Protein Binding Pocket Research Articles

Bcl-xL Dynamics under the Lens of Protein Structure Networks.

Understanding the finely orchestrated interactions leading to or preventing programmed cell death (apoptosis) is of utmost importance in cancer research because the failure of these systems could eventually lead to the onset of the disease. In this regard, the maintenance of a delicate balance between the promoters and inhibitors of mitochondrial apoptosis is crucial, as demonstrated by the interplay among the Bcl-2 family members. In particular, B-cell lymphoma extra-large (Bcl-xL) is a target of interest due to the forefront role of its dysfunctions in cancer development. Bcl-xL prevents apoptosis by binding both the pro-apoptotic BH3-only proteins, like PUMA, and the noncanonical partners, such as p53, at different sites. An allosteric communication between the BH3-only protein binding pocket and the p53 binding site, mediating the release of p53 from Bcl-xL upon PUMA binding, has been postulated and supported by nuclear magnetic resonance and other biophysical data. The molecular details of this mechanism, especially at the residue level, remain unclear. In this work, we investigated the distal communication between these two sites in Bcl-xL in its free state and when bound to PUMA. We also evaluated how missense mutations of Bcl-xL found in cancer samples might impair this communication and therefore the allosteric mechanism. We employed all-atom explicit solvent microsecond molecular dynamics simulations, analyzed through a Protein Structure Network approach and integrated with calculations of changes in free energies upon cancer-related mutations identified by genomics studies. We found a subset of candidate residues responsible for both maintaining protein stability and for conveying structural information between the two binding sites and hypothesized possible communication routes between specific residues at both sites.

Baicalein Binds to TLR4, Inhibits Colorectal Cancer Growth and Metastasis via the TLR4/HIF/VEGF Axis

Background: Lipopolysaccharide(LPS) inserts into the hydrophobic binding pocket of the myeloid differentiation protein 2(MD-2) that bound to toll-like receptor 4(TLR4). TLR4 antagonists have been designed based on the structure of lipid A, the innermost regions of LPS. However, these antagonists have poor bioavailability and may be toxic. Furthermore, the presence of lipid A moiety is not necessary for driving TLR4 activation. Therefore, compound directly binds to TLR4 is a better strategy to inhibit TLR4 activity. Methods: Biophysical techniques were used to examine the direct binding between baicalein and TLR4. With colorectal cancer(CRC) as models, coupled with drug-target-disease network, protein-protein interaction network and functional studies, the effect and the associated underlying mechanism of action upon the binding baicalein to TLR4 were examined. Findings: We evidently show a direct physical binding of baicalein to TLR4 in molecular docking, surface plasmon resonance biosensor analysis and bio-layer interferometry analysis. With CRC cells as model, we demonstrate the binding of baicalein to TLR4 with cellular thermal shift assay; which interrupts the binding of LPS to TLR4-MD-2 in the cells. Baicalein inhibits TLR4 activity, reduces CRC cell viability and migration in TLR4-dependent manner. Drug–targets–disease network and protein-protein interaction network highlight hypoxia inducible factor(HIF-1α) and vascular endothelial growth factor(VEGF) as downstream of TLR4, which are further validated in cell models. Involvement of TLR4/HIF-1α/VEGF axis in the anti-CRC and anti-angiogenic effect of baicalein is demonstrated in CRC-bearing mice and chick-chorioallantoic-membrane assay, respectively. Our study provides evidence to support the translation of baicalein into TLR4-targeting therapeutics. Funding Information: This work was partially supported by Research Grant Council of HKSAR HKBU-22103017-ECS, Innovation & Technology Commission #PRP/015/19FX, National Natural Science Foundation of China #SCM-2016-NSFC-003 and Natural Science Foundation of Guangdong Province #2018A0303130122 to HYK; the National Natural Science Foundation of China (82074019 and 81703705), Characteristic innovation projects of universities in Guangdong Province (2020KTSCX030), the Opening Project of Zhejiang Provincial Preponderant and Characteristic Subject of Key University (Traditional Chinese Pharmacology), Zhejiang Chinese Medical University (ZYAOX2018010) to ST. Declaration of Interests: The authors declare that they have no conflict of interest. Ethics Approval Statement: Animal experiments were approved by the Guangzhou University of Chinese Medicine Animal Care and Use Committee (Guangzhou, China), and conducted according to the ethical standards and national guidelines.

SARS-COV-2 Spike Glycoprotein as Inhibitory Target for In silico Screening of Natural Compounds

Coronavirus disease (Covid-19) caused by SARS-Cov-2 has raised global health concerns without approved drugs to manage this life-threatening disease. This study aimed to predict the inhibitory potential of quercetin-3-o-rutinoside against SARS-Cov-2 spike glycoprotein. Targeting the SARS-Cov-2 Nucleocapsid spike glycoprotein (pdb id: 6m3m) is gaining importance. In this present study, the relationship between plant-derived natural drug and spike glycoprotein was predicted using in silico computational approach. The results were evaluated according to the glide (Schrodinger) dock score. Among the five (5) screened natural compounds, quercetin-3-o-rutinoside has the best docking score (-9.296) with the target. Molecular dynamic (MD) simulation analysis was performed for 1000ps to confirm the spike protein's stability behavior and quercetin-3-o-rutinoside complex. The MD simulation analysis validated the stability of quercetin-3-o-rutinoside in the spike protein binding pocket as a potent inhibitor. The pharmacokinetics screening of the natural compounds showed that quercetin-3-o-rutinoside possesses good oral bioavailability with no side effects.

Imperatorin alleviated endometriosis by inhibiting the activation of PI3K/Akt/NF-κB pathway in rats

AimsMost therapeutic drugs of endometriosis have been contraceptives but symptoms recur in up to 75% of cases, which makes it a presses need to try to find novel and safer therapeutic drugs. Imperatorin is a furanocoumarin existing in many plants, possessing multiple activities, including anti-inflammatory. The purpose of this study was to assess the effects and mechanisms of imperatorin in endometriosis. Main methodsEctopic endometrial volume and hematoxylin-eosin staining were used to estimate the effects of imperatorin in experimental endometriosis model rats. Potential mechanisms of imperatorin in endometriosis were systematically analyzed by network pharmacology and molecular docking. Western blotting and enzyme-linked immunosorbent assay were employed to evaluate proteins expression and cytokines levels in PI3K/Akt/NF-κB pathway. Key findingsImperatorin could significantly inhibit the growth and ameliorate the histopathological features of ectopic endometrium in experimental endometriosis rats. Network pharmacology approaches showed that imperatorin might regulate inflammatory response and cellular function via primarily affecting PI3K-Akt pathway, Endocrine resistance, Th17 cell differentiation in endometriosis. Moreover, 7 core targets (PIK3CA, AKT1, SRC, MAPK8, MAPK14, ERBB2 and CCND1) resulted from the intersection of KEGG and PPI network topological analysis were used to dock with imperatorin, which indicated that imperatorin could preferably fit in the binding pocket of the above target proteins, except for CCND1. Lastly, imperatorin markedly inhibited the activation of PI3K/Akt/NF-κB pathway via suppressing the phosphorylation levels of PI3K, Akt and p65 in the ectopic endometrium tissue. SignificanceOur findings revealed that imperatorin is a significant multi-target natural active ingredient for treatment endometriosis.

Influence of the Environment on Shaping the Absorption of Monomeric Infrared Fluorescent Proteins.

Infrared fluorescent proteins (iRFPs) are potential candidates for deep-tissue in vivo imaging. Here, we provide molecular-level insights into the role of the protein environment in the structural stability of the chromophore within the protein binding pocket through the flexible hydrogen-bonding network using molecular dynamics simulation. Furthermore, we present systematic excited-state analysis to characterize the nature of the first two excited states and the role of the environment in shaping the nature of the chromophore’s excited states within the hybrid quantum mechanics/molecular mechanics framework. Our results reveal that the environment red-shifts the absorption of the chromophore by about 0.32 eV compared to the isolated counterpart, and besides the structural stability, the protein environment does not alter the nature of the excited state of the chromophore significantly. Our study contributes to the fundamental understanding of the excited-state processes of iRFPs in a complex environment and provides a design principle for developing iRFPs with desired spectral properties.

Allelic characterization and protein structure analysis reveals the involvement of splice site mutation for growth habit differences in Lablab purpureus (L.) Sweet

BackgroundInterrelationship between growth habit and flowering played a key role in the domestication history of pulses; however, the actual genes responsible for these traits have not been identified in Indian bean. Determinate growth habit is desirable due to its early flowering, photo-insensitivity, synchronous pod maturity, ease in manual harvesting and short crop duration. The present study aimed to identify, characterize and validate the gene responsible for growth habit by using a candidate gene approach coupled with sequencing, multiple sequence alignment, protein structure prediction and binding pocket analysis. ResultsTerminal flowering locus was amplified from GPKH 120 (indeterminate) and GNIB-21 (determinate) using the primers designed from PvTFL1y locus of common bean. Gene prediction revealed that the length of the third and fourth exons differed between the two alleles. Allelic sequence comparison indicated a transition from guanine to adenine at the end of the third exon in GNIB 21. This splice site single-nucleotide polymorphism (SNP) was validated in germplasm lines by sequencing. Protein structure analysis indicated involvement of two binding pockets for interaction of terminal flowering locus (TFL) protein with other proteins. ConclusionThe splice site SNP present at the end of the third exon of TFL locus is responsible for the transformation of shoot apical meristem into a reproductive fate in the determinate genotype GNIB 21. The splice site SNP leads to absence of 14 amino acids in mutant TFL protein of GNIB 21, rendering the protein non-functional. This deletion disturbed previously reported anion-binding pocket and secondary binding pocket due to displacement of small β-sheet away from an external loop. This finding may enable the modulation of growth habit in Indian bean and other pulse crops through genome editing.

Black pepper and piperine induce anticancer effects on leukemia cell line.

The black pepper, most commonly used in Indian cuisines for ages, is considered as "king of spices." The present study evaluates the anticancer potential of black pepper and its main constituent, i.e. alkaloid piperine, against human leukemia cell line, K-562 cells. Gas chromatography-mass spectrometry (GC-MS) analysis confirmed the presence of piperine in black pepper extract. The methanolic extract of black pepper (BP-M) and pure piperine (PIP) showed a strong cytotoxic effect against this cell line. Both BP-M and PIP generated apoptotic bodies in K-562 cells and caused nuclear condensation as visualized by fluorescent microscopy, which was further confirmed by flow cytometry analysis. BP-M and PIP also generated reactive oxygen species in K-562 cells as established by flow cytometry. The translation of Bax, caspase-3 and caspase-9 genes was found to be upregulated with subsequent downregulation of Bcl-2 gene. The anti-proliferative effect of both BP-M and PIP was also observed by trypan blue staining and was further confirmed by the downregulated expression of proliferating cell nuclear antigen (PCNA). The molecular docking studies showed the binding of PIP with PCNA and Bcl-2 and supported the in vitro findings. The docking studies also proposed the binding of PIP to ADP binding pocket of Apaf-1 protein. Taken together, these findings signify the anticancer potential of both black pepper and PIP, thus proposing black pepper as a potent nutraceutical for preventing the progression of chronic myeloid leukemia.

OctSurf: Efficient hierarchical voxel-based molecular surface representation for protein-ligand affinity prediction

Voxel-based 3D convolutional neural networks (CNNs) have been applied to predict protein-ligand binding affinity. However, the memory usage and computation cost of these voxel-based approaches increase cubically with respect to spatial resolution and sometimes make volumetric CNNs intractable at higher resolutions. Therefore, it is necessary to develop memory-efficient alternatives that can accelerate the convolutional operation on 3D volumetric representations of the protein-ligand interaction. In this study, we implement a novel volumetric representation, OctSurf, to characterize the 3D molecular surface of protein binding pockets and bound ligands. The OctSurf surface representation is built based on the octree data structure, which has been widely used in computer graphics to efficiently represent and store 3D object data. Vanilla 3D-CNN approaches often divide the 3D space of objects into equal-sized voxels. In contrast, OctSurf recursively partitions the 3D space containing the protein-ligand pocket into eight subspaces called octants. Only those octants containing van der Waals surface points of protein or ligand atoms undergo the recursive subdivision process until they reach the predefined octree depth, whereas unoccupied octants are kept intact to reduce the memory cost. Resulting non-empty leaf octants approximate molecular surfaces of the protein pocket and bound ligands. These surface octants, along with their chemical and geometric features, are used as the input to 3D-CNNs. Two kinds of CNN architectures, VGG and ResNet, are applied to the OctSurf representation to predict binding affinity. The OctSurf representation consumes much less memory than the conventional voxel representation at the same resolution. By restricting the convolution operation to only octants of the smallest size, our method also alleviates the overall computational overhead of CNN. A series of experiments are performed to demonstrate the disk storage and computational efficiency of the proposed learning method. Our code is available at the following GitHub repository: https://github.uconn.edu/mldrugdiscovery/OctSurf.

Reversible Michael Addition of an Engineered Cysteine Residue to a Light Activated Ligand, a New Design Strategy for a Synthetic Photoswitchable Fluorescent Protein

Reversible photoswitchable fluorescent probes can transit between two different optical states when triggered by light. Because of the ability to switch, they become useful in live cell super-resolution microscopy (e.g. RESOLFT, psSIM, STORM, PALM), information storage, and optical control of protein activity. Currently, only a handful of fluorescent proteins and synthetic dyes exhibit reversible photoswitchability. Hence, there is a growing interest for new systems with enhanced functionality. We are currently focused on utilizing a synthetic ligand capable of reversible Michael addition of an active cysteine residue, within the binding pocket of human cellular retinoid binding protein (hCRBPII).

Probing CAS database as prospective antiviral agents against SARS-CoV-2 main protease

The pandemic of COVID-19 has an unprecedented impact on global health and economy. The novel SARS-CoV-2 is recognized as the etiological agent of current outbreak. Because of its contagious human-to-human transmission, it is an utmost global health emergency at present. To mitigate this threat many scientists and researchers are racing to develop antiviral therapy against the virus. Unfortunately, to date no vaccine or antiviral therapeutic is approved thus there is an urgent need to discover antiviral agent to help the individual who are at high risk. Virus main protease or chymotrypsin-like protease plays a pivotal role in virus replication and transcription; thus, it is considered as an attractive drug target to combat the COVID-19. In this study, multistep structure based virtual screening of CAS antiviral database is performed for the identification of potent and effective small molecule inhibitors against chymotrypsin-like protease of SARS-CoV-2. Consensus scoring strategy combine with flexible docking is used to extract potential hits. As a result of extensive virtual screening, 4 hits were shortlisted for MD simulation to study their stability and dynamic behavior. Insight binding modes demonstrated that the selected hits stabilized inside the binding pocket of the target protein and exhibit complementarity with the active site residues. Our study provides compounds for further in vitro and in vivo studies against SARS-CoV-2.

Furan-2-carboxamide derivative, a novel microtubule stabilizing agent induces mitotic arrest and potentiates apoptosis in cancer cells

The vital role played by microtubules in the cell division process, marks them as a potential druggable target to decimate cancer. A novel furan-2-carboxamide based small molecule, is a selective microtubule stabilizing agent (MSA) with IC50 ranging from 4 µM to 8 µM in different cancer cell lines. Inhibition of tubulin polymerization or stabilization of tubulin polymers abrogates chromosomal segregation during cell division, results in cell cycle arrest and leads to cell death due to the delayed repair mechanism. A novel furan-2-carboxamide based small molecule exhibited potent anti-proliferative and anti-metastatic property In-Vitro against the panel of cancer cells. Annexin V-FITC/PI, double staining reveals potent cytotoxic effect of SH09 against HeLa cells. FACS analysis displays induction of G2/M arrest and accumulation of subG1 population of cells upon treatment with SH09. Molecular docking study unveils SH09 binding affinity to the Taxol binding pocket of tubulin proteins and MM-GBSA also confirms strong binding energies of SH09 with tubulin proteins.

Three Dimensional Quantitative Structure Activity Relationship and Molecular Docking Studies of Flavonoids as Reverse Transcriptase Inhibitors

A set of 29 flavonoid molecules are used to generate comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models. The best CoMFA model showed a cross-validated correlation coefficient (q2) = 0.762, noncross- validated correlation coefficient (r2) = 0.939, standard error of estimate (S) = 0.038 and F = 396. And that for CoMSIA model were q2 = 0.758, r2 = 0.957, S = 0.063 and F = 236. The models show a high predictive ability, validated by 11 favonoid molecules. The docking studies shows the hydrogen bonding interaction is mostly responsible for binding of the flavonoids molecules in the binding pocket of HIV 1-RT protein (3HVT.pdb).

Phytochemical profile of Cespedesia spathulata leaves (Ochnaceae) and its effect on tyrosinase enzyme.

Phytochemical studies of Cespedesia spathulata (Ochnaceae) leaves using 1H, 13C NMR, and GC-MS have led to the isolation of some metabolites identified for the first time in these species such as cathechin, epicatechin, vitexin, orientin, 6''-O-acetyl-vitexin, sitosterol, stigmasterol, phytol, 4,5-dihydrovomifoliol and a mixture of aliphatic methyl esters, together with ochnaflavone, which was previously isolated from this plant. The modulating activity of some fractions and compounds from Cespedesia spathulata towards tyrosinase enzyme was assayed by spectroscopic and theoretical means/experiments. The dichloromethane fraction (133 μg mL-1) and ochnaflavone (333 μM) inhibited tyrosinase activity by 20 % and 2.0 %, respectively, whereas the ethyl acetate fraction (666 μg mL-1) and ±catechins (catechin and epicatechin - 800 μM) activated it by 104 % and 384 %, respectively. Quantum chemical calculations suggested that catechin and epicatechin are better activators than L-DOPA by interacting with Cu (II) ions. Molecular docking results suggested that hydrogen bonding and hydrophobic interactions are the main binding forces between each tyrosinase activator and the amino acid residues inside the active protein binding pocket.

General Theory of Fragment Linking in Molecular Design: Why Fragment Linking Rarely Succeeds and How to Improve Outcomes.

Linking two fragments binding in nearby subpockets together has become an important technique in fragment-based drug discovery to optimize the binding potency of fragment hits. Despite the expected favorable translational and orientational entropic contribution to the binding free energy of the linked molecule, brute force enumeration of chemical linker for linking fragments is rarely successful, and the vast majority of linked molecules do not exhibit the expected gains of binding potency. In this paper, we examine the physical factors that contribute to the change of binding free energy from fragment linking and develop a method to rigorously calculate these different physical contributions. We find from these analyses that multiple confounding factors make successful fragment linking strategies rare, including (1) possible change of the binding mode of the fragments in the linked state compared to separate binding of the fragments, (2) unfavorable intramolecular strain energy of the bioactive conformation of the linked molecule, (3) unfavorable interaction between the linker and the protein, (4) favorable interaction energies between two fragments in solution when not chemically linked that offset the expected entropy loss for the formation of fragment pair, (5) complex compensating configurational entropic effects beyond the simplistic rotational and translational analysis. We here have applied a statistically mechanically rigorous approach to compute the fragment linking coefficients of 10 pharmaceutically interesting systems and quantify the contribution of each physical component to the binding free energy of the linked molecule. Based on these studies, we have found that the change in the relative configurational entropy of the two fragments in the protein binding pocket (a term neglected to our knowledge in all previous analyses) substantially offsets the favorable expected rotational and translational entropic contributions to the binding free energy of the linked molecule. This configurational restriction of the fragments in the binding pocket of the proteins is found to be, in our analysis, the dominant reason why most fragment linking strategies do not exhibit the expected gains of binding potency. These findings have further provided rich physical insights, which we expect should facilitate more successful fragment linking strategies to be formulated in the future.

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features.

The virtual screening of large numbers of compounds against target protein binding sites has become an integral component of drug discovery workflows. This screening is often done by computationally docking ligands into a protein binding site of interest, but this has the drawback of a large number of poses that must be evaluated to obtain accurate estimates of protein-ligand binding affinity. We here introduce a fast pre-filtering method for ligand prioritization that is based on a set of machine learning models and uses simple pose-invariant physicochemical descriptors of the ligands and the protein binding pocket. Our method, Rapid Screening with Physicochemical Descriptors + machine learning (RASPD+), is trained on PDBbind data and achieves a regression performance that is better than that of the original RASPD method and traditional scoring functions on a range of different test sets without the need for generating ligand poses. Additionally, we use RASPD+ to identify molecular features important for binding affinity and assess the ability of RASPD+ to enrich active molecules from decoys.

Anisotine and amarogentin as promising inhibitory candidates against SARS-CoV-2 proteins: a computational investigation

The coronavirus disease 2019 (COVID-19) pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents an unprecedented challenge to global public health with researchers striving to find a possible therapeutic candidate that could limit the spread of the virus. In this context, the present study employed an in silico molecular interaction-based approach to estimate the inhibitory potential of the phytochemicals from ethnomedicinally relevant Indian plants including Justicia adhatoda, Ocimum sanctum and Swertia chirata, with reported antiviral activities against crucial SARS-CoV-2 proteins. SARS-CoV-2 proteins associated with host attachment and viral replication namely, spike protein, main protease enzyme Mpro and RNA-dependent RNA polymerase (RdRp) are promising druggable targets for COVID-19 therapeutic research. Extensive molecular docking of the phytocompounds at the binding pockets of the viral proteins revealed their promising inhibitory potential. Subsequent assessment of physicochemical features and potential toxicity of the compounds followed by robust molecular dynamics simulations and analysis of MM-PBSA energy scoring function revealed anisotine against SARS-CoV-2 spike and Mpro proteins and amarogentin against SARS-CoV-2 RdRp as potential inhibitors. It was interesting to note that these compounds displayed significantly higher binding energy scores against the respective SARS-CoV-2 proteins compared to the relevant drugs that are currently being targeted against them. Present research findings confer scopes to explore further the potential of these compounds in vitro and in vivo towards deployment as efficient SARS-CoV-2 inhibitors and development of novel effective therapeutics. Communicated by Ramaswamy H. Sarma

Unraveling individual host-guest interactions in molecular recognition from first principles quantum mechanics: Insights into the nature of nicotinic acetylcholine receptor agonist binding.

Drug binding to a protein target is governed by a complex pattern of noncovalent interactions between the ligand and the residues in the protein's binding pocket. Here we introduce a generally applicable, parameter-free, computational method that allows for the identification, quantification, and analysis of the key ligand-residue interactions responsible for molecular recognition. Our strategy relies on Local Energy Decomposition analysis at the "gold-standard" coupled cluster DLPNO-CCSD(T) level. In the study case shown in this paper, nicotine and imidacloprid binding to the nicotinic acetylcholine receptor, our approach provides new insights into how individual amino acids in the active site determine sensitivity and selectivity of the ligands, extending and refining classical pharmacophore hypotheses. By inference, the method is applicable to any kind of host/guest interactions with potential applications in industrial biocatalysis and protein engineering.

Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching.

Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin-TBA complex. In the free GQ, T3 is solvent-exposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (Kd) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQ-folding aptamers in the absence of DNA topology switching.

A Comprehensive Overview of Structure-Activity Relationships of Small-Molecule Splicing Modulators Targeting SF3B1 as Anticancer Agents.

The pre-mRNA splicing factor SF3B1 shows recurrent mutations among hematologic malignancies and some solid tumors. In 2007, the identification of two cytotoxic natural products, which showed splicing inhibition by binding to SF3b, prompted the development of small-molecule splicing modulators of SF3B1 as therapeutics for cancer. Recent studies suggested that spliceosome-mutant cells are preferentially sensitive to pharmacologic splicing modulation; therefore, exploring the clinical utility of splicing modulator therapies in patients with spliceosome-mutant hematologic malignancies who have failed current therapies is greatly needed, as these patients have few treatment options. H3B-8800 had unique pharmacological activity and exhibited favorable data in phase I clinical trials to treat patients with advanced myeloid malignancies, indicating that further clinical trials are promising. The most established small-molecule modulators of SF3B1 can be categorized into three classes: the bicycles, the monopyranes, and the 12-membered macrolides. This review provides a comprehensive overview of the structure-activity relationships of small-molecule SF3B1 modulators, with a detailed analysis of interactions between modulators and protein binding pocket. The future strategy for splicing modulators development is also discussed.

Discovery of anaplastic lymphoma kinase inhibitors from natural product library: A holistic in silico approach.

Over the years, phytochemical compounds have shown compelling evidences in exhibiting powerful antitumor properties. Moreover, due to the lack of safety and high cost of cancer therapies, opportunities are being sought out in these compounds as an alternative treatment modality. Therefore, in the present study, 1,574 compounds from NPACT library were examined to excavate potent and nontoxic anaplastic lymphoma kinase (ALK) inhibitors. Notably, two pharmacophore hypotheses (AAAHP and DDRRR) were generated using ligand-based and energy-based techniques, respectively, to eliminate false-positive prediction in database screening. Furthermore, molecular docking and Prime MM/GBSA analysis were performed on the screened compounds to examine inhibitory activity against ALK. The analysis revealed that the two hits, namely, NPACT00018 and NPACT01077, exhibited better docking scores, binding energies, and also ensured excellent drug-likeness properties than the reference compound, crizotinib. Finally, the results were subjected to molecular dynamics studies to gain insight into the stability of these compounds in the binding pocket of ALK protein. Indeed, the useful predictions generated by the present computational models are of immense importance and could further speed up the anticancer drug development in the near future.