Unraveling the structural and functional dimensions of SARS-CoV2 proteins in the context of COVID-19 pathogenesis and therapeutics.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) has emerged as the causative agent behind the global pandemic of Coronavirus Disease 2019 (COVID-19). As the scientific community strives to comprehend the intricate workings of this virus, a fundamental aspect lies in deciphering the myriad proteins it expresses. This knowledge is pivotal in unraveling the complexities of the viral machinery and devising targeted therapeutic interventions. The proteomic landscape of SARS-CoV2 encompasses structural, non-structural, and open-reading frame proteins, each playing crucial roles in viral replication, host interactions, and the pathogenesis of COVID-19. This comprehensive review aims to provide an updated and detailed examination of the structural and functional attributes of SARS-CoV2 proteins. By exploring the intricate molecular architecture, we have highlighted the significance of these proteins in viral biology. Insights into their roles and interplay contribute to a deeper understanding of the virus's mechanisms, thereby paving the way for the development of effective therapeutic strategies. As the global scientific community strives to combat the ongoing pandemic, this synthesis of knowledge on SARS-CoV2 proteins serves as a valuable resource, fostering informed approaches toward mitigating the impact of COVID-19 and advancing the frontier of antiviral research.

Structural Modelling of Platelet Activating Factor Acetyl Hydrolase in Leishmania donovani, Trypanosoma cruzi, and Trypanosoma brucei: Implications on Therapeutics for Leishmaniasis, Chagas Disease, and Sleeping Sickness.

Purpose: Leishmaniasis, Chagas disease, and sleeping sickness are caused by protozoa Leishmania donovani, Trypanosoma cruzi, and Trypanosoma brucei, respectively. Platelet activating factor acetyl hydrolase (PAF-AH) is an inflammatory protein implicated in pathogenesis of these three infections, thereby making them attractive drug targets. Methods: PAF-AH sequences were retrieved from UniProt and aligned using Clustal Omega. Homologous models of parasitic proteins were built based on crystal structure of human PAF-AH and validated using PROCHECK server. Volumes of substrate-binding channel were calculated using the ProteinsPlus program. High throughput virtual screening using Glide program in Schrodinger was done with ZINC drug library against parasitic PAF-AH enzymes. Complexes with best hits were energy-minimized and subjected to 100 ns molecular dynamic simulation and analyzed. Results: PAF-AH enzyme sequences from protozoa Leishmania donovani, Trypanosoma cruzi, Trypanosoma brucei, and human have a minimum of 34% sequence similarity with each other. Corresponding structures show a globular conformation consisting of twisted ß-pleated sheets, flanked by α-helices on either side. Catalytic triad of serine-histidine-aspartate is conserved. Substrate-binding channel residues are conserved to an extent, with a lower channel volume in human as compared to target enzymes. Drug screening resulted in identification of three molecules that had better affinities than the substrate to the target enzymes. These molecules fulfill Lipinski's rules for drug likeness and also bind with less affinity to the human counterpart, thereby establishing a high selective index. Conclusion: Structures of PAF-AH from protozoan parasites and humans belong to the same family of enzymes and have a similar three-dimensional fold. However, they show subtle variations in residue composition, secondary structure composition, substrate-binding channel volume, and conformational stability. These differences result in certain specific molecules being potent inhibitors of the target enzymes while simultaneously having weaker binding to human homologue.

Computational and Biophysical Characterization of Heterocyclic Derivatives of Anthraquinone against Human Aurora Kinase A.

Human Aurora kinase A (AurA) has recently garnered the attention of researchers worldwide as a promising effective mitotic drug target for its involvement in cancer and related inflammatory anomalies. This study has explored the binding affinity of newly identified heteroarene-fused anthraquinone derivatives against AurA. Molecular docking analyses showed that all the heteroanthraquinone compounds bind to AurA with different affinities. Molecular dynamics simulation studies revealed that the compounds maintained relatively stable binding modes in the active site pocket while inducing minimal conformational changes in the AurA structure, interacting with key residues through several noncovalent interactions, including hydrogen bonds. Fluorescence spectroscopy and biolayer interferometry binding assays with synthesized compounds against recombinantly expressed AurA further verified their binding efficacy. Naphthoisatine 3 proved to be the best binder, with compounds anthraimidazole 5 and anthrathiophene 2 showing comparable results. Overall, this study indicates decent binding of heterocyclic derivatives of anthraquinone with the target AurA, which can further be assessed by performing enzymatic assays and cellular studies. The studies also highlight the applicability of the heteroarene-fused anthraquinone scaffold to construct selective and potent inhibitors of Aurora kinases after necessary structural modifications for the development of new anticancer drugs.

Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern.

BACKGROUND: The genome of SARS-CoV-2, is mutating rapidly and continuously challenging the management and preventive measures adopted and recommended by healthcare agencies. The spike protein is the main antigenic site that binds to the host receptor hACE-2 and is recognised by antibodies. Hence, the mutations in this site were analysed to assess their role in differential infectivity of lineages having these mutations, rendering the characterisation of these lineages as variants of concern (VOC) and variants of interest (VOI). METHODS: In this work, we examined the genome sequence of SARS-CoV-2 VOCs and their phylogenetic relationships with the other PANGOLIN lineages. The mutational landscape of WHO characterized variants was determined and mutational diversity was compared amongst the different severity groups. We then computationally studied the structural impact of the mutations in receptor binding domain of the VOCs. The binding affinity was quantitatively determined by molecular dynamics simulations and free energy calculations. RESULTS: The mutational frequency, as well as phylogenetic distance, was maximum in the case of omicron followed by the delta variant. The maximum binding affinity was for delta variant followed by the Omicron variant. The increased binding affinity of delta strain followed by omicron as compared to other variants and wild type advocates high transmissibility and quick spread of these two variants and high severity of delta variant. CONCLUSION: This study delivers a foundation for discovering the improved binding knacks and structural features of SARS-CoV-2 variants to plan novel therapeutics and vaccine candidates against the virus.

Structural analysis of LpqY, a substrate-binding protein from the SugABC transporter of Mycobacterium tuberculosis, provides insights into its trehalose specificity.

The LpqY-SugABC transporter of Mycobacterium tuberculosis (Mtb) salvages residual trehalose across the cell membrane, which is otherwise lost during the formation of cell-wall glycoconjugates in the periplasm. LpqY, a substrate-binding protein from the SugABC transporter, acts as the primary receptor for the recognition of trehalose, leading to its transport across the cell membrane. Since trehalose is crucial for the survival and virulence of Mtb, trehalose receptors should serve as important targets for novel drug design against tuberculosis. In order to comprehend the detailed architecture and substrate specificity, the first crystal structures of both apo and trehalose-bound forms of M. tuberculosis LpqY (Mtb-LpqY) are presented here at 2.2 and 1.9 Šresolution, respectively. The structure exhibits an N-lobe and C-lobe and is predominantly composed of a globular α/ß domain connected by a flexible hinge region concealing a deep binding cleft. Although the trehalose-bound form of Mtb-LpqY revealed an open ligand-bound conformation, the glucose moieties of trehalose are seen to be strongly held in place by direct and water-mediated hydrogen bonds within the binding cavity, producing a Kd of 6.58 ± 1.21 µM. These interactions produce a distinct effect on the stereoselectivity for the α-1,1-glycosidic linkage of trehalose. Consistent with the crystal structure, molecular-dynamics simulations further validated Asp43, Asp97 and Asn151 as key residues responsible for strong and stable interactions throughout a 1 µs time frame, thus capturing trehalose in the binding cavity. Collectively, the results provide detailed insights into how the structure and dynamics of Mtb-LpqY enable it to specifically bind trehalose in a relaxed conformation state.

Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins.

The Human Aurora Kinase (AURK) protein family is the key player of cell cycle events including spindle assembly, kinetochore formation, chromosomal segregation, centrosome separation, microtubule dynamics, and cytokinesis. Their aberrant expression has been extensively linked with chromosomal instability in addition to derangement of multiple tumor suppressors and oncoprotein regulated pathways. Therefore, the AURK family of kinases is a promising target for the treatment of various types of cancer. Over the past few decades, several potential inhibitors of AURK proteins have been identified and have reached various phases of clinical trials. But very few molecules have currently crossed the safety criteria due to their various toxic side effects. In the present study, we have adopted a computational polypharmacological strategy and identified four novel molecules that can target all three AURKs. These molecules were further investigated for their binding stabilities at the ATP binding pocket using molecular dynamics based simulation studies. The molecules selected adopting a multipronged computational approach can be considered as potential AURKs inhibitors for cancer therapeutics.

Heteroarene-fused anthraquinone derivatives as potential modulators for human aurora kinase B.

The quest for effective anticancer therapeutics continues to be extensively pursued. Over the past century, several drugs have been developed, however, a majority of these drugs have a poor therapeutic index and increased toxicity profile. Hence, there still exists ample opportunity to discover safe and effective anticancer drugs. Aurora Kinase B (AurB), a member of the Aurora kinase family and a key regulator of mitotic cell division, is found to be frequently overexpressed in a variety of human cancers and has thus emerged as an attractive target for the design of anticancer therapeutics. In the present study, a structure-based scaffold hopping approach was utilized to modify the heterocyclic moiety of (S)-3-(3-aminopyrrolidine-1-carbonyl)-4,11-dihydroxy-2-methylanthra [2,3-b]furan-5,10-dione (anthrafuran 1) to generate a series of heteroarene-fused anthraquinone derivatives, which were then subjected to virtual screening for the identification of potential AurB inhibitors. The obtained hits were subsequently synthesized and evaluated by using a combination of in silico and biophysical techniques for elucidating their in vitro binding and inhibition activity with recombinantly expressed AurB. Four identified hits presented an improved binding profile as compared to their parent analog anthrafuran 1. One derivative, anthrathiophene 2 demonstrated excellent in vitro inhibition of AurB (7.3 µM).

Biochemical and biophysical characterization of nucleotide binding domain of Trehalose transporter from Mycobacterium tuberculosis.

The SugABC is an ABC transporter in Mycobacterium tuberculosis which is proposed to be involved in the process of Trehalose import, but till date the proteins of this transporter complex have not been functionally characterized. This transport process is driven by the nucleotide binding domain SugC of SugABC transporter. To understand the functional role of SugC, we expressed and purified the protein in E.coli. Our purification result shows, Mtb SugC exists as a monomer in solution but forms dimers upon binding to ATP. It is stable at pH 7.5 as analyzed by CD spectroscopy and showed maximum activity at this pH as estimated by Michaelis-Menten's kinetics for Mg-ATP at a KM of 0.15 mM. The SugCH193A mutant was observed to have a reduced catalytic activity implying that H193 is one of the residues involved in the hydrolysis of ATP. The molecular modeling further revealed that, like E.coli MalK, MtbSugC also has an ATPase domain and a regulatory domain. Despite having low sequence homology with other nucleotide binding domains of ABC transporters, the structure and functional motifs of MtbSugC are conserved. Thus, we show that SugC is a functional ATPase domain of SugABC transporter in Mycobacterium tuberculosis.

Evaluation of α-synuclein and apolipoprotein E as potential biomarkers in cerebrospinal fluid to monitor pharmacotherapeutic efficacy in dopamine dictated disease states of Parkinson's disease and schizophrenia.

BACKGROUND AND OBJECTIVE: Dopamine plays an important role in the disease pathology of Parkinson's disease and schizophrenia. These two neuropsychiatric disorders represent disease end points of the dopaminergic spectrum where Parkinson's disease represents dopamine deficit and schizophrenia represents dopamine hyperactivity in the mid-brain. Therefore, current treatment strategies aim to restore normal dopamine levels. However, during treatment patients develop adverse effects due to overshooting of physiological levels of dopamine leading to psychosis in Parkinson's disease, and extrapyramidal symptoms in schizophrenia. Absence of any laboratory tests hampers modulation of pharmacotherapy. Apolipoprotein E and α-synuclein have an important role in the neuropathology of these two diseases. The objective of this study was to evaluate cerebrospinal fluid (CSF) concentrations of apolipoprotein E and α-synuclein in patients with these two diseases so that they may serve as biomarkers to monitor therapy in Parkinson's disease and schizophrenia. METHODS: Drug-naïve Parkinson's disease patients and Parkinson's disease patients treated with dopaminergic therapy, neurological controls, schizophrenic patients treated with antidopaminergic therapy, and drug-naïve schizophrenic patients were recruited for the study and CSF was collected. Enzyme-linked immunosorbent assays were carried out to estimate the concentrations of apolipoprotein E and α-synuclein. Pathway analysis was done to establish a possible role of these two proteins in various pathways in these two dopamine dictated diseases. RESULTS: Apolipoprotein E and α-synuclein CSF concentrations have an inverse correlation along the entire dopaminergic clinical spectrum. Pathway analysis convincingly establishes a plausible hypothesis for their co-regulation in the pathogenesis of Parkinson's disease and schizophrenia. Each protein by itself or as a combination has encouraging sensitivity and specificity values of more than 55%. CONCLUSION: The dynamic variation of these two proteins along the spectrum is ideal for them to be pursued as pharmacotherapeutic biomarkers in CSF to monitor pharmacological efficacy in Parkinson's disease and schizophrenia.

Structural insights into the substrate binding mechanism of novel ArgA from Mycobacterium tuberculosis.

The Mycobacterium tuberculosis (Mtb) Rv2747 gene encodes for a functional protein known as ArgA, which plays an important role in the first step of the l-arginine biosynthesis pathway. ArgA transfers the acetyl group from the acetyl-CoA to either l-glutamate or l-glutamine, which are the known substrates. Here, we present two crystal structures of ArgA: one complexed with CoA and product bound N-acetylglutamine and the other complexed with acetyl-CoA and the inhibitor l-arginine at 2.3 and 3.0 Šresolution respectively. The Mtb ArgA protomer was found to have a "V" cleft and a "ß" bulge, archetypal of a classical GCN5-related N-acetyltransferase superfamily of proteins. The product bound form implies that ArgA can also acetylate l-glutamine like l-glutamate. The active site is strongly inhibited by l-arginine resulting in a closed conformation of ArgA and both l-arginine and N-acetylglutamine were found to occupy at the same active site. Together with structural analysis, molecular docking studies, microscale thermophoresis and enzyme inhibition assays, we conclude that l-glutamine, l-glutamate and l-arginine, all occupy at the same active site of ArgA. Furthermore in case of Mtb ArgA, l-arginine does not act as an allosteric inhibitor unlike other N-acetylglutamate synthase family of proteins.