In silico modeling of Plasmodium falciparum chloroquine resistance transporter protein and biochemical studies suggest its key contribution to chloroquine resistance

Chloroquine (CQ) has been used for decades as the primary chemotherapeutic drug for the treatment of malaria. The emergence of drug resistance in Plasmodium falciparum has been considered to be because of the excessive use of antimalarial drugs worldwide. Moreover, the intense distribution and prevalence of chloroquine-resistant strains in endemic regions has aided the incidence of more complications to malaria treatment and control. Due to the lack of literature that portrays evident molecular mechanisms of drug resistance, it has been difficult to understand the drug resistance conferred by Plasmodium species. Intensive research on CQ drug resistance has identified the association of P. falciparum chloroquine resistance transporter protein (PfCRT), which belongs to the drug/metabolite transporter and EamA-like superfamily. Additionally, it has shown that K76 T mutation in PfCRT protein has mainly attributed to CQ resistance than other mutations. This study deals with the development of an in silico model of the PfCRT protein and its interaction with the CQ ligand molecule as well as the biochemical and biophysical characterization of the transmembrane domain 1 (TMD 1) peptide of the PfCRT protein. The physiochemical analysis of the PfCRT protein identified basic differences between the wild and mutant forms of the protein, as well as identifying the high hydrophobic nature of the mutant-type protein. The tertiary structure of the PfCRT protein was predicted and interaction with CQ revealed different active pocket binding regions in both the wild and mutant form of PfCRT proteins. The CQ²⁺ molecule interacts with TMD 10 of the wild-type PfCRT protein, whereas it interacts with TMD 1 of the mutant-type protein. Studies on the TMD 1 peptide revealed the insertion of the peptide in the micelles adopting stable alpha-helical structure. Binding studies with the CQ molecule detected high binding affinity toward the mutant-type TMD 1 peptide rather than the wild-type, thus confirming that the TMD 1 peptide is involved in substrate selectivity. Our findings help to characterize the structure of the PfCRT protein and the role played by the TMD 1 region in CQ resistance using in silico and biochemical approaches. Molecular docking and ligand binding studies confirm that TMD 1 is involved in substrate selectivity and aids in CQ efflux, thereby contributing to the parasite's CQ drug resistance mechanism.

Mechanistic insights into the activity of Ptf1-p48 (pancreas transcription factor 1a): probing the interactions levels of Ptf1-p48 with E2A-E47 (transcription factor E2-alpha) and ID3 (inhibitor of DNA binding 3)

Ptf1-p48 (Pancreas specific transcription factor 1a) is transcription regulatory protein known for the activation of exocrine specific genes. Downregulation of its expression formulates early stages of pancreatic adenocarcinoma as deduced by its association with oncogenic bHLH (Basic Helix-Loop-Helix) protein ID3 (Inhibitor of DNA binding 3) protein whose overexpression induces cytoplasmic mislocalization of Ptf1-p48. The precise mechanism and/or functional role of Ptf1-p48in promoting pancreatic cancer is vague. The structural features of the Ptf1-p48 and its dimerization with E47 (Transcription factor E2-alpha) and ID3 mediated by their HLH (Helix-Loop-Helix) domain were perceived through MD (Molecular Dynamics) simulations of 50 ns. The interactions formed by the HLH domain in both Ptf1-E47 and Ptf1-ID3 complexes are favored by the synergistic movement of their domain helices. Accordingly, in the Ptf1-E47 complex α7 of Ptf1-p48 and α1 helix of E47 along with the loop residues of their HLH domain exhibit transitions marked by inward movement toward each other and forms polar and charged interactions. In the Ptf1-ID3 complex, α8 of Ptf1-p48 moves toward the α3 helix of ID3 and forms hydrogen bonds. The interface analysis also reveals better interface in the Ptf1-p48 complex than the Ptf1-ID3 evident by energetics and number of hydrogen bonds. The interactions in each of these complexes, supported by angular displacement and mode vector analyzes, comprehensibly describe the considerable structural changes induced upon dimer formation. It thereby gives an insight into the interfaces that could help in designing of potential inhibitors for ID3 to curb the cancer cell growth.

Structural transition of ETS1 from an auto-inhibited to functional state upon association with the p16INK4anative and mutated promoter region

Detailed elucidation of structural changes invoked on transcriptional factors and their target genes upon their association is pivotal for understanding the genetic level regulations imposed in several diseases including ovarian cancer.

Interacting mechanism of ID3 HLH domain towards E2A/E12 transcription factor - An Insight through molecular dynamics and docking approach

Inhibitor of DNA binding protein 3 (ID3) has long been characterized as an oncogene that implicates its functional role through its Helix-Loop-Helix (HLH) domain upon protein-protein interaction. An insight into the dimerization brought by this domain helps in identifying the key residues that favor the mechanism behind it. Molecular dynamics (MD) simulations were performed for the HLH proteins ID3 and Transcription factor E2-alpha (E2A/E12) and their ensemble complex (ID3-E2A/E12) to gather information about the HLH domain region and its role in the interaction process. Further evaluation of the results by Principal Component Analysis (PCA) and Free Energy Landscape (FEL) helped in revealing residues of E2A/E12: Lys570, Ala595, Val598, and Ile599 and ID3: Glu53, Gln63, and Gln66 buried in their HLH motifs imparting key roles in dimerization process. Furthermore the T-pad analysis results helped in identifying the key fluctuations and conformational transitions using the intrinsic properties of the residues present in the domain region of the proteins thus specifying their crucial role towards molecular recognition. The study provides an insight into the interacting mechanism of the ID3-E2A/E12 complex and maps the structural transitions arising in the essential conformational space indicating the key structural changes within the helical regions of the motif. It thereby describes how the internal dynamics of the proteins might regulate their intrinsic structural features and its subsequent functionality.

(Z)-3-(1-Hy-droxy-3-oxobut-1-en-yl)-6-nitro-2H-chromen-2-one

In the title compound, C(13)H(9)NO(6), the coumarin system has the benzene ring aligned at 0.61 (18)° with respect to the pyrone ring. An intra-molecular O-H⋯O hydrogen bond stabilizes the mol-ecular conformation and a C-H⋯O contact also occurs. In the crystal, weak C-H⋯O inter-actions link the mol-ecules, forming inversion dimers.

Structure prediction of Bestrophin for the induced - fit docking of anthocyanins

Bestrophin, an integral membrane protein existing in basolateral region of the retina is a propitious target for drug discovery. Mutations in the Bestrophin protein cause Best Vitelliform Macular Dystrophy (BVMD) leading to retinal damages and loss of visual acuity. Owing to the lack of three dimensional structure and related structural homologs in the protein data bank, we modeled the bestrophin protein using Robetta ab initio method. Further, no treatment is available for the disease. In this situation, anthocyanins from natural sources are reported to combat retinal damages. Hence, we identified anthocyanins from Syzygium cumini fruit skin using Electrospray Ionization tandem mass spectrometry. These compounds were docked into the predicted bestrophin model to study the interactions within the active site. The results may provide a valuable insight into the structure of bestrophin and efficacy of anthocyanins in molecular docking studies.

ABBREVIATIONS

PTP - Putative transmembrane proteins, VMD - Vitelliform macular dystrophy, BVMD - Best's vitelliform macular dystrophy, RPE - Retinal pigment epithelium, ESI-MS/MS - Electrospray Ionization Tandem Mass Spectrometry, UNIPROT - Universal Protein Resource, PSIPRED - Protein secondary structure prediction, TMH - Transmembrane Helices, SCFS - Syzygium cumini fruit skin DP - Declustering Potential IFD - Induced Fit Docking.

6-Amino-3,4-dimethyl-4-phenyl-2H,4H-pyrano[2,3-c]pyrazole-5-carbonitrile

In the title compound, C₁₅H₁₄N₄O, the pyrazole ring is aligned at 88.23 (4)° with respect to the aromatic ring and at 3.75 (4)° with respect to the pyran ring. In the crystal, N—H⋯N hydrogen bonds link adjacent mol­ecules into a linear chain motif. C—H⋯N inter­actions are also observed.