Computational Biology and Chemistry

Tuberculosis (TB) is one of the life-threatening infectious diseases with prehistoric origins and occurs in almost all habitable parts of the world. TB mainly affects the lungs, and its etiological agent is Mycobacterium tuberculosis (Mtb). In ...

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• TB is an infectious disease occurs in almost all habitable parts of the world.
• InhA has already been proved a potential target for TB drug development.
• In-silico and ML approaches used to screen SelleckChem database against InhA.

Bioactive cobalt (II) macrocyclic complexes [Co(N₄O₄ML₁)Cl₂]-[Co(N₄O₄ML₃)Cl₂] have been synthesized by using the macrocyclic ligands [N₄O₄ML₁], [N₄O₄ML₂], and [N₄O₄ML₃] that have an N₄O₄ core. These three macrocyclic ligands were all isolated in ...

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• We have synthesized diaminonaphthalene-based macrocyclic complexes of Co(II).
• Complexes were examined utilizing different analytical, and spectroscopic techniques.
• A distorted octahedral geometry has been assigned for Co(II) ...

Cancer is the most prevalent disease globally, which presents a significant challenge to the healthcare industry, with breast and lung cancer being predominant malignancies. This study used RNA-seq data from the TCGA database to identify ...

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• TNFAIP8 and SUOX identified as biomarkers for lung and breast cancer, respectively.
• Compounds derived from the Euphorbia ammak plant were screened.
• Stigmasterol binds better known inhibitor of TNFAIP8.
• Stigmasterol identified ...

Latest studies confirmed that abnormal function of histone deacetylase (HDAC) plays a pivotal role in formation of tumors and is a potential therapeutic target for treating breast cancer. In this research, in-silico drug discovery approaches via ...

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• QSAR model was generated with good statistical results based on indazole derivatives as potential HDAC inhibitors.
• Compounds C32, C26 and C31 from model 3 had relatively higher inhibitory activity with pIC50 of 9.30103, 9.1549 and ...

The local disruptions caused by the genes of one disease can influence the pathways associated with the other diseases resulting in comorbidity. For gene therapies, it is necessary to prioritize the key genes that regulate common biological ...

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• Effective identification of key comorbid genes via clustering of weighted subgraph of PPIN.
• Identified key comorbid genes of ALS-SMA: TP53, YWHAZ, KRT31, FUS, USP2, ESR1, SMN1, TRAF2, APP and MEOX2.
• Identified key comorbid genes of ...

Hepatocellular carcinoma (HCC) persists to be one of the most devastating and deadliest malignancies globally. Recent research into the molecular signaling networks entailed in many malignancies has given some prominent insights that can be ...

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• PRL-3 contributes to the advancement, incursion, and metastasis of HCC.
• PRL-3 antagonists may be advantageous for combating HCC metastasis.
• Drug repurposing could serve as an effective method to speed up and minimize the expenses ...

The rise of drug resistance in Plasmodium falciparum, rendering current treatments ineffective, has hindered efforts to eliminate malaria. To address this issue, the study employed a combination of Systems Biology approach and a structure-based ...

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• Malaria, a life-threatening disease caused by the coccidian protozoa parasite, infects the human circulatory system.
• A metabolic pathway selection and protein-protein interaction network were used to determine the best target.
• The ...

Alpha-glucosidase (maltase, sucrase, isomaltase and glucoamylase) activities which are involved in carbohydrate metabolism are present in human intestinal maltase-glucoamylase (MGAM) and sucrase-isomaltase (SI). Hence, these proteins are ...

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• Artocarpus heterophyllus leaf aqueous active fraction (AHL-AAF) subjected to LC-ESI-MS/MS.
• AHL-AAF inhibited mammalian glucosidases activities.
• AHL-AAF active molecules interacted with human glucosidase in silico .
• MD ...

Endocannabinoid system plays a pivotal role in controlling neuroinflammation, and modulating this system may not only aid in managing symptoms of neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Multiple sclerosis, ...

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• Role of endocannabinoid system in neuroinflammation associated conditions such as Alzheimer’s disease, Multiple sclerosis, neuropathy and epilepsy.
• Bias signaling potential of CBD and its possible pathway in eliciting the response via ...

Amidst the Zn²⁺-dependant isoforms of the HDAC family, HDAC6 has emerged as a potential target associated with an array of diseases, especially cancer and neuronal disorders like Rett’s Syndrome, Alzheimer’s disease, Huntington’s disease, etc. ...

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• HDAC6 is a well-recognized target for drug design and discovery.
• ML model and fragment-based structural analysis were performed on quinazoline-based HDAC6 inhibitors.
• The models were validated on other external sets to prove the ...

The computational method has been proven to be a promising means for pre-screening large-scale anticancer drug combinations to support precision oncology applications. Pioneering efforts have been made to develop machine learning technology for ...

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• A framework named SNSynergy is developed for predicting synergistic effects to new cell lines and new drug combinations.
• An assumption that similar cell lines and similar drug combinations have similar synergistic effects is proposed.

Cancer is one of the wide-ranging diseases which have a high mortality rate impacting globally. This scenario can be switched by early detection and correct precision treatment, a major concern for cancer patients. Clinicians can figure out the ...

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• Microsoft genomics services have been utilized for accelerated Secondary Analysis using GATK best practices.
• The data is secured and protected with Microsoft Azure's data security protocols.
• MSI Analysis & TMB Analysis tools are ...

Accurate classification of membrane proteins like ion channels and transporters is critical for elucidating cellular processes and drug development. We present DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs) and multi-...

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• Novel Integration: Integrating ProtTrans and ESM1b boosts ion channel and transporter protein identification.
• Diverse Convolution: Filters across 4-64 residues capture local and global motifs for nuanced structure recognition.
• ...

Being widely accepted tools in computational drug search, the (Q)SAR methods have limitations related to data incompleteness. The proteochemometrics (PCM) approach expands the applicability area by using description for both protein and ligand ...

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• A scheme for filtering data on protease inhibitors from the ChEMBL database has been proposed.
• The original descriptors are based on the 3D alignment of proteins and structural descriptors of ligands.
• The models have been obtained ...

COVID-19, a novel ailment, has received comparatively fewer drugs for its treatment. Side Effects (SE) of a COVID-19 drug could cause long-term health issues. Hence, SE prediction is essential in COVID-19 drug development. Efficient models are ...

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• Proposed a novel K1K2NN method based on neighbours to predict side effects of the COVID drug from 17 molecules' drug descriptor and 1D chemical drug structure, which have not yet been utilized to predict adverse COVID drug reactions.
• ...

Virtual screening-based molecular similarity and fingerprint are crucial in drug design, target prediction, and ADMET prediction, aiding in identifying potential hits and optimizing lead compounds. However, challenges such as lack of ...

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• FaissMolLib accomplishes the screening of 2.8 million compounds in only 0.05 seconds.
• FaissMolLib shows lower mean deviation across all the molecular properties compared toTanimoto.
• FaissMolLib is available for free at http://...

Artificial intelligence (AI) has revolutionized structural biology by predicting protein 3D structures with near-experimental accuracy. Here, short backbone N-O distances in high-resolution crystal structures were compared to those in three-...

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• AI has dramatically changed the predictions of the three-dimensional structures of proteins.
• However, the accuracy of predicted atomic positions must be estimated.
• Positional standard errors in AI-based protein 3D models are 3.5–6 ...

Diabetic mellitus (DM) is a chronic disorder, and type 2 DM (T2DM) is the most prevalent among all categories (nearly 90%) across the globe every year. With the availability of potential drugs, the prevalence rate has remained uncontrollable, ...

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• Therapeutic repurposing of natural indole-derivatives.
• Anti-diabetic potency of plant and marine derived indoles.
• Computational platform to select potential antidiabetic candidates.

Due to its emerging resistance to first-line anti-TB medications, tuberculosis (TB) is one of the most contagious illness in the world. According to reports, the effectiveness of treating TB is severely impacted by drug resistance, notably ...

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• The mutations significantly impact FE2+ binding residues and their arrangement in the active centre.
• It is observed that the pncA mutants lose their structural stability and strong binding affinity compared to the WT.
• The flap ...

The methylation and demethylation of lysine and arginine side chains are fundamental processes in gene regulation and disease development. Histone lysine methylation, controlled by histone lysine methyltransferases (KMTs) and histone lysine ...

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• The interactions between KDM4E/6B and their selective inhibitors are investigated to clarify the selectivity mechanism.
• Crucial amino acids of KDM4E/6B are explored, to reveal the main contributor for molecular interactions.
• ...

The physical interactions between proteins are largely determined by the structural properties at their binding interfaces. It was found that the binding interfaces in distinctive protein complexes are highly similar. The structural properties ...

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• We decomposed protein-protein binding interfaces into pairs of interacting fragments.
• We employed a generative model to encode these interface fragment pairs in a low-dimensional latent space.
• We found that the conformational space ...

Clear cell renal cell carcinoma (ccRCC) frequently progresses to advanced stages due to tumor thrombus (TTs) formation. In this study, we aimed to investigate the role of coagulation-related pathway activation in the progression of ccRCC.

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• Identify the correlation between coagulation and the tumor microenvironment in renal cell carcinoma.
• Develop a coagulation-related prognostic model for risk stratification and prognosis prediction in renal cell carcinoma.
• MMP9 is ...

Protein stability is a critical aspect of molecular biology and biochemistry, hinges on an intricate balance of thermodynamic and structural factors. Determining protein stability is crucial for understanding and manipulating biological ...

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• CNN based ML model was developed for protein stability prediction.
• The stability prediction is dependent on ∆G, Tm, ∆Cp and number of di-sulphide bonds.
• Validation with experimental dataset yielded high accuracy in classification ...

Sodium-glucose co-transporter 2 (SGLT2) is one of the important targets against type II diabetes mellitus. A typical SGLT2 inhibitor acts by inhibiting glucose reabsorption, thus lowering the blood glucose level. Unlike SGLT1, SGLT2 is ...

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• SGLT2, crucial for type II diabetes and key target in drug design.
• Present work used ligand-based and structure-based methods for compound discovery.
• 3D-QSAR screens 10 thousand compounds; docking studies performed for inhibitors.

Human Carbonic anhydrase IX (hCA IX) is found to be an essential biomarker for the treatment of hypoxic tumors in both the early and metastatic stages of cancer. Due to its active function in maintaining pH levels and overexpression in hypoxic ...

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• Pharmacophore model was developed in search of selective hCA IX inhibitors.
• Molecular docking studies revealed 186 hits from zinc database.
• Three lead compounds were identified based on molecular dynamics simulations.
• Toxicity ...

Clinical studies have already illustrated the associations between gut microbes and diseases, yet fundamental questions remain unclear that how we can universalize this knowledge. Considering the important role of human gut microbial composition ...

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• Metagenomics provides a way to analyze and understand the microbes and their role in a community manner.
• Disease-specific gut microbiome study may help to understand disease-specific microbial diversity and microbial shifting.
• Five ...

Glutathione reductase (GR) is a two dinucleotide binding domain flavoprotein (tDBDF) that catalyzes the reduction of glutathione disulfide to glutathione coupled to the oxidation of NADPH to NADP⁺. An interesting feature of GR and other tDBDFs is ...

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• Active site Lys-66 must be in its neutral state for a thermodynamically favorable reduction of FAD by NADPH.
• Protonated Lys-66 promotes the reverse reaction (reduction of NADP+ by FADH−).
• An equivalent residue is present in related ...

Cumulative global prevalence of the emergent monkeypox (MPX) infection in the non-endemic countries has been professed as a global public health predicament. Lack of effective MPX-specific treatments sets the baseline for designing the current ...

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• Re-emergence of monkeypox infection stimulated the need to develop potential therapeutics.
• AlphaFold2 with a high pLDDT score and MD simulation predicted nearly accurate structure of F13.
• Molecular docking and all-atoms MD ...

Cichorium glandulosum, a common traditional Chinese medicine used by Uyghur and Mongolian ethnic groups, is recognized for its potential to ameliorate metabolic disorders. However, the specific efficacy and mechanisms of Cichorium glandulosum in ...

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• Screening the extraction parts of aqueous extract of Cichorium glandulosum against hyperuricemia combined with hyperlipidemia.
• Analysis of the composition of n-butanol extracted parts of Cichorium glandulosum using LC-MS/MS.
• ...