The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10.

The mitochondria are responsible for producing energy within the cell, and in mitochondrial myopathy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein called coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), which is found in the mitochondria and is involved in the regulation of mitochondrial function. G58R mutation has been shown to disrupt the normal function of CHCHD10, leading to mitochondrial dysfunction and ultimately to the development of mitochondrial myopathy. The structures of G58R mutant CHCHD10 and how G58R mutation impacts the wild-type CHCHD10 protein at the monomeric level are unknown. To address this problem, we conducted homology modeling, multiple run molecular dynamics simulations and bioinformatics calculations. We represent herein the structural ensemble properties of the G58R mutant CHCHD10 (CHCHD10G58R) in aqueous solution. Moreover, we describe the impacts of G58R mutation on the structural ensembles of wild-type CHCHD10 (CHCHD10WT) in aqueous solution. The dynamics properties as well as structural properties of CHCHD10WT are impacted by the mitochondrial myopathy-related G58R mutation. Specifically, the secondary and tertiary structure properties, root mean square fluctuations, Ramachandran diagrams and results from principal component analysis demonstrate that the CHCHD10WT and CHCHD10G58R proteins possess different structural ensemble characteristics and describe the impacts of G58R mutation on CHCHD10WT. These findings may be helpful for designing new treatments for mitochondrial myopathy.Communicated by Ramaswamy H. Sarma.

Frontotemporal Dementia-Related V57E Mutation Impairs Mitochondrial Function and Alters the Structural Properties of CHCHD10.

The V57E pathological variant of the mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10) plays a role in frontotemporal dementia. The wild-type and V57E mutant CHCHD10 proteins contain intrinsically disordered regions, and therefore, these regions hampered structural characterization of these proteins using conventional experimental tools. For the first time in the literature, we represent that the V57E mutation is pathogenic to mitochondria as it increases mitochondrial superoxide and impairs mitochondrial respiration. In addition, we represent here the structural ensemble properties of the V57E mutant CHCHD10 and describe the impacts of V57E mutation on the structural ensembles of wild-type CHCHD10 in aqueous solution. We conducted experimental and computational studies for this research. Namely, MitoSOX Red staining and Seahorse Mito Stress experiments, atomic force microscopy measurements, bioinformatics, homology modeling, and multiple-run molecular dynamics simulation computational studies were conducted. Our experiments show that the V57E mutation results in mitochondrial dysfunction, and our computational studies present that the structural ensemble properties of wild-type CHCHD10 are impacted by the frontotemporal dementia-associated V57E genetic mutation.

Effects of the Jokela type of spinal muscular atrophy-related G66V mutation on the structural ensemble characteristics of CHCHD10.

The G66V pathological variant of the coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), mitochondrial, plays a role in Jokela type spinal muscular atrophy. The wild-type and G66V mutant-type CHCHD10 proteins contain intrinsically disordered regions, and therefore, their structural ensemble studies have been experiencing difficulties using conventional tools. Here, we show our results regarding the first characterization of the structural ensemble characteristics of the G66V mutant form of CHCHD10 and the first comparison of these characteristics with the structural ensemble properties of wild-type CHCHD10. We find that the structural properties, potential of mean force surfaces, and principal component analysis show stark differences between these two proteins. These results are important for a better pathology, biochemistry and structural biology understanding of CHCHD10 and its G66V genetic variant and it is likely that these reported structural properties are important for designing more efficient treatments for the Jokela type of spinal muscular atrophy disease.

Novel Thioether-Bridged 2,6-Disubstituted and 2,5,6-Trisubstituted Imidazothiadiazole Analogues: Synthesis, Antiproliferative Activity, ADME, and Molecular Docking Studies.

In this study, starting from 2-amino-1,3,4-thiadiazole derivatives (3-5), a new series of 2,6-disubstituted (compounds 7-15) and 2,5,6-trisubstituted (compounds 16-33) imidazo[2,1-b][1,3,4]-thiadiazole derivatives were synthesized using cyclization and Mannich reaction mechanisms, respectively. All synthesized compounds were characterized by 1 H-NMR, 13 C-NMR, FT-IR, elemental analysis, and mass spectroscopy techniques. Also, X-ray diffraction analysis were used for compounds 4, 7, 11, 17, and 19. The cytotoxic effects of the new compounds on the viability of colon cancer cells (DLD-1), lung cancer cells (A549), and liver cancer cells (HepG2) were investigated using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) method in vitro. Compound 15 was found to be the most potent anticancer drug candidate in this series with an IC50 value of 3.63 µM against HepG2 for 48 h. Moreover, the absorption, distribution, metabolism, and excretion (ADME) parameters of the synthesized compounds were calculated and thus, their potential to be safe drugs was evaluated. Finally, to support the biological activity experiments, molecular docking studies of these compounds were carried out on three different target cancer protein structures (PDB IDs: 5ETY, 1M17, and 3GCW), and the amino acids that play key roles in the binding of the compounds to these proteins were determined.

Structures of the Wild-Type and S59L Mutant CHCHD10 Proteins Important in Amyotrophic Lateral Sclerosis-Frontotemporal Dementia.

The S59L genetic mutation of the mitochondrial coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10) is involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The wild-type and mutant forms of this protein contain intrinsically disordered regions, and their structural characterization has been facing challenges. Here, for the first time in the literature, we present the structural ensemble properties of the wild-type and S59L mutant form of CHCHD10 in an aqueous solution environment at the atomic level with dynamics. Even though available experiments suggested that the S59L mutation may not change the structure of the CHCHD10 protein, our structural analysis clearly shows that the structure of this protein is significantly affected by the S59L mutation. We present here the secondary structure components with their abundances per residue, the tertiary structure properties, the free energy surfaces based on the radius of gyration and end-to-end distance values, the Ramachandran plots, the quantity of intramolecular hydrogen bonds, and the principal component analysis results. These results may be crucial in designing more efficient treatment for ALS and FTD diseases.

Design and various in silico studies of the novel curcumin derivatives as potential candidates against COVID-19 -associated main enzymes.

The novel coronavirus disease (COVID-19) is a highly contagious disease caused by the SARS-CoV-2 virus, leading severe acute respiratory syndrome in patients. Although various antiviral drugs and their combinations have been tried so far against SARS-CoV-2 and they have shown some effectiveness, there is still a need for safe and cost-effective binding inhibitors in the fight against COVID-19. Therefore, phytochemicals in nature can be a quick solution due to their wide therapeutic spectrum and strong antiviral, anti-inflammatory, and antioxidant properties. In this context, the low toxicity, and high pharmacokinetic properties of curcumin, which is a natural phytochemical, as well as the easy synthesizing of its derivatives reveal the need for investigation of its various derivatives as inhibitors against coronaviruses. The present study focused on curcumin derivatives with reliable ADME profile and high molecular binding potency to different SARS-CoV-2 target enzymes (3CLPro, PLpro, NSP7/8/12, NSP7/8/12 +RNA, NSP15, NSP16, Spike, Spike+ACE). In the molecular docking studies, the best binding scores for the 22 proposed curcumin derivatives were obtained for the PLpro protein. Furthermore, MD simulations were performed for high-affinity ligand-PLpro protein complexes and subsequently, Lys157, Glu161, Asp164, Arg166, Glu167, Met208, Pro247, Pro248, Tyr264, Tyr273 and Asp302 residues of PLpro was determined to play key role for ligand binding by Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis. The results of the study promise that the proposed curcumin derivatives can be potent inhibitors against SARS-CoV-2 and be converted into pharmaceutical drugs. It is also expected that the findings may provide guiding insights to future design studies for synthesizing different antiviral derivatives of phytochemicals.

Synthesis, in vitro cytotoxicity, molecular docking and ADME study of some indolin-2-one linked 1,2,3-triazole derivatives.

In pursuit of an anticancer lead, a library of 1,2,3-triazole derivatives (7a-x) was prepared, characterized and screened for in vitro cytotoxicity in different cell lines. Most of the compounds proved to be cytotoxic with IC50 values in the low micromolar range. Further studies showed that the most active compound 7c induces caspase-dependent apoptosis in Jurkat cells by activating both the intrinsic and the extrinsic apoptotic pathways and perturbs cell-cycle progression. Moreover, 7c did not show any genotoxic activity. Molecular docking simulations were performed against epidermal growth factor receptor (EGFR). Docking experiments showed that, compounds 7c, 7o and 7 v bind within active sites of epidermal growth factor receptor EGFR (Pdb ID: 6P8Q) by strong hydrogen bonds with residue MET793, Pi-Sulfur with residue MET790 and Pi-Alkyl type interactions with residues LEU788, ALA743. The SwissADME webserver investigation suggested that most of the synthesized compounds follow the rules of drug-likeness.

Synthesis, in silico ADME, molecular docking and in vitro cytotoxicity evaluation of stilbene linked 1,2,3-triazoles.

Series of (E)-1-benzyl-4-((4-styrylphenoxy)methyl)-1H-1,2,3-triazoles 7a-x were obtained by Wittig reaction between 4-((1-benzyl-1H-1,2,3-triazol-4-yl)methoxy)benzaldehydes 5a-d and benzyl triphenylphosphonium halides 6a-f in benzene. The structures of the synthesized compounds were confirmed by FTIR, NMR (1H and 13C NMR) spectroscopy, and mass spectrometry. All synthesized compounds were screened for their cytotoxic activity against human cancer cell lines including pancreatic carcinoma, colorectal carcinoma, lung carcinoma, and leukemias such as acute lymphoblastic, chronic myeloid, and non-Hodgkinson lymphoma cell lines. In vitro cytotoxicity data showed that compounds 7c, 7e, 7h, 7j, 7k, 7r, and 7w were moderately cytotoxic (11.6-19.3 µM) against the selected cancer cell lines. These cytotoxicity findings were supported using molecular docking studies of the compounds against 1TUB receptor. The drug-likeness properties of the compounds evaluated by in silico ADME analyses. Resveratrol linked 1,2,3-triazoles were more sensitive towards human carcinoma cell lines but least sensitive towards leukemia and lymphoma cell lines.

Structural analyses and force fields comparison for NACore (68-78) and SubNACore (69-77) fibril segments of Parkinson's disease.

The α-synuclein fibrils are a pathological hallmark of Parkinson's disease (PD) and are abundant in the brains of PD patients. These amyloid fibrils can aggregate into distinct polymorphism under different physical conditions. Therefore, these different fibril polymorph formations should be considered in drug design studies targeting amyloid fibrils. Recently, the atomic structures of two small fibril segments of α-synuclein, named NACore (68-78) and SubNACore (69-77), have been crystallized. These segments are critical for cytotoxicity and fibril formation. Therefore, elucidation of interface interactions between pair sheets of the NACore and SubNACore is significant for the clarification of the mechanism of fibril formation in PD. In this context, molecular dynamics (MD) simulation technique is a convenient tool to investigate interface interactions of these segments at the atomic level. However, the accuracy of these simulations depends on the utilized force fields. Therefore, we have tested the dependence of interface interactions and stabilities of these small amyloid fibrils on various force fields. From the results of triple long (100 ns) MD simulations, we inferred for the stability investigations of the NACore and SubNACore that CHARMM27 and GROMOS53A6 are the most convenient force fields whereas AMBER99SB-ILDN is the most unfavorable one. Consequently, it is expected that our findings will guide the selection of the appropriate force field for simulations between these segments and possible inhibitors of this disease.

Experimental and theoretical studies of electrochemical oxidation of nicotinamide adenine dinucleotide at the modified SWCNT and graphene oxide.

In recent years, nicotinamide adenine dinucleotide (NADH) and its oxidized form (NAD+) have withdrawn a substantial attention since they possess a significant place in both biosensor and biofuel cell studies. However, the transformation of NADH to NAD+ brings about the surface passivation and fouling at the most of corresponding conductive materials; consequently, significant decrease takes place in the current. In order to overcome these drawbacks, we have performed the surface functionalization of single-walled carbon nanotube (SWCNT) and graphene oxide (GO) immobilized onto glassy carbon surface with dihydroxybenzene (di-HB) using solid-phase synthesis methodology. The di-HB-modified SWCNT and GO were found to exhibit great catalytic activity as they reduce required overpotential of electrochemical oxidation of NADH and lead to enhancement in the peak current, compared with unmodified carbon electrodes. Molecular docking simulation technique was also carried out to enlighten attained experimental findings in detail, and we have found that increase in the binding affinity of NAD+ to functionalized carbon surfaces with di-HB is related to formation of hydrogen bonding interactions Furthermore, our experimental and theoretical outputs were also found to be quite consistent in terms of reactivity of modified surfaces to NADH oxidation.