Inhibitors against New Delhi metallo-betalactamase-1 (NDM-1) and its variants endemic in Indian settings along with the laboratory functional gain mutant of NDM-1

PURPOSE

The emergence of NDM-1 producing bacteria has become common in both hospital and community settings, but no inhibitor has yet been available for clinical treatment. Hence, demanding the urgent need of NDM-1 inhibitors, we initiated to screen broad spectrum inhibitors against NDM natural variants and laboratory mutant.

METHODS

We used docking and molecular dynamics simulations, in silico pharmacokinetic investigations, and density functional theory calculation to characterize molecules. Furthermore, an in vitro study, including MIC, kinetics, and fluorescence study were carried out to confirm the efficacies of the selected compounds.

RESULTS

According to the findings of the computational studies, three compounds were effective against NDM variants. Fourfold reduction in MIC of imipenem and meropenem was observed when combined with inhibitors (D2573, D2148, and D63) against blaNDM-1, blaNDM-4, blaNDM-6, and blaNDM-1Q123A, while twofold reduction in MIC of imipenem and meropenem was observed against blaNDM-5 and blaNDM-7. Similarly in the presence of inhibitors (D2573, D2148, and D63) the efficiency of nitrocefin hydrolysis by NDM-4, NDM-6, and Q123A decreases to much more extent as compared to NDM-5 and NDM-7. These results showed that the efficacy of these broad spectrum inhibitors decreases with increasing resistance of NDM variants.

CONCLUSION

This is the first time inhibitors were tested against different NDM natural variants which are endemic in Indian settings. Moreover, a functional gain laboratory mutant was also checked for their efficacies. We may propose these molecules for the pre-clinical trial to further translate.

Mechanistic Approach of Effective Combination of Antibiotics Against Clinical Bacterial Strains Having New Delhi Metallo-Beta-Lactamase Variants and Functional Gain Laboratory Mutant

Antimicrobial resistance has emerged as a serious issue for physicians and health-care workers treating infections that could lead to the next pandemic. One of the key resistance mechanisms is beta-lactamases. Although several beta-lactamase inhibitors in combination with antibiotics have been created and are being utilized in clinical settings, resistance to these formulations has also been evolving in the bacterial population due to their distinct targets. In this study we used effective combination of antibiotic as an approach to inhibit multidrug resistance bacteria. We used four combinations and checked its efficacy against NDM (New Delhi Metallo-beta-lactamase) variants and functional gain laboratory mutant by employing FICI, enzyme kinetics, fluorescence and computational biology approaches (Docking and Molecular Dynamics Simulation). FICI values of all the combinations were either less than 0.5 or equal to 0.5. Binding features acquired by spectroscopic techniques showed important interaction and complex formation between drugs and enzymes with decreased ksv and kq values. In steady-state kinetics, a reduction in hydrolytic efficiency of enzymes was shown by cooperative binding behaviour when they were treated with different drugs. We have also tested functional gain laboratory mutant developed in our lab, keeping in view that if in future upcoming variants of this kind be emerged then these mutants could also be subsided by combinational therapy. This study identifies three other combinations better than fluoroquinolones effective against NDM variants and laboratory mutant.

Enhancement in chaperone activity of human αA-crystallin by nanochaperone gold nanoparticles: Multispectroscopic studies on their molecular interactions

The chaperone activity of human αA-crystallin (HAA) against aggregation of human γD-crystallin (HGD) was enhanced by gold nanoparticles (AuNPs). Chaperone activity of HAA was almost doubled in the presence of 5.5 nM gold nanoparticles (AuNPs). To decipher this effect at molecular level, interactions between HAA and AuNPs were studied using fluorescence and circular dichroism spectroscopic techniques. The nanoparticles were synthesized and characterized by using TEM and dynamic light scattering (DLS). TEM and DLS studies revealed that bioconjugation of AuNPs with HAA did not cause any significant change in the size of the nanoparticles. AuNPs had caused static quenching of tryptophan (Trp) fluorescence, which was confirmed through determination of excited state lifetime of Trp residue of HAA in absence and the presence of AuNPs. The association and quenching constant for HAA-AuNPs conjugation were ∼ 10⁹ M^-1. Hydrogen bonding and van der Waals interactions were found to be involved in HAA-AuNPs complex. Polarity of Trp microenvironment in HAA was not perturbed by AuNPs as supported by synchronous and three-dimensional fluorescence spectroscopy. Far-UV CD spectra suggested that the secondary structure of HAA was not significantly affected by AuNPs.

Broad-Spectrum Inhibitors against Class A, B, and C Type β-Lactamases to Block the Hydrolysis against Antibiotics: Kinetics and Structural Characterization

The emergence of antibiotic resistance has led to a global crisis for the physician to handle infection control issues. All antibiotics, including colistin, have lost efficiency against emerging drug-resistant bacterial strains due to the production of metallo-β-lactamases (MBLs) and serine-β-lactamases (SBLs). Therefore, it is of the utmost importance to design inhibitors against these enzymes to block the hydrolytic action against antibiotics being used. Although various novel β-lactamase inhibitors are being authorized or are under clinical studies, the coverage of their activity spectrum does not include MDR organisms expressing multiple classes of β-lactamases at a single time. This study reports three novel broad-spectrum inhibitors effective against both SBLs and MBLs. Virtual screening, molecular docking, molecular dynamics simulations, and an in silico pharmacokinetic study were performed to identify the lead molecules with broad-spectrum ability to inhibit the hydrolysis of β-lactam. The selected compounds were further assessed by in vitro cell assays (MIC, 50% inhibitory concentration [IC₅₀], kinetics, and fluorescence against class A, B, and C type β-lactamases) to confirm their efficacies. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay was performed to check the toxicity of screened lead molecules. All three selected inhibitors were found to reduce MIC and showed good affinity against all the SBLs and MBLs produced by class A, B, and C type β-lactamases. These nontoxic novel non-β-lactam broad-spectrum inhibitors bind to the active site residues of selected β-lactamases, which are crucial for β-lactam antibiotic hydrolysis. These inhibitors may be proposed as a future drug candidate in combination with antibiotics as a single formulation to control infection caused by resistant strains. Hence, this study plays a significant role in the cure of infections caused by antibiotic-resistant bacteria.

IMPORTANCE Several inhibitors for usage in conjunction with antibiotics have been developed. However, to date, there is no commercially available broad-spectrum β-lactamase inhibitor that targets both MBLs and SBLs. Here, we showed three novel broad-spectrum inhibitors with promising results through computational techniques and in vitro studies. These inhibitors are effective against both SBLs and MBLs and hence could be used as future drug candidates to treat infections caused by multidrug-resistant bacteria producing both types of enzymes (SBLs and MBLs).

Chemically synthesised flavone and coumarin based isoxazole derivatives as broad spectrum inhibitors of serine β-lactamases and metallo-β-lactamases: a computational, biophysical and biochemical study

The β-lactam antibiotics are the most effective medicines for treating bacterial infections. Resistance to them, particularly through the production of β-lactamases, which can hydrolyse all kinds of β-lactams, poses a threat to their continued use. The synthesised flavone and coumarin based isoxazole derivatives have the potential to be used as broad-spectrum inhibitors of the mechanistically different serine-(SBL) and metallo-β-lactamases (MBL). The synthesised compounds were discovered as potent β-lactamase inhibitors using molecular docking and in silico pharmacokinetic analysis. We studied the binding of chemically synthesised inhibitors to clinically significant β-lactamases of class A, B, and C using biophysical and biochemical approaches, and computational analyses. These molecules follow Lipinski's rule of five and have acceptable solubility, permeability, and oral bioavailability. These molecules were found to be non-toxic and non-carcinogenic. MIC results suggest that these molecules restore the antibiotic efficacy against class A, B, and C β-lactamases. Kinetics data showed that these molecules reduce the catalytic efficiency of clinically relevant class A, B, and C β-lactamases. Fluorescence study showed significant interaction between these flavone-/coumarin-based isoxazole derivatives and class A/B/ C β-lactamases. This study showed promising effect of these new generation compounds as broad spectrum β-lactamase inhibitors of both SBLs and MBLs.Communicated by Ramaswamy H. Sarma.

Multispectroscopic studies on the molecular interactions between bovine gamma-globulin and borohydride-capped silver nanoparticles

Interactions between bovine gamma-globulin (BGG) and borohydride-capped silver nanoparticles (BAgNPs) were studied using dynamic light scattering and spectroscopic techniques like UV-Vis, fluorescence and circular dichroism. The results were compared with earlier reported^[1] interactions between γ-globulin and citrate-coated AgNPs (CAgNPs). BAgNPs were synthesized and characterized. Irrespective of the coating on AgNPs, nanoparticles had formed ground state complexes with the protein. CAgNPs as well as BAgNPS had caused static quenching of tryptophan (Trp) fluorescence of the protein. The change in the capping agent from citrate to borohydride weakened the binding of nanoparticles with the protein. But the same change in capping agent had increased the- fluorescence quenching efficiency of AgNPs. Hydrogen bonding and van der Waals interactions were involved in BGG-BAgNPs complex similar to the CAgNPs complex with γ-globulin. Polarity of the Trp microenvironment in BGG was not altered by BAgNPs contrary to CAgNPs as supported by synchronous and three-dimensional fluorescence. Resonance light scattering experiment also suggested nano-bio conjugation. Far-UV and near-UV CD spectra respectively pointed towards changes in the secondary and tertiary structure of BGG by BAgNPs, which was not observed in case of CAgNPs.

Probing heat and oxidation induced conformational changes of molecular chaperone artemin by excitation-emission fluorescence spectroscopy

Artemin is a potent molecular chaperone, which protects Artemia embryos undergoing encystment against extreme environmental stresses. In the present work, we have examined the structural changes of artemin from A. urmiana upon exposure to oxidant and heat, by using CD measurements as well as excitation-emission fluorescence spectroscopy as a powerful tool for monitoring the conformational transitions and molecular interactions in proteins. We have also provided here the first document on reporting the three dimensional fluorescence spectra of a protein using ANS. Totally, the fluorescence results indicated that the microenvironments of tyrosine and tryptophan residues and the hydrophobic pockets as well as the polypeptide backbone or secondary structure of the chaperone were influenced in responses to heat and H₂O₂ in different degrees. Moreover, the native state of artemin did not induce a considerable exposure of the internal non-polar groups to the solvent. Besides, the excitation-emission spectra of heated artemin by ANS revealed new emission peaks at 430-450 nm when it was excited at 330 nm, which suggests probable exposure of new binding sites for hydrophobic or electrostatic interactions of the protein with ANS. The protein also showed a greater conformational sensitivity to the temperature fluctuations compared to oxidation. Here, we presented some evidence in support of the relation between artemin and its stress dependent activation in vitro and in vivo. This study can expect that the EEM fluorescence spectroscopy could provide a promising tool to study conformational transitions of proteins.

Study on the interaction of ertugliflozin with human serum albumin in vitro by multispectroscopic methods, molecular docking, and molecular dynamics simulation

Ertugliflozin is a potent and selective inhibitor of sodium-dependent glucose cotransporters 2 (SGLT2) and used as a monotherapy to improve glycemic control in adult patients with type 2 diabetes. In this study, ertugliflozin binding to human serum albumin (HSA) was investigated by multispectroscopic and computer simulations. The fluorescence spectra demonstrated that the quenching mechanism of ertugliflozin and HSA was static quenching. Thermodynamic parameters indicated that hydrogen bonding and van der Waals forces played a key role in the binding. Fluorescence competition experiments and molecular docking revealed that ertugliflozin bound to HSA sites II. In three-dimensional fluorescence, circular dichroism spectroscopy, and molecular dynamics simulation, ertugliflozin did not affect the basic skeleton structure of HSA but slightly increased the α-helical structure content and changed the microenvironment around amino acid residues. Results provide valuable information on the basis of the interaction of ertugliflozin with HSA.

Interactions of Bromocarbazoles with Human Serum Albumin Using Spectroscopic Methods

The 1,3,6,8-tetrabromocarbazole and 3-bromocarbazole have attracted great attention in the ecotoxicology field recently as hazardous environmental contaminants. In this study, the quenching mechanism of these two substances binding with human serum albumin (HSA) has been investigated with spectroscopic methods. Through fluorescence quenching and binding site experiments with steady-state fluorescence and UV-Vis spectra, the intrinsic fluorescence of HSA quenched by 1,3,6,8-tetrabromocarbazole and 3-bromocarbazole both in static process, are activated by binding to site II (subdomain IIIA) of the HSA. In addition, it was not only found that the conformation and secondary structure of the proteins changes, but also that their spontaneous binding processes were driven by electrostatic interactions as well as hydrophobic forces for HSA-1,3,6,8-tetrabromocarbazole, and by typical hydrophobic forces for HSA-3-bromocarbazole. The above studies are beneficial to enhance our understanding of the ecotoxicology and environmental behaviors of halogenated carbazoles.

Insights into the interaction mechanism between tiagabine hydrochloride and two serum albumins

Tiagabine hydrochloride (TGB) is a widely used anticonvulsive drug for the treatment of epilepsy. To better understand the interactions of TGB with plasma proteins, human serum albumin (HSA) and bovine serum albumin (BSA) were selected as model proteins. TGB slightly increased thermal stability of the proteins as confirmed by VP-capillary differential scanning calorimetric (DSC) measurements. Isothermal titration calorimeter (ITC) results showed that TGB could be combined with HSA and BSA moderately, which was also corroborated by fluorescence analysis. Besides, the thermodynamic parameters (ΔH > 0, ΔS > 0) indicated that hydrophobic forces played a major role in the formulation of TGB-HSA and TGB-BSA complexes. Moreover, the main binding sites of TGB to HSA and BSA were also examined by classical fluorescent probe (dansylsarcosine and dansylamide) experiments, showing that TGB and dansylsarcosine competitively interacted with HSA and BSA at the same binding sites. Additionally, TGB had no obvious effect on the conformation change of HSA and BSA as indicated by spectroscopic analyses. This study provides useful information about the interaction mechanism of TGB and serum albumins, which could help to better utilize TGB in biomedical field.

Comparative investigation of binding interactions between three steroidal compounds and human serum albumin: Multispectroscopic and molecular modeling techniques

Steroidal compounds have attracted great attentions in biomedical and pharmacological areas. The investigation of structural influences during protein-compound interactions helps in understanding both the biological effects and the mechanism behind bioactivities of steroidal compounds. Herein, the structural influences of three steroidal complexes were investigated based on their binding interactions with human serum albumin (HSA) by multispectroscopic methods and molecular modeling techniques. Three steroidal compounds bonded with HSA to form three HSA-compound complexes, and van der Waals force and hydrogen bond played major roles in stabilizing these complexes. Detailed binding conformation of three steroidal compounds and HSA was further investigated by molecular modeling techniques. The changes of microenvironments and conformations of HSA were significant and the biological activity of HSA was weakened in the present of three steroidal compounds. The space steric hindrance was responsible for differences in the binding interactions between HSA and three steroidal compounds. These results provided the molecular understanding of binding interactions of protein with steroidal compounds and the strategy for research of structural influences.

Potential inhibitors designed against NDM-1 type metallo-β-lactamases: an attempt to enhance efficacies of antibiotics against multi-drug-resistant bacteria

NDM-1 and its variants are the most prevalent types of metallo-β-lactamases, hydrolyze almost all antibiotics of β-lactam group leading to multiple-drug resistance in bacteria. No inhibitor has yet been obtained for NDM-1 or other class of metallo-β-lactamases. Therefore, strategies to identify novel anti-β-lactamase agents with specific mechanisms of action are the need of an hour. In this study, we have reported the discovery of novel non-β-lactam inhibitors against NDM-1 by multi-step virtual screening approach. The potential for virtually screened drugs was estimated through in vitro cell assays. Five chemical compounds were finally purchased and evaluated experimentally for their efficacies to inhibit NDM-1 producing bacterial cells, in vitro. The dissociation constants (Kd), association constant (Ka), stoichiometry (n) and binding energies (ΔG) of compounds with the respective targets were determined using isothermal titration calorimetry (ITC). Molecular dynamic simulation carried out for 25 ns revealed that these complexes were stable throughout the simulation with relative RMSD in acceptable range. Moreover, Microbiological and kinetic studies further confirmed high efficacies of these inhibitors by reducing the minimum inhibitory concentration (MIC) and catalysis of antibiotics by β-lactamases in the presence of inhibitors. Therefore, we conclude that these potential inhibitors may be used as lead molecules for future drug candidates.

Investigation on the interaction of antibacterial drug moxifloxacin hydrochloride with human serum albumin using multi-spectroscopic approaches, molecular docking and dynamical simulation

Investigating the interactions of moxifloxacin hydrochloride with human serum albuminviamulti-spectroscopic approaches, molecular docking and dynamical simulation.

Synthesis and study on the binding of thiazol-2(3H)-ylidine derivative with human serum albumin using spectroscopic and molecular docking methods

In this article, a facile and convenient synthesis of thiazol-2(3H)-ylidine derivatives of fatty acid (3a-c) is described. The binding of N'-(4,5-dimethyl-3-penylthiazol-2(3H)-ylidine)octadec-9-enehydrazide (3a) with human serum albumin (HSA) is explored using various spectral methods and molecular docking. Fluorescence quenching results show that 3a induces conformational changes in HSA and the polarity around the tryptophan residues is increased. Stern-Volmer quenching plots at different temperatures (298, 305 and 312 K) show that the fluorescence quenching mechanism is static quenching. Synchronous fluorescence, 3D fluorescence spectra, circular dichroism and Fourier transform infrared spectroscopy are used to determine the structural change in HSA on interaction with 3a. Förster resonance energy transfer analysis shows that the binding distance (r₀  = 2.78 nm) between HSA (Trp214) and 3a is within the of range 2-8 nm for quenching to occur. The molecular docking study also confirms that 3a is located in subdomain IIA (site I) of HSA and is stabilized by hydrogen bonding and hydrophobic forces.

The binding properties of metandienone and human serum albumin by comparing with other five similar compounds

Metandienone (MET) is an exogenous anabolic androgenic steroid. The interaction between MET and human serum albumin (HSA) was investigated by molecular modeling and different optical techniques. There was no possibility of energy transfer, and the fluorescence quenching of HSA induced by MET was mainly due to the complex formation. The differences of binding ability between MET and compounds 1-5 were significantly caused by space steric hindrance. The single crystallographic data of two steroids (compounds 4 and 5) were obtained in the methanol at the first time. In addition, the binding ability was slightly affected by -OH, -CH₃ , and -COCH₃ . The results of displacement experiment demonstrated that the MET binding site was mainly located in site 1 of HSA. H-bonding and van der Waals forces were significant in the MET-HSA binding. MET played an insignificant role on the local conformation change in HSA.

Multispectroscopic Investigation of the Interaction Between two Ruthenium(II) Arene Complexes of Curcumin Analogs and Human Serum Albumin

The interaction between two ruthenium(II) arene complexes of curcumin analogs and human serum albumin (HSA) was systematically investigated by multispectroscopic techniques. The fluorescence spectral results indicated that two complexes quenched the intrinsic fluorescence of HSA through static quenching mode. The quenching constants and the corresponding thermodynamic parameters at different temperatures were calculated. The binding interactions of two complexes with HSA resulted in the complex formation of complex-HSA, and the van der Waals interactions and hydrogen bond interactions played major roles in the complex stabilization. The distances between HSA and two complexes were obtained according to fluorescence resonance energy transfer theory. The site competitive replacement experiments illustrated that two complexes mainly bounded with HSA on site I. The results of synchronous fluorescence spectra, three-dimensional fluorescence spectra, FT-IR spectra, and circular dichroism spectra indicated that the secondary structure of HSA was changed at the present of two complexes. The results of mass spectrometry further validated the binding interaction and the binding number between two complexes and HSA.

In vitro interaction investigation between three Ru(ii) arene complexes and human serum albumin: structural influences

In vitro interactions between three Ru(ii) arene complexes and human serum albumin were systematically investigated by multi-spectroscopic techniques.

Exploring the thermodynamics and conformational aspects of nicotinic acid binding with bovine serum albumin: a detailed calorimetric, spectroscopic and molecular docking study

An attempt to obtain a physicochemical and conformational outlook on the binding interaction of vitamin B₃ (NA) with a model transport protein BSA using calorimetry, light scattering, molecular docking, and spectroscopic techniques.

Determination of potential main sites of apixaban binding in human serum albumin by combined spectroscopic and docking investigations

Probing apixaban binding to human serum albumin: combining spectroscopic methods and docking investigations.

Insights into the fatty acid ester norethisterone enanthate binding to human albumin: fluorescence, circular dichroism, and docking investigations

Fatty acid ester norethisterone enanthate binding to human albumin.

Combined spectroscopy and cyclic voltammetry investigates the interaction between [(η6-p-cymene)Ru(benzaldehyde-N(4)-phenylthiosemicarbazone)Cl]Cl anticancer drug and human serum albumin

The interaction between Ru anticancer drug and HSA was investigated systematically under physiological conditions.