP, using Well-tempered metadynamics (WT-MtD) simulations. The experimental in vitro assays show that both TPP and CH2-TPP repress the gene expression to the same extent. The calculated binding energies correlate well with the experimental study and show the same trend of binding affinity of ligands for the TPP riboswitch. The root mean square fluctuation profiles suggest that the CH2-TPP and TPP trigger higher fluctuations in P1 and L3 region, and such fluctuations in the P1 region is involved in the gene regulation process. The metal ion mediated contact of TPP ligand with pyrophosphate binding helix is found to be critical in the gene regulation process. The simulation results corroborate the experimental observations that the role of conformational changes occurring in different riboswitch regions upon ligand binding is essential to repress the gene expression process. This work sheds light on the subtle change in the ligand structure that can induce a more considerable impact on binding affinity and efficacy of ligands with riboswitch.
Assuntos
Riboswitch , Difosfatos , Expressão Gênica , Conformação de Ácido Nucleico , Riboswitch/genética , Tiamina , Tiamina Pirofosfato/metabolismoRESUMO
Selective adsorption of CO2 from flue gas is extremely significant because of its increasing concentration in air and its deleterious effect on the environment. In this work, we have explored metal-ion-bound prismane molecules for selective CO2 adsorption from the flue gas mixture. The Ca2+-bound prismane complex exhibits superior CO2 selectivity and adsorption capacity. The calculated binding energy and molecular electrostatic potential (MESP) analysis showed that the rectangular face of prismane binds strongly with metal ions as compared to its triangular face. The CBS-QB3 and density functional theory-based functional M06-2X/6-311+G(d) calculations show that the prismane molecule can bind to one Li+, K+, Mg2+, and Ca2+ ion with favorable binding energy. The metal-ion-bound prismane complexes have been examined for their CO2, N2, and CH4 adsorption capacity. Prismane-Ca2+ can bind with six CO2 molecules strongly with an average binding energy of -18.1 kcal/mole as compared to six N2 (-12.6) and five CH4 (-13.4) gas molecules. The gravimetric density calculated for the CO2-adsorbed prismane-Ca2+ complex has been found to be 69.1 wt %. The discrete hydrocarbon structure for selective separation of CO2 is rare in the literature and can have potential applications for cost-effective CO2 capture from the flue gas mixture.
RESUMO
Antiviral drug therapy against SARS-CoV-2 is not yet established and posing a serious global health issue. Remdesivir is the first antiviral compound approved by the US FDA for the SARS-CoV-2 treatment for emergency use, targeting RNA-dependent RNA polymerase (RdRp) enzyme. In this work, we have examined the action of remdesivir and other two ligands screened from the library of nucleotide analogues using docking and molecular dynamics (MD) simulation studies. The MD simulations have been performed for all the ligand-bound RdRp complexes for the 30 ns time scale. This is one of the earlier reports to perform the MD simulations studies using the SARS-CoV-2 RdRp crystal structure (PDB ID 7BTF). The MD trajectories were analyzed and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) calculations were performed to calculate the binding free energy. The binding energy data reveal that compound-17 (-59.6 kcal/mol) binds more strongly as compared to compound-8 (-46.3 kcal/mol) and remdesivir (-29.7 kcal/mol) with RdRp. The detailed analysis of trajectories shows that the remdesivir binds in the catalytic site and forms a hydrogen bond with the catalytic residues from 0 to 0.46 ns. Compound-8 binds in the catalytic site but does not form direct hydrogen bonds with catalytic residues. Compound-17 showed the formation of hydrogen bonds with catalytic residues throughout the simulation process. The MD simulation results such as hydrogen bonding, the center of mass distance analysis, snapshots at a different time interval, and binding energy suggest that compound-17 binds strongly with RdRp of SARS-CoV-2 and has the potential to develop as a new antiviral against COVID-19. Further, the frontier molecular orbital analysis and molecular electrostatic potential (MESP) iso-surface analysis using DFT calculations shed light on the superior binding of compound-17 with RdRp compared to remdesivir and compound-8. The computed as well as the experimentally reported pharmacokinetics and toxicity parameters of compound-17 is encouraging and therefore can be one of the potential candidates for the treatment of COVID-19.
Assuntos
Monofosfato de Adenosina/análogos & derivados , Alanina/análogos & derivados , Antivirais/metabolismo , RNA-Polimerase RNA-Dependente de Coronavírus/antagonistas & inibidores , Inibidores Enzimáticos/metabolismo , SARS-CoV-2/enzimologia , Monofosfato de Adenosina/química , Monofosfato de Adenosina/metabolismo , Monofosfato de Adenosina/farmacocinética , Monofosfato de Adenosina/toxicidade , Alanina/química , Alanina/metabolismo , Alanina/farmacocinética , Alanina/toxicidade , Antivirais/química , Antivirais/farmacocinética , Antivirais/toxicidade , Células CACO-2 , Domínio Catalítico , RNA-Polimerase RNA-Dependente de Coronavírus/química , RNA-Polimerase RNA-Dependente de Coronavírus/metabolismo , Teoria da Densidade Funcional , Inibidores Enzimáticos/química , Inibidores Enzimáticos/farmacocinética , Inibidores Enzimáticos/toxicidade , Humanos , Ligação de Hidrogênio , Modelos Químicos , Simulação de Acoplamento Molecular , Simulação de Dinâmica Molecular , Ligação Proteica , TermodinâmicaRESUMO
Antibiotics resistance is becoming a serious problem associated with fatalities and suffering patients. New antibiotics that can target the broader spectrum of cellular processes are warranted. One of the recent approaches in this regard is to target the special type of RNA riboswitches in bacteria. In this report, we have explored the mechanistic pathways of ligand-dependent conformational changes of flavin mononucleotide (FMN) riboswitch using molecular dynamics (MD) simulation studies. Cognate ligands FMN and riboflavin (RBF) have shown very different behavior with FMN riboswitch in terms of their role in the gene regulation process. These two ligands have similar scaffold, except the terminal phosphate group in FMN ligand. The MD simulations reveal that the binding of FMN ligand with the riboswitch does not lead to global folding of structure, rather lead to local changes in riboswitch structure. The binding free energy calculated with molecular mechanics Poisson-Boltzmann surface area method suggests the stronger binding of FMN than RBF to the riboswitch and electrostatic energy contributes chiefly to stabilize the complex. Further, the hydrogen bonding analysis identified the key binding site residues G11, G32, G62 of the riboswitch with FMN and RBF. The critical role of the phosphate group in the FMN ligand for binding with the active site of a riboswitch is also borne out in this study. These results unravel the importance of functional groups in natural ligands on designing newer ligands for FMN riboswitch as new antibiotics in the future.Communicated by Ramaswamy H. Sarma.
Assuntos
Riboswitch , Mononucleotídeo de Flavina/genética , Mononucleotídeo de Flavina/metabolismo , Humanos , Ligantes , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Riboflavina , Riboswitch/genéticaRESUMO
Communicated by Ramaswamy H. Sarma.
Assuntos
Riboswitch , Adenina , Conformação de Ácido Nucleico , Pirimidinonas , Pirróis , Riboswitch/genéticaRESUMO
We report herein detailed structural insights into the ligand recognition modes guiding bromodomain selectivity, enrichment analysis and docking-based database screening for the identification of the FDA-approved drugs that have potential to be the human BRD4 inhibitors. Analysis of multiple X-ray structures prevailed that the lysine-recognition sites are highly conserved, and apparently, the dynamic ZA loop guides the specific ligand-recognition. The protein-ligand interaction profiling revealed that both BRD2 and BRD4 shared hydrophobic interaction of bound ligands with PRO-98/PRO-82, PHE-99/PHE-83, LEU-108/LEU-92 and direct H-bonding with ASN-156/ASN-140 (BRD2/BRD4), while on the other hand the water-mediated H-bonding of bound ligands with PRO-82, GLN-85, PRO-86, VAL-87, ASP-88, LEU-92, TYR-97 and MET-132, and aromatic π-π stacking with TRP-81 prevailed as unique interaction in BRD4, and were not observed in BRD2. Subsequently, through ROC curve analysis, the best enrichment was found with PDB-ID 4QZS of BRD4 structures. Finally, through docking-based database screening study, we found that several drugs have better binding affinity than the control candidate lead (+)-JQ1 (Binding affinity = -7.9 kcal/mol), a well-known BRD4 inhibitor. Among the top-ranked drugs, azelastine, a selective histamine H1 receptor antagonist, showed the best binding affinity of -9.3 kcal/mol and showed interactions with several key residues of the acetyl lysine binding pocket. Azelastine may serve as a promising template for further medicinal chemistry. These insights may serve as basis for structure-based drug design, drug repurposing and the discovery of novel BRD4 inhibitors. Communicated by Ramaswamy H. Sarma.
Assuntos
Proteínas de Ciclo Celular/antagonistas & inibidores , Preparações Farmacêuticas/metabolismo , Proteínas/metabolismo , Fatores de Transcrição/antagonistas & inibidores , Sítios de Ligação , Desenho de Fármacos , Reposicionamento de Medicamentos/métodos , Humanos , Ligantes , Simulação de Acoplamento Molecular/métodos , Simulação de Dinâmica Molecular , Ligação Proteica , Domínios ProteicosRESUMO
Spermine and spermidine serve as the key biomarkers for early-stage cancer diagnosis. This work reports a rapid, highly selective, and noninvasive sensing platform for spermine/spermidine. The hybrid material, developed in this work, has been characterized by UV-vis, IR, powder XRD, SEM, EDX, and rheological studies. Storage modulus (G') and loss modulus (Gâ³) measurements infer that embedding boronic acid integrated coumarin softens the agarose gel fibers at room temperature. Stress resistance measurement and subsequent imaging further confirms the softness of the hybrid hydrogel over pure agarose gel and homogeneous distribution of the dye in the hybrid matrix as well. The soft hydrogel with a limit-of-detection (LOD) value of 6 µM showed a nearly 27-fold fluorescence enhancement for spermine. The hybrid hydrogel matrix can be useful within a wide concentration window (6 µM-2.5 mM spermine). Response time (≤7 s) confirms rapid detection ability of the material. Noninterference from various metal ions, common anions, monosaccharides, nucleobases, and amino acids, particularly, histidine, arginine, lysine, ornithine, glutamine, etc., makes the hybrid hydrogel suitable for the real-time measurement of spermine in human urinary and blood samples. Furthermore, noninterference from other biogenic amines supports the highly selective nature of the hybrid gel. The ability to measure spermine in urinary samples by the probe offers a noninvasive nature of the sensing platform. Overall, we envisioned that the hybrid material formulation would be useful for diagnosing early-stage tumors and assessing the recovery of patients undergoing chemotherapeutic treatment.