Potential molecular mechanisms underlying the ameliorative effect of Cola nitida (Vent.) Schott & Endl. on insulin resistance in rat skeletal muscles

ETHNOPHARMACOLOGICAL RELEVANCE

Cola nitida (Vent.) Schott & Endl. are among the common medicinal plants employed in traditional medicine for treating diabetes and its complications.

AIM OF THE STUDY

The present study investigated the effect of Cola nitida infusion on the expression of key genes involved in insulin signaling vis-à-vis Insulin receptor substrate 1 (IRS-1), tumor protein P53 gene, glucose transporter type 4 (GLUT4), phosphoinositide 3-kinases (PI3K) and B-cell lymphoma-2 (BCL2) in skeletal muscles of type 2 diabetic (T2D) rats.

METHODS

Type 2 diabetic rats were administered C. nitida infusion at low and high doses (150 and 300 mg/kg bodyweight, respectively), while a high dose of the infusion was also administered to a normal toxicological group. Metformin served as the standard antidiabetic drug. The rats were sacrificed at the end of the experimental period. Their psoas muscles were harvested and assayed for the expressions of IRS1, p53, GLUT4, PI3K and BCL2. The studied genes were further subjected to enrichment analysis using the ShinyGO 0.76 online software.

RESULTS

Induction of T2D upregulated the expressions of IRS-1, p53, PI3K and BCL2 in psoas muscles, while concomitantly downregulating GLUT4 expression. These expressions were significantly reversed in type 2 diabetic rats treated with C. nitida infusion, and the results were statistically significant compared to metformin. Gene enrichment analysis revealed that the genes were linked to intrinsic pathways and biological processes involved in insulin resistance. The infusion further improved muscle glucose uptake, ex vivo. Molecular docking and molecular dynamics stimulation of C. nitida infusion phytoconstituents, caffeine and theobromine with IRS-1, p53, GLUT4, PI3K and BCL2 revealed a strong binding affinity as evident by the RMSD and RMSF values.

CONCLUSION

These results indicate the potentials of C. nitida infusion to improve glucose homeostasis in skeletal muscles of type 2 diabetic rats.

Investigation of Simultaneous and Sequential Cooperative Homotropic Inhibitor Binding to the Catalytic Chamber of SARS-CoV-2 RNA-dependent RNA Polymerase (RdRp)

In our previous report, the unique architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp), which harbours two distinctive binding sites, was fully characterized at molecular level. The significant differences in the two binding sites BS1 and BS2 in terms of binding pockets motif, as well as the preferential affinities of eight anti-viral drugs to each of the two binding sites were described. Recent Cryogenic Electron Microscopy (Cryo-EM) studies on the RdRp revealed that two suramin molecules, a SARS-CoV-2 inhibitor, bind to RdRp in two different sites with distinctive interaction landscape. Here, we provide the first account of investigating the combined inhibitor binding to both binding sites, and whether the binding of two inhibitors molecules concurrently is "Cooperative binding" or not. It should be noted that the binding of inhibitors to different sites do not necessary constitute mutually independent events, therefore, we investigated two scenarios to better understand cooperativity: simultaneous binding and sequential binding. It has been demonstrated by binding free energy calculations (MM/PBSA) and piecewise linear potential (PLP) interaction energy analysis that the co-binding of two suramin molecules is not cooperative in nature; rather, when compared to individual binding, both molecules adversely affect one another's binding affinities. This observation appeared to be primarily due to RdRp's rigidity, which prevented both ligands from fitting comfortably within the catalytic chamber. Instead, the suramin molecules showed a tendency to change their orientation within the binding pockets in order to maintain their binding to the protein, but at the expense of the ligand internal energies. Although co-binding resulted in the loss of several important key interactions, a few interactions were conserved, and these appear to be crucial in preserving the binding of ligands in the active site. The structural and mechanistic details of this study will be useful for future research on creating and developing RdRp inhibitors against SARS-CoV-2.

Therapeutic Path to Triple Knockout: Investigating the Pan-inhibitory Mechanisms of AKT, CDK9, and TNKS2 by a novel 2-Phenylquinazolinone derivative in Cancer Therapy- An In-Silico Investigation

BACKGROUND

Blocking the oncogenic Wnt//β-catenin pathway has of late been investigated as a viable therapeutic approach in the treatment of cancer. This involves the multi-targeting of certain members of the tankyrase-kinase family; tankyrase 2 (TNKS2), protein kinase B (AKT), and cyclin-dependent kinase 9 (CDK9), which propagate the oncogenic Wnt/β-catenin signalling pathway.

METHODS

During a recent investigation, the pharmacological activity of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one was repurposed to serve as a 'triple-target' inhibitor of TNKS2, AKT and CDK9. Yet, the molecular mechanism that surrounds its multi-targeting activity remains unanswered. As such, this study aims to explore the pan-inhibitory mechanism of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one towards AKT, CDK9, and TNKS2, using in silico techniques.

RESULTS

Results revealed favourable binding affinities of -34.17 kcal/mol, -28.74 kcal/mol, and -27.30 kcal/mol for 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one towards TNKS2, CDK9, and AKT, respectively. Pan-inhibitory binding of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one is illustrated by close interaction with specific residues on tankyrase-kinase. Structurally, 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one had an impact on the flexibility, solvent-accessible surface area, and stability of all three proteins, which was illustrated by numerous modifications observed in the unbound as well as the bound states of the structures, which evidenced the disruption of their biological function. Prediction of the pharmacokinetics and physicochemical properties of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one further established its inhibitory potential, evidenced by the favourable absorption, metabolism, excretion, and minimal toxicity properties.

CONCLUSION

The following structural insights provide a starting point for understanding the pan-inhibitory activity of 2-(4-aminophenyl)-7-chloro-3H-quinazolin-4-one. Determining the criticality of the interactions that exist between the pyrimidine ring and catalytic residues could offer insight into the structure-based design of innovative tankyrase-kinase inhibitors with enhanced therapeutic effects.

Enzyme-responsive biomimetic solid lipid nanoparticles for antibiotic delivery against hyaluronidase-secreting bacteria

In this work, a potent hyaluronidase inhibitor (ascorbyl stearate (AS)) was successfully employed to design vancomycin-loaded solid lipid nanoparticles (VCM-AS-SLNs) with biomimetic and enzyme-responsive features, to enhance the antibacterial efficacy of vancomycin against bacterial-induced sepsis. The VCM-AS-SLNs prepared were biocompatible and had appropriate physicochemical parameters. The VCM-AS-SLNs showed an excellent binding affinity to the bacterial lipase. The in vitro drug release study showed that the release of the loaded vancomycin was significantly accelerated by the bacterial lipase. The in silico simulations and MST studies confirmed the strong binding affinity of AS and VCM-AS-SLNs to bacterial hyaluronidase compared to its natural substrate. This binding superiority indicates that AS and VCM-AS-SLNs could competitively inhibit the effect of hyaluronidase enzyme, and thus block its virulence action. This hypothesis was further confirmed using the hyaluronidase inhibition assay. The in vitro antibacterial studies against sensitive and resistant Staphylococcus aureus revealed that the VCM-AS-SLNs had a 2-fold lower minimum inhibitory concentration, and a 5-fold MRSA biofilm elimination compared to the free vancomycin. Furthermore, the bactericidal-kinetic showed a 100% bacterial clearance rate within 12 hours of treatment with VCM-AS-SLNs, and less than 50 % eradication after 24 hours for the bare VCM. Therefore, the VCM-AS-SLN shows potential as an innovative multi-functional nanosystem for effective and targeted delivery of antibiotics.

The Unusual Architecture of RNA-Dependent RNA Polymerase (RdRp)'s Catalytic Chamber Provides a Potential Strategy for Combination Therapy against COVID-19

The unusual and interesting architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) was recently explored using Cryogenic Electron Microscopy (Cryo-EM), which revealed the presence of two distinctive binding cavities within the catalytic chamber. In this report, first, we mapped out and fully characterized the variations between the two binding sites, BS1 and BS2, for significant differences in their amino acid architecture, size, volume, and hydrophobicity. This was followed by investigating the preferential binding of eight antiviral agents to each of the two binding sites, BS1 and BS2, to understand the fundamental factors that govern the preferential binding of each drug to each binding site. Results showed that, in general, hydrophobic drugs, such as remdesivir and sofosbuvir, bind better to both binding sites than relatively less hydrophobic drugs, such as alovudine, molnupiravir, zidovudine, favilavir, and ribavirin. However, suramin, which is a highly hydrophobic drug, unexpectedly showed overall weaker binding affinities in both binding sites when compared to other drugs. This unexpected observation may be attributed to its high binding solvation energy, which disfavors overall binding of suramin in both binding sites. On the other hand, hydrophobic drugs displayed higher binding affinities towards BS1 due to its higher hydrophobic architecture when compared to BS2, while less hydrophobic drugs did not show a significant difference in binding affinities in both binding sites. Analysis of binding energy contributions revealed that the most favorable components are the ΔE_ele, ΔE_vdw, and ΔG_gas, whereas ΔG_sol was unfavorable. The ΔE_ele and ΔG_gas for hydrophobic drugs were enough to balance the unfavorable ΔG_sol, leaving the ΔE_vdw to be the most determining factor of the total binding energy. The information presented in this report will provide guidelines for tailoring SARS-CoV-2 inhibitors with enhanced binding profiles.

Revealing the Role of the Arg and Lys in Shifting Paradigm from BTK Selective inhibition to the BTK/HCK Dual inhibition- Delving into the Inhibitory Activity of KIN-8194 Against BTK, and HCK in the Treatment of Mutated 〖BTK〗^Cys481 Waldenström Macroglobulinemia: A computational Approach

BACKGROUND

Despite the early success of Bruton's tyrosine kinase (BTK) inhibitors in the treatment of Waldenström macroglobulinemia (WM), these single-target drug therapies have limitations in their clinical applications, such as drug resistance. Several alternative strategies have been developed, including the use of dual inhibitors, to maximize the therapeutic potential of these drugs.

OBJECTIVE

Recently, the pharmacological activity of KIN-8194 was repurposed to serve as a 'dual-target' inhibitor of BTK and Hematopoietic Cell Kinase (HCK). However, the structural dual inhibitory mechanism remains unexplored, hence the aim of this study.

METHODS

Conducting predictive pharmacokinetic profiling of KIN-8194, as well as demonstrating a comparative structural mechanism of inhibition against the above-mentioned enzymes.

RESULTS

Our results revealed favourable binding affinities of -20.17 kcal/mol, and -35.82 kcal/mol for KIN-8194 towards HCK and BTK, respectively. Catalytic residues Arg137/174 and Lys42/170 in BTK and Arg303 and Lys75/173/244/247 in HCK were identified as crucial mediators of the dual binding mechanism of KIN-8194, corroborated by high per-residue energy contributions and consistent high-affinity interactions of these residues. Prediction of the pharmacokinetics and physicochemical properties of KIN-8194 further established its inhibitory potential, evidenced by the favourable absorption, metabolism, excretion, and minimal toxicity properties. Structurally, KIN-8194 impacted the stability, flexibility, solvent-accessible surface area, and rigidity of BTK and HCK, characterized by various alterations observed in the bound and unbound structures, which proved enough to disrupt their biological function.

CONCLUSION

These structural insights provided a baseline for the understanding of the dual inhibitory activity of KIN-8194. Establishing the cruciality of the interactions between the KIN-8194 and Arg and Lys residues could guide the structure-based design of novel dual BTK/HCK inhibitors with improved therapeutic activities.

The antioxidant and antidiabetic potentials of polyphenolic-rich extracts of Cyperus rotundus (Linn.)

In this study, the rhizome of Cyperus rotundus L was investigated for its antioxidant and antidiabetic effects using in vitro and in silico experimental models. Its crude extracts (ethyl acetate, ethanol and aqueous) were screened in vitro for their antioxidant activity using ferric-reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH), as well as their inhibitory effect on α-glucosidase enzyme. Subsequently, the extracts were subjected to Gas Chromatography-Mass Spectrometry (GC-MS) analysis to elucidate their possible bioactive compounds. Furthermore, computational molecular docking of selected phenolic compounds was conducted to determine their mode of α-glucosidase inhibitory activity. The aqueous extract displayed the highest level of total phenolic content and significantly higher scavenging activity in both FRAP and DPPH assays compared to ethyl acetate and ethanol extracts. In FRAP and DPPH assays, IC₅₀ values of aqueous extract were 448.626 µg/mL and 418.74 µg/mL, respectively. Aqueous extract further presented higher α-glucosidase inhibitory activity with an IC₅₀ value of 383.75 µg/mL. GC-MS analysis revealed the presence of the following phenolic compounds: 4-methyl-2-(2,4,4-trimethylpentan-2-yl) phenol, Phenol,2-methyl-4-(1,1,3,3-tetramethylbutyl)- and 1-ethoxy-2-isopropylbenzene. Molecular docking study revealed 1-ethoxy-2-isopropylbenzene formed two hydrogen bonds with the interacting residues in the active site of α-glucosidase enzyme. Furthermore, 4-methyl-2-(2,4,4-trimethylpentan-2-yl) phenol had the lowest binding energy inferring the best affinity for α-glucosidase active site. These results suggest the possible antioxidant and antidiabetic potential of Cyperus rotundus.Communicated by Ramaswamy H. Sarma.

Battling BTK mutants with noncovalent inhibitors that overcome Cys481 and Thr474 mutations in Waldenström macroglobulinemia therapy: structural mechanistic insights on the role of fenebrutinib

Recently, the non-covalent Bruton tyrosine kinase (BTK) inhibitor fenebrutinib was presented as a therapeutic option with strong inhibitory efficacy against a single (C481S) and double (T474S/C481S) BTK variant in the treatment of Waldenström macroglobulinemia (WM). However, the molecular events surrounding its inhibition mechanism towards this variant remain unresolved. Herein, we employed in silico methods such as molecular dynamic simulation coupled with binding free energy estimations to explore the mechanistic activity of the fenebrutinib on (C481S) and (T474S/C481S) BTK variant, at a molecular level. Our investigations reveal that amino acid arginine contributed immensely to the total binding energy, this establishing the cruciality of amino acid residues, Arg132 and Arg156 in (C481S) and Arg99, Arg137, and Arg132 in (T474S/C481S) in the binding of fenebrutinib towards both BTK variants. The structural orientations of fenebrutinib within the respective hydrophobic pockets allowed favorable interactions with binding site residues, accounting for its superior binding affinity by 24.5% and relative high hydrogen bond formation towards (T474S/C481S) when compared with (C481S) BTK variants. Structurally, fenebrutinib impacted the stability, flexibility, and solvent accessible surface area of both BTK variants, characterized by various alterations observed in the bound and unbound structures, which proved enough to disrupt their biological function. Findings from this study, therefore, provide insights into the inhibitory mechanism of fenebrutinib at the atomistic level and reveal its high selectivity towards BTK variants. These insights could be key in designing and developing BTK mutants' inhibitors to treat Waldenström macroglobulinemia (WM).

Probing Alterations in MDM2 Catalytic Core Structure Effect of Garcinia Mangostana Derivatives: Insight from Molecular Dynamics Simulations

The MDM2-p53 protein-protein interaction is a promising model for researchers to design, study, and discover new anticancer drugs. The design of therapeutically active compounds that can maintain or restore the binding of MDM2 to p53 has been found to limit the oncogenic activities of both. This led to the current development of a group of xanthone-core and cis-imidazoline analogs compounds, among which γ-Mangostin (GM), α-Mangostin (AM), and Nutlin exhibited their MDM2-p53 interaction inhibitory effects. Therefore, in this study, we seek to determine the mechanisms by which these compounds elicit MDM2-p53 interaction targeting. Unique to the binding of GM, AM, and Nutlin, from our findings, they share the same three active site residues Val76, Tyr50, and Gly41, which represent the top active side residues that contribute to high electrostatic energy. Consequently, the free binding energy contributed enormously to the binding of these compounds, which culminated in the high binding affinities of GM, AM, and Nutlin with high values. Furthermore, GM, AM, and Nutlin commonly interrupted the stable and compact conformation of MDM2 coupled with its active site, where Cα deviations were relatively high. We believe that our findings would assist in the design of more potent active anticancer drugs.

Co-Binding of JQ1 and Venetoclax Exhibited Synergetic Inhibitory Effect for Cancer Therapy; Potential Line of Treatment for the Waldenström Macroglobulinemia Lymphoma

In recent times, the development of combination therapy has been a focal point in drug discovery. This article explores the potential synergistic effect of co-administration of Bcl2 inhibitor Venetoclax and BET inhibitor JQ1. We envisioned that the 'dual-site'-binding of Bcl2 has significant prospects and paves the way for the next round of rational design of potent Waldenström macroglobulinemia (WM) therapy. The preferential binding mechanisms of the multi-catalytic sites of the Bcl2 enzyme have been a subject of debate in the literature. This study conducted a systematic procedure to explore the preferred binding modes and the structural effects of co-binding at each catalytic active site. Interestingly, a mutual enhanced binding effect was observed - Venetoclax increased the binding affinity of JQ1 by 11.5 %, while JQ1 boosted the binding affinity of Venetoclax by 16.3 % when compared with individual inhibition of each drug. This synergistic binding effect has significantly increased protein stability, with substantial correlated movements and multiple van der Waals interactions. The structural and thermodynamic insights unveiled in this report would assist the future design of improved combined therapy against WM.

Talazoparib Dual-targeting on Poly (ADP-ribose) Polymerase-1 and -16 Enzymes Offers a Promising Therapeutic Strategy in Small Cell Lung Cancer Therapy: Insight from Biophysical Computations

In recent times, inhibition of poly (ADP-ribose) polymerase (PARP) enzymes by pharmacological drugs has attracted much attention as an anticancer therapy. As reported, PARP-16 has been discovered as a novel anticancer target for small cell lung cancer, and that the inhibition of both PARP-16 and PARP-1 by talazoparib can increase the overall effectiveness of talazoparib in the SCLC treatment. In this study, we employed computational approaches to investigate the differential inhibitory potency of Talazoparib on PARP-1 and PARP-16. Talazoparib has excellent PARP-1 and PARP-16 binding activities, as revealed by the ΔG_bind (total binding energy). Pp16-tpb had binding energy of -34.85 kcal/mol, while pp1-tpb had a binding energy of -26.36 kcal/mol. The binding activity of Talazoparib on both PARP-1 and PARP-16 was significantly influenced by van der Waal and electrostatic interactions. Correspondingly, according to the findings of this study, binding residues with total binding energy greater than 1.00 kcal/mol contributed considerably to the Talazoparib's binding activities on PARP-1 and PARP-16. We believe the findings of this study will pave the way for developing dual targeting of PARP enzymes as a strategy for small-cell lung cancer treatment.

Multi-catalytic Sites Inhibition of Bcl2 Induces Expanding of Hydrophobic Groove: A New Avenue Towards Waldenström Macroglobulinemia Therapy

B-cell lymphoma 2 (Bcl2) is a key protein regulator of apoptosis. The hydrophobic groove in Bcl2 is a unique structural feature to this class of enzymes and found to have a profound impact on protein overall structure, function, and dynamics. Dynamics of the hydrophobic groove is an essential determinant of the catalytic activity of Bcl2, an implicated protein in Waldenström macroglobulinemia (WM). The mobility of α3-α4 helices around the catalytic site of the protein remains crucial to its activity. The preferential binding mechanisms of the multi-catalytic sites of the Bcl2 enzyme have been a subject of debate in the literature. In addition to our previous report on the same protein, herein, we further investigate the preferential binding modes and the conformational implications of Venetoclax-JQ1 dual drug binding at both catalytic active sites of Bcl2. Structural analysis revealed asymmetric α3-α4 helices movement with the expansion of the distance between the α3 and α4 helix in Venetoclax-JQ1 dual inhibition by 15.2% and 26.3%, respectively when compared to JQ1 and Venetoclax individual drug inhibition-resulting in remarkable widening of hydrophobic groove. Moreso, a reciprocal enhanced binding effect was observed: Venetoclax increased the binding affinity of JQ1 by 11.5%, while the JQ1 fostered the binding affinity of Venetoclax by 16.3% compared with individual inhibition of each drug. This divergence has also resulted in higher protein stability, and prominent correlated motions were observed with the least fluctuations and multiple van der Waals interactions. Findings offer vital conformational dynamics and structural mechanisms of enzyme-single ligand and enzyme-dual ligand interactions, which could potentially shift the current therapeutic protocol of Waldenström macroglobulinemia.

Distinguishing the optimal binding mechanism through reversible and irreversible inhibition analysis of HSP72 protein in cancer therapy

Over the past two decades, covalent inhibitors have gained much interest and are living up to their reputation as a powerful tool in drug discovery. Covalent inhibitors possess several significant advantages, including increased biochemical efficiency, prolonged duration and the ability to target shallow, solvent-exposed substrate-binding domains. One of the enzymes that have been both covalently and non-covalently targeted is the heat shock protein 72 (HSP72). This elevated enzyme expression in cancer cells may be responsible for tumorigenesis and tumor progression by providing chemotherapy resistance. A critical gap remains in the molecular understanding of the structural mechanism's covalent and non-covalent binding to HSP72. In this study, we explore the most optimal binding mechanism in the inhibition of the HSP72. Based on the molecular dynamic analyses, it was evident that the non-covalent complex showed more stability than the covalent complex. The covalent ligand, however, was more able to induce and stabilize the sealed conformation of the HSP72-NBD ATP binding domain throughout the. Also, the non-covalent ligand does not induce any significant conformational change as it remained close to the shape of the unbound complex; and the affinity is only dependent on the multiple hydrogen bonds in contrast to the covalent ligand. This is supported by the secondary structure elements and principal component analysis that was more dominant in the covalently inhibited complex. Covalent bond induced the α-helices sealed conformation of the HSP72-NBD; based on our findings, this will prevent other small molecules from interacting at the ATP binding site domain. Moreover, inhibition of the ATP binding domain can directly affect the ATPs protein folding mechanism of the HSP72 enzyme. The essential dynamic analysis presented in this report compliments the binding mechanism of HSP72, establishing covalent inhibition as the preferred method of inhibiting the HSP72 protein. The findings from this study may assist in the design of more target-specific HSP72 covalent inhibitors exploring the surface-exposed lysine residues.

Coupling of HSP72 α-Helix Subdomains by the Unexpected Irreversible Targeting of Lysine-56 over Cysteine-17; Coevolution of Covalent Bonding

Covalent inhibition has recently gained a resurgence of interest in several drug discovery areas. The expansion of this approach is based on evidence elucidating the selectivity and potency of covalent inhibitors when bound to particular amino acids of a biological target. The unexpected covalent inhibition of heat shock protein 72 (HSP72) by covalently targeting Lys-56 instead of Cys-17 was an interesting observation. However, the structural basis and conformational changes associated with this preferential coupling to Lys-56 over Cys-17 remain unclear. To resolve this mystery, we employed structural and dynamic analyses to investigate the structural basis and conformational dynamics associated with the unexpected covalent inhibition. Our analyses reveal that the coupling of the irreversible inhibitor to Lys-56 is intrinsically less dynamic than Cys-17. Conformational dynamics analyses further reveal that the coupling of the inhibitor to Lys-56 induced a closed conformation of the nucleotide-binding subdomain (NBD) α-helices, in contrast, an open conformation was observed in the case of Cys-17. The closed conformation maintained the crucial salt-bridge between Glu-268 and Lys-56 residues, which strengthens the interaction affinity of the inhibitor nearly identical to adenosine triphosphate (ADP/Pi) bound to the HSP72-NBD. The outcome of this report provides a substantial shift in the conventional direction for the design of more potent covalent inhibitors.