Current Research in Structural Biology最新文献

{"title":"Structural basis for the binding of the cancer targeting scorpion toxin, ClTx, to the vascular endothelia growth factor receptor neuropilin-1","authors":"Gagan Sharma ,&nbsp;Carolyne B. Braga ,&nbsp;Kai-En Chen ,&nbsp;Xinying Jia ,&nbsp;Venkatraman Ramanujam ,&nbsp;Brett M. Collins ,&nbsp;Roberto Rittner ,&nbsp;Mehdi Mobli","doi":"10.1016/j.crstbi.2021.07.003","DOIUrl":"10.1016/j.crstbi.2021.07.003","url":null,"abstract":"<div><p>Chlorotoxin (ClTx) is a 36-residue disulfide-rich peptide isolated from the venom of the scorpion <em>Leiurus quinquestriatus.</em> This peptide has been shown to selectively bind to brain tumours (gliomas), however, with conflicting reports regarding its direct cellular target. Recently, the vascular endothelial growth factor receptor, neuropilin-1 (NRP1) has emerged as a potential target of the peptide. Here, we sought to characterize the details of the binding of ClTx to the b1-domain of NRP1 (NRP1-b1) using solution state nuclear magnetic resonance (NMR) spectroscopy. The 3D structure of the isotope labelled peptide was solved using multidimensional heteronuclear NMR spectroscopy to produce a well-resolved structural ensemble. The structure points to three putative protein-protein interaction interfaces, two basic patches (R14/K15/K23 and R25/K27/R36) and a hydrophobic patch (F6/T7/T8/H10). The NRP1-b1 binding interface of ClTx was elucidated using ¹⁵N chemical shift mapping and included the R25/K27/R36 region of the peptide. The thermodynamics of binding was determined using isothermal titration calorimetry (ITC). In both NMR and ITC measurements, the binding was shown to be competitive with a known NRP1-b1 inhibitor. Finally, combining all of this data we generate a model of the ClTx:NRP1-b1 complex. The data shows that the peptide binds to the same region of NRP1 that is used by the SARS-CoV-2 virus for cell entry, however, via a non-canonical binding mode. Our results provide evidence for a non-standard NRP1 binding motif, while also providing a basis for further engineering of ClTx to generate peptides with improved NRP1 binding for future biomedical applications.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 179-186"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.07.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39318610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Replacement of heme by soluble guanylate cyclase (sGC) activators abolishes heme-nitric oxide/oxygen (H-NOX) domain structural plasticity","authors":"Aikaterini I. Argyriou ,&nbsp;Garyfallia I. Makrynitsa ,&nbsp;Georgios Dalkas ,&nbsp;Dimitra A. Georgopoulou ,&nbsp;Konstantinos Salagiannis ,&nbsp;Vassiliki Vazoura ,&nbsp;Andreas Papapetropoulos ,&nbsp;Stavros Topouzis ,&nbsp;Georgios A. Spyroulias","doi":"10.1016/j.crstbi.2021.11.003","DOIUrl":"10.1016/j.crstbi.2021.11.003","url":null,"abstract":"<div><p>The gasotransmitter nitric oxide (NO) is a critical endogenous regulator of homeostasis, in major part via the generation of cGMP (cyclic guanosine monophosphate) from GTP (guanosine triphosphate) by NO's main physiological receptor, the soluble guanylate cyclase (sGC). sGC is a heterodimer, composed of an α1 and a β1 subunit, of which the latter contains the heme-nitric oxide/oxygen (H-NOX) domain, responsible for NO recognition, binding and signal initiation. The NO/sGC/cGMP axis is dysfunctional in a variety of diseases, including hypertension and heart failure, especially since oxidative stress results in heme oxidation, sGC unresponsiveness to NO and subsequent degradation. As a central player in this axis, sGC is the focus of intense research efforts aiming to develop therapeutic molecules that enhance its activity. A class of drugs named sGC “activators” aim to replace the oxidized heme of the H-NOX domain, thus stabilizing the enzyme and restoring its activity. Although numerous studies outline the pharmacology and binding behavior of these compounds, the static 3D models available so far do not allow a satisfactory understanding of the structural basis of sGC's activation mechanism by these drugs. Herein, application NMR describes different conformational states during the replacement of the heme by a sGC activators. We show that the two sGC activators (BAY 58-2667 and BAY 60-2770) significantly decrease the conformational plasticity of the recombinant H-NOX protein domain of <em>Nostoc</em> sp. cyanobacterium, rendering it a lot more rigid compared to the heme-occupied H-NOX. NMR methodology also reveals, for the first time, a surprising bi-directional competition between reduced heme and these compounds, pointing to a highly dynamic regulation of the H-NOX domain. This competitive, bi-directional mode of interaction is also confirmed by monitoring cGMP generation in A7r5 vascular smooth muscle cells by these activators. We show that, surprisingly, heme's redox state impacts differently the bioactivity of these two structurally similar compounds. In all, by NMR-based and functional approaches we contribute unique experimental insight into the dynamic interaction of sGC activators with the H-NOX domain and its dependence on the heme redox status, with the ultimate goal to permit a better design of such therapeutically important molecules.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 324-336"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6d/d1/main.PMC8640258.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39583633","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The phosphatidylglycerol phosphate synthase PgsA utilizes a trifurcated amphipathic cavity for catalysis at the membrane-cytosol interface","authors":"Bowei Yang ,&nbsp;Hebang Yao ,&nbsp;Dianfan Li ,&nbsp;Zhenfeng Liu","doi":"10.1016/j.crstbi.2021.11.005","DOIUrl":"10.1016/j.crstbi.2021.11.005","url":null,"abstract":"<div><p>Phosphatidylglycerol is a crucial phospholipid found ubiquitously in biological membranes of prokaryotic and eukaryotic cells. The phosphatidylglycerol phosphate (PGP) synthase (PgsA), a membrane-embedded enzyme, catalyzes the primary reaction of phosphatidylglycerol biosynthesis. Mutations in <em>pgsA</em> frequently correlate with daptomycin resistance in <em>Staphylococcus aureus</em> and other prevalent infectious pathogens. Here we report the crystal structures of <em>S. aureus</em> PgsA (<em>Sa</em>PgsA) captured at two distinct states of the catalytic process, with lipid substrate (cytidine diphosphate-diacylglycerol, CDP-DAG) or product (PGP) bound to the active site within a trifurcated amphipathic cavity. The hydrophilic head groups of CDP-DAG and PGP occupy two different pockets in the cavity, inducing local conformational changes. An elongated membrane-exposed surface groove accommodates the fatty acyl chains of CDP-DAG/PGP and opens a lateral portal for lipid entry/release. Remarkably, the daptomycin resistance-related mutations mostly cluster around the active site, causing reduction of enzymatic activity. Our results provide detailed mechanistic insights into the dynamic catalytic process of PgsA and structural frameworks beneficial for development of antimicrobial agents targeting PgsA from pathogenic bacteria.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 312-323"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/88/88/main.PMC8640168.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39583632","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cyclohexyl-α maltoside as a highly efficient tool for membrane protein studies","authors":"Julie Winkel Missel ,&nbsp;Nina Salustros ,&nbsp;Eva Ramos Becares ,&nbsp;Jonas Hyld Steffen ,&nbsp;Amalie Gerdt Laursen ,&nbsp;Angelica Struve Garcia ,&nbsp;Maria M. Garcia-Alai ,&nbsp;Čeněk Kolar ,&nbsp;Pontus Gourdon ,&nbsp;Kamil Gotfryd","doi":"10.1016/j.crstbi.2021.03.002","DOIUrl":"10.1016/j.crstbi.2021.03.002","url":null,"abstract":"<div><p>Membrane proteins (MPs) constitute a large fraction of the proteome, but exhibit physicochemical characteristics that impose challenges for successful sample production crucial for subsequent biophysical studies. In particular, MPs have to be extracted from the membranes in a stable form. Reconstitution into detergent micelles represents the most common procedure in recovering MPs for subsequent analysis. n-dodecyl-β-D-maltoside (DDM) remains one of the most popular conventional detergents used in production of MPs. Here we characterize the novel DDM analogue 4-trans-(4-trans-propylcyclohexyl)-cyclohexyl α-maltoside (t-PCCαM), possessing a substantially lower critical micelle concentration (CMC) than the parental compound that represents an attractive feature when handling MPs. Using three different types of MPs of human and prokaryotic origin, <em>i.e.</em>, a channel, a primary and a secondary active transporter, expressed in yeast and bacterial host systems, respectively, we investigate the performance of t-PCCαM in solubilization and affinity purification together with its capacity to preserve native fold and activity. Strikingly, t-PCCαM displays favorable behavior in extracting and stabilizing the three selected targets. Importantly, t-PCCαM promoted extraction of properly folded protein, enhanced thermostability and provided negatively-stained electron microscopy samples of promising quality. All-in-all, t-PCCαM emerges as competitive surfactant applicable to a broad portfolio of challenging MPs for downstream structure-function analysis.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 85-94"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2021.03.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39163167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures","authors":"Athi N. Naganathan,&nbsp;Adithi Kannan","doi":"10.1016/j.crstbi.2021.09.003","DOIUrl":"10.1016/j.crstbi.2021.09.003","url":null,"abstract":"<div><p>Protein sequences and structures evolve by satisfying varied physical and biochemical constraints. This multi-level selection is enabled not just by the patterning of amino acids on the sequence, but also via coupling between residues in the native structure. Here, we employ an energetically detailed statistical mechanical model with millions of microstates to extract such long-range structural correlations, <em>i.e.</em> thermodynamic coupling free energies, from a diverse family of protein structures. We find that despite the intricate and anisotropic distribution of coupling patterns, the majority of residues (&gt;70%) are only marginally coupled contributing to functional motions and catalysis. Physical origins of ‘sectors’, determinants of native ensemble heterogeneity in extant, ancient and designed proteins, and the basis for allostery emerge naturally from coupling free energies. The statistical framework highlights how evolutionary selection and optimization occur at the level of global interaction network for a given protein fold impacting folding, function, and allosteric outputs.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 257-267"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4d/5e/main.PMC8526763.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39561259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hypervariability of accessible and inaccessible conformational space of proteins","authors":"Ashraya Ravikumar,&nbsp;Narayanaswamy Srinivasan","doi":"10.1016/j.crstbi.2021.09.001","DOIUrl":"10.1016/j.crstbi.2021.09.001","url":null,"abstract":"<div><p>Proteins undergo motions in a range of amplitudes, from domain motions to backbone rotations, leading to changes in (φ,ψ) torsion angles and small-scale bond vibrations and angle bending. Here, we study the extent of variations in (φ,ψ) values in proteins and the effects of bond geometry variations due to vibrational motions in a protein on the accessible, (steric clash-free) (φ,ψ) space. We perform 1-fs timestep unconstrained molecular dynamics simulations on super-high-resolution protein structures. Extent of variations in bond geometry during the simulation is within acceptable ranges of bond lengths and angles. However, the steric clash-free (φ,ψ) space continuously changes as seen in bond geometry-specific (φ,ψ) steric maps at the residue level during simulations. (φ,ψ) regions that have steric clash at one timepoint can become steric clash-free at a different timepoint through minor adjustments to backbone bond lengths and angles. Also instances of (φ,ψ) transitions from the left to right half of the (φ,ψ) map in consecutive snapshots of the trajectory are seen. Although the two quadrants are separated by a steric clash-prone region, corresponding to a high-energy barrier, height of this barrier is lowered by adjusting the bond geometry such that a bridging region of steric clash-free, low-energy (φ,ψ) values is formed. We demonstrate the idea of dynamically varying nature of acceptable and accessible (φ,ψ) steric space in proteins, which has implications for protein folding; proteins could sample (φ,ψ) space which is originally considered to be inaccessible, during folding, through minor adjustments to their backbone bond geometry.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 229-238"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/02/f5/main.PMC8473459.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39483613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features","authors":"Saman Fatihi ,&nbsp;Surabhi Rathore ,&nbsp;Ankit K. Pathak ,&nbsp;Deepanshi Gahlot ,&nbsp;Mitali Mukerji ,&nbsp;Nidhi Jatana ,&nbsp;Lipi Thukral","doi":"10.1016/j.crstbi.2021.11.002","DOIUrl":"10.1016/j.crstbi.2021.11.002","url":null,"abstract":"<div><p>The recent release of SARS-CoV-2 genomic data from several countries has provided clues into the potential antigenic drift of the coronavirus population. In particular, the genomic instability observed in the spike protein necessitates immediate action and further exploration in the context of viral-host interactions. By temporally tracking 527,988 SARS-CoV-2 genomes, we identified invariant and hypervariable regions within the spike protein. We evaluated combination of mutations from SARS-CoV-2 lineages and found that maximum number of lineage-defining mutations were present in the N-terminal domain (NTD). Based on mutant 3D-structural models of known Variants of Concern (VOCs), we found that structural properties such as accessibility, secondary structural type, and intra-protein interactions at local mutation sites are greatly altered. Further, we observed significant differences between intra-protein networks of wild-type and Delta mutant, with the latter showing dense intra-protein contacts. Extensive molecular dynamics simulations of D614G mutant spike structure with hACE2 further revealed dynamic features with 47.7% of mutations mapping on flexible regions of spike protein. Thus, we propose that significant changes within spike protein structure have occurred that may impact SARS-CoV-2 pathogenesis, and repositioning of vaccine candidates is required to contain the spread of COVID-19 pathogen.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 290-300"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9f/ce/main.PMC8590475.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39898585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual targeting of 3CLpro and PLpro of SARS-CoV-2: A novel structure-based design approach to treat COVID-19","authors":"Sajjan Rajpoot,&nbsp;Manikandan Alagumuthu,&nbsp;Mirza S. Baig","doi":"10.1016/j.crstbi.2020.12.001","DOIUrl":"10.1016/j.crstbi.2020.12.001","url":null,"abstract":"<div><p>With the rapid growth of the COVID-19 (coronavirus disease 2019) pandemic across the globe, therapeutic attention must be directed to fight the novel severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). However, developing new antiviral drugs and vaccines is time-consuming, so one of the best solutions to tackle this virus at present is to repurpose ready-to-use drugs. This paper proposes the repurposing of the Food and Drug Administration (FDA)-approved, purchasable, and naturally occurring drugs for preventive and therapeutic use. We propose to design a dual-inhibitor for the SARS-CoV-2 cysteine proteases—3 Chemotrypsin-like protease or main protease (3CL^pro or M^pro) and Papain-like protease (PL^pro) responsible for processing the translated polyprotein chain from the viral RNA yielding functional viral proteins. For virtual screening, an unbiased blind docking was performed from which the top nine dual-targeting inhibitors for 3CL^pro and PL^pro were selected. The nine repurposed drugs, block the catalytic dyad (His41 and Cys145) of 3CL^pro as well as the catalytic triad (Cys111, His272, and Asp286) of PL^pro. Repurposing known drugs will not only pave the way for rapid in-vitro and in-vivo studies to battle the SARS-CoV-2 but will also expedite the quest for a potent anti-coronaviral drug.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 9-18"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2020.12.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38722936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Testing the length limit of loop grafting in a helical repeat protein","authors":"Juliane F. Ripka,&nbsp;Albert Perez-Riba ,&nbsp;Piyush K. Chaturbedy,&nbsp;Laura S. Itzhaki","doi":"10.1016/j.crstbi.2020.12.002","DOIUrl":"10.1016/j.crstbi.2020.12.002","url":null,"abstract":"<div><p>Alpha-helical repeat proteins such as consensus-designed tetratricopeptide repeats (CTPRs) are exceptionally stable molecules that are able to tolerate destabilizing sequence alterations and are therefore becoming increasingly valued as a modular platform for biotechnology and biotherapeutic applications. A simple approach to functionalize the CTPR scaffold that we are pioneering is the insertion of short linear motifs (SLiMs) into the loops between adjacent repeats. Here, we test the limits of the scaffold by inserting 17 highly diverse amino acid sequences of up to 58 amino acids in length into a two-repeat protein and examine the impact on protein folding, stability and solubility. The sequences include three SLiMs that bind oncoproteins and eleven naturally occurring linker sequences all predicted to be intrinsically disordered but with conformational preferences ranging from compact globules to expanded coils. We show that the loop-grafted proteins retain the native CTPR structure and are thermally stable with melting temperatures above 60 ​°C, despite the longest loop sequence being almost the same size as the CTPR scaffold itself (68 amino acids). Although the main determinant of the effect of stability was found to be loop length and was relatively insensitive to amino acid composition, the relationship between protein solubility and the loop sequences was more complex, with the presence of negatively charged amino acids enhancing the solubility. Our findings will help us to fully realize the potential of the repeat-protein scaffold, allowing a rational design approach to create artificial modular proteins with customized functional capabilities.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 30-40"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.crstbi.2020.12.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39163207","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential of Withaferin-A, Withanone and Caffeic Acid Phenethyl ester as ATP-competitive inhibitors of BRAF: A bioinformatics study","authors":"Vidhi Malik ,&nbsp;Vipul Kumar ,&nbsp;Sunil C. Kaul ,&nbsp;Renu Wadhwa ,&nbsp;Durai Sundar","doi":"10.1016/j.crstbi.2021.11.004","DOIUrl":"10.1016/j.crstbi.2021.11.004","url":null,"abstract":"<div><p>Serine/threonine-protein kinase B-raf (BRAF) plays a significant role in regulating cell division and proliferation through MAPK/ERK pathway. The constitutive expression of wild-type BRAF (BRAF^WT) and its mutant forms, especially V600E (BRAF^V600E), has been linked to multiple cancers. Various synthetic drugs have been approved and are in clinical trials, but most of them are reported to become ineffective within a short duration. Therefore, combinational therapy involving multiple drugs are often recruited for cancer treatment. However, they lead to toxicity and adverse side effects. In this computational study, we have investigated three natural compounds, namely Withaferin-A (Wi-A), Withanone (Wi-N) and Caffeic Acid Phenethyl ester (CAPE) for anti-BRAF^WT and anti-BRAF^V600E activity. We found that these compounds could bind stably at ATP-binding site in both BRAF^WT and BRAF^V600E proteins. In-depth analysis revealed that these compounds maintained the active conformation of wild-type BRAF protein by inducing αC-helix-In, DFG-In, extended activation segment and well-aligned R-spine residues similar to already known drugs Vemurafenib (VEM), BGB283 and Ponatinib. In terms of binding energy, among the natural compounds, CAPE showed better affinity towards both wild-type and V600E mutant proteins than the other two compounds. These data suggested that CAPE, Wi-A and Wi-N have potential to block constitutive autophosphorylation of BRAF and hence warrant <em>in vitro</em> and <em>in vivo</em> experimental validation.</p></div>","PeriodicalId":10870,"journal":{"name":"Current Research in Structural Biology","volume":"3 ","pages":"Pages 301-311"},"PeriodicalIF":2.8,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c9/ae/main.PMC8714769.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39681757","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}