Dakshinamurthy Sivakumar

Treating acute myeloid leukemia (AML) by targeting FMS-like tyrosine kinase 3 (FLT-3) is considered an effective treatment strategy. By using AI-assisted hit optimization, we discovered a novel and highly selective compound with desired drug-like properties with which to target the FLT-3(D835Y) mutant. In the current study, we applied an AI-assisted de novo design approach to identify a novel inhibitor of FLT-3(D835Y). A recurrent neural network containing long short-term memory cells (LSTM)… عرض المزيد

Treating acute myeloid leukemia (AML) by targeting FMS-like tyrosine kinase 3 (FLT-3) is considered an effective treatment strategy. By using AI-assisted hit optimization, we discovered a novel and highly selective compound with desired drug-like properties with which to target the FLT-3(D835Y) mutant. In the current study, we applied an AI-assisted de novo design approach to identify a novel inhibitor of FLT-3(D835Y). A recurrent neural network containing long short-term memory cells (LSTM) was implemented to generate potential candidates related to our in-house hit compound (PCW-1001). Approximately 10,416 hits were generated from 20 epochs, and the generated hits were further filtered using various toxicity and synthetic feasibility filters. Based on the docking and free energy ranking, the top compound was selected for synthesis and screening. عرض أقل

Binding free energy estimation of drug candidates to their biomolecular target is one of the best quantitative estimators in computer-aided drug discovery. Accurate binding free energy estimation is still a challengeable task even after decades of research, along with the complexity of the algorithm, time-consuming procedures, and reproducibility issues. In this review, we have discussed the advantages and disadvantages of diverse free energy methods like Thermodynamic Integration (TI)… عرض المزيد

Binding free energy estimation of drug candidates to their biomolecular target is one of the best quantitative estimators in computer-aided drug discovery. Accurate binding free energy estimation is still a challengeable task even after decades of research, along with the complexity of the algorithm, time-consuming procedures, and reproducibility issues. In this review, we have discussed the advantages and disadvantages of diverse free energy methods like Thermodynamic Integration (TI), Bennett's Acceptance Ratio (BAR), Free Energy Perturbation (FEP), and alchemical methods. Moreover, we discussed the possible application of the machine learning method in proteinligand binding free energy estimation.

Keywords: Free energy, Bennett's acceptance ratio (BAR), alchemical methods, machine learning, computer-aided drug discovery, thermodynamic integration (TI). عرض أقل

The urgent need for novel and effective drugs against the SARS-CoV-2 coronavirus pandemic has stimulated research worldwide. The Papain-like protease (PLpro), which is essential for viral replication, shares a similar active site structural architecture to other cysteine proteases. Here, we have used representatives of the Ovarian Tumor Domain deubiquitinase family OTUB1 and OTUB2 along with the PLpro of SARS-CoV-2 to validate and rationalize the binding of inhibitors from previous SARS-CoV… عرض المزيد

The urgent need for novel and effective drugs against the SARS-CoV-2 coronavirus pandemic has stimulated research worldwide. The Papain-like protease (PLpro), which is essential for viral replication, shares a similar active site structural architecture to other cysteine proteases. Here, we have used representatives of the Ovarian Tumor Domain deubiquitinase family OTUB1 and OTUB2 along with the PLpro of SARS-CoV-2 to validate and rationalize the binding of inhibitors from previous SARS-CoV candidate compounds. By forming a new chemical bond with the cysteine residue of the catalytic triad, covalent inhibitors irreversibly suppress the protein’s activity. Modeling covalent inhibitor binding requires detailed knowledge about the compounds’ reactivities and binding. Molecular Dynamics refinement simulations of top poses reveal detailed ligand-protein interactions and show their stability over time. The recently discovered selective OTUB2 covalent inhibitors were used to establish and validate the computational protocol. Structural parameters and ligand dynamics are in excellent agreement with the ligand-bound OTUB2 crystal structures. For SARS-CoV-2 PLpro, recent covalent peptidomimetic inhibitors were simulated and reveal that the ligand-protein interaction is very dynamic. The covalent and non-covalent docking plus subsequent MD refinement of known SARS-CoV inhibitors into DUBs and the SARS-CoV-2 PLpro point out a possible approach to target the PLpro cysteine protease from SARS-CoV-2. The results show that such an approach gives insight into ligand-protein interactions, their dynamic character, and indicates a path for selective ligand design. عرض أقل

PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibitors BAY73-6691R, BAY73-6691S, 28r, 28s, 3r, 3s, PF-0447943, PF-4181366, and 4r to elucidate the differences in their interaction patterns in the presence of different metal systems such as Zn/Mg, Mg/Mg, and Zn/Zn. The initial complexes were… عرض المزيد

PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibitors BAY73-6691R, BAY73-6691S, 28r, 28s, 3r, 3s, PF-0447943, PF-4181366, and 4r to elucidate the differences in their interaction patterns in the presence of different metal systems such as Zn/Mg, Mg/Mg, and Zn/Zn. The initial complexes were generated by molecular docking followed by molecular dynamics simulation for 100 ns in triplicate for each system to understand the interactions’ stability. The results were carefully analyzed, focusing on the ligands’ non-bonded interactions with PDE9 in different metal systems عرض أقل

The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTU ubiquitin aldehyde binding 1 (OTUB1) and OTUB2 are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics… عرض المزيد

The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTU ubiquitin aldehyde binding 1 (OTUB1) and OTUB2 are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases, but differ in their configuration and protonation states. The OTUB1 protein had a pre-arranged catalytic site, with strong electrostatic interactions between the active-site residues His-265 and Asp-267. In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding, did the catalytic triad in OTUB2 re-arrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His-224 and Asn-226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors. عرض أقل

Abstract
Pyridine nucleotide cofactors play important roles in biocatalytic processes that generate value-added chemicals for the pharmaceutical and food industries. Because of the high price of these pyridine cofactors, cofactor regeneration is highly desirable. However, recycling the oxidized form of cofactors, especially NADP+, remains a challenge. Here, we cloned and characterized an NADH oxidase from Lactobacillus reuteri (LreNox) which can oxidize both NADH and NADPH. Unlike many other… عرض المزيد

Abstract
Pyridine nucleotide cofactors play important roles in biocatalytic processes that generate value-added chemicals for the pharmaceutical and food industries. Because of the high price of these pyridine cofactors, cofactor regeneration is highly desirable. However, recycling the oxidized form of cofactors, especially NADP+, remains a challenge. Here, we cloned and characterized an NADH oxidase from Lactobacillus reuteri (LreNox) which can oxidize both NADH and NADPH. Unlike many other Noxs, LreNox showed equal catalytic efficiency towards NADH and NADPH. To the best our knowledge, LreNox has the highest activity towards NADPH as a substrate compared to other wild type Noxs. Homology modeling and substrate docking studies provided insights into the dual substrate specificity of LreNox. Gly155, Ser179, and His184 in the LreNox substrate binding pocket, which are absent in other Noxs structures, are crucial for NADPH recognition, providing more space for interactions with the additional phosphate group present in NADPH. We also explored the utility of LreNox for NADP+ regeneration in l-sorbose production by coupling it with a sorbitol dehydrogenase. The turn over number (TTN) improved ~53-fold after using LreNox as the NADP+ recycling enzyme. This study demonstrates that LreNox could potentially be used for the regeneration of NAD(P)+ in commercial applications.

Keywords
NADH oxidaseCofactor regenerationHomology modelingRare l-sugars عرض أقل

Multi-enzymatic cascade reactions have garnered the attention of many researchers as an approach for converting CO2 into methanol. The cascade reaction used in this study includes the enzymes a formate dehydrogenase (ClFDH), a formaldehyde dehydrogenase (BmFaldDH), and an alcohol dehydrogenase (YADH) from Clostridium ljungdahlii, Burkholderia multivorans, and Saccharomyces cerevisiae, respectively. Because this cascade reaction requires NADH as a cofactor, phosphite dehydrogenase (PTDH) was… عرض المزيد

Multi-enzymatic cascade reactions have garnered the attention of many researchers as an approach for converting CO2 into methanol. The cascade reaction used in this study includes the enzymes a formate dehydrogenase (ClFDH), a formaldehyde dehydrogenase (BmFaldDH), and an alcohol dehydrogenase (YADH) from Clostridium ljungdahlii, Burkholderia multivorans, and Saccharomyces cerevisiae, respectively. Because this cascade reaction requires NADH as a cofactor, phosphite dehydrogenase (PTDH) was employed to regenerate the cofactor. The multi-enzymatic cascade reaction, along with PTDH, yielded 3.28 mM methanol. The key to the success of this cascade reaction was a novel formaldehyde dehydrogenase, BmFaldDH, the enzyme catalyzing reduction of formate to formaldehyde. The methanol yield was further improved by incorporation of 1-ethyl-3-methylimidazolium acetate, resulting in 7.86 mM of methanol. A 500-fold increase in total turnover number was observed for the ClFDH-BmFaldDH-YADH cascade system compared to the Candida boidinii FDH-Pseudomonas putida FaldDH-YADH system. We provided detailed insights into the enzymatic reduction of CO2 by determining the thermodynamic parameters (Kd and ΔG) using isothermal titration calorimetry. Furthermore, we demonstrated a novel time-dependent formaldehyde production from CO2. Our results will aid in the understanding and development of a robust multienzyme catalyzed cascade reaction for the reduction of CO2 to value-added chemicals. عرض أقل

Upgrading ethanol to higher order alcohols is desired but difficult using current biotechnological methods. In this study, we designed a completely artificial reaction pathway for upgrading ethanol to acetoin, 2,3-butanediol, and 2-butanol in a cell-free bio-system composed of ethanol dehydrogenase, formolase, 2,3-butanediol dehydrogenase, diol dehydratase, and NADH oxidase. Under optimized conditions, acetoin, 2,3-butanediol, and 2-butanol were produced at 88.78%, 88.28%, and 27.25% of the… عرض المزيد

Upgrading ethanol to higher order alcohols is desired but difficult using current biotechnological methods. In this study, we designed a completely artificial reaction pathway for upgrading ethanol to acetoin, 2,3-butanediol, and 2-butanol in a cell-free bio-system composed of ethanol dehydrogenase, formolase, 2,3-butanediol dehydrogenase, diol dehydratase, and NADH oxidase. Under optimized conditions, acetoin, 2,3-butanediol, and 2-butanol were produced at 88.78%, 88.28%, and 27.25% of the theoretical yield from 100 mM ethanol, respectively. These results demonstrate that this artificial synthetic pathway is an environmentally-friendly novel approach for upgrading bio-ethanol to acetoin, 2,3-butanediol, and 2-butanol. عرض أقل

In this study, we determined that DPI was toxic to breast cancer cell lines as individual drug as well as in combination with DOX. Moreover, immunofluorescence and confocal studies showed that DPI decreases DOX induced YB-1 nuclear translocation and increases DOX accumulation in breast cancer cell line. A G1/G0 phase cell cycle arrest and apoptosis was also induced by DPI. Moreover, DPI modulated YB-1 downstream targets such as p53, caspase-3, CDK-1 which are involved in cell cycle progression… عرض المزيد

In this study, we determined that DPI was toxic to breast cancer cell lines as individual drug as well as in combination with DOX. Moreover, immunofluorescence and confocal studies showed that DPI decreases DOX induced YB-1 nuclear translocation and increases DOX accumulation in breast cancer cell line. A G1/G0 phase cell cycle arrest and apoptosis was also induced by DPI. Moreover, DPI modulated YB-1 downstream targets such as p53, caspase-3, CDK-1 which are involved in cell cycle progression and apoptosis. Further, metastatic functional analysis revealed that DPI inhibits cell adhesion, migration, invasion in aggressive metastatic cell line and inhibits angiogenesis in chick embryonic chorioallantoic membrane (CAM) model. Meanwhile, DPI alters the expression of YB-1 downstream targets which are involved in metastasis such as VEGFR, caveolin, E-cadherin, cytokeratins, desmin and vimentin in MDA-MB-231 xenograft in chick embryonic CAM membrane. The results clearly demonstrated that DPI inhibited YB-1 nuclear translocation, thereby exhibited anti-apoptotic, anti-proliferative and anti-metastatic activities and increases the therapeutic potential of commercial breast cancer drug doxorubicin. عرض أقل

Cancer cells evade apoptosis, which is regulated by proteins of Bcl-2 family in the intrinsic pathways. Numerous experimental three-dimensional (3D) structures of the apoptotic proteins and the proteins bound with small chemical molecules/peptides/proteins have been reported in the literature. In this review article, the 3D structures of the Bcl-2 family proteins from Homo sapiens and as well complex structures of the anti-apoptotic proteins bound with small molecular inhibitors reported in the… عرض المزيد

Cancer cells evade apoptosis, which is regulated by proteins of Bcl-2 family in the intrinsic pathways. Numerous experimental three-dimensional (3D) structures of the apoptotic proteins and the proteins bound with small chemical molecules/peptides/proteins have been reported in the literature. In this review article, the 3D structures of the Bcl-2 family proteins from Homo sapiens and as well complex structures of the anti-apoptotic proteins bound with small molecular inhibitors reported in the literature to date have been comprehensively listed out and described in detail. Moreover, the molecular mechanisms by which the Bcl-2 family proteins modulate the apoptotic processes and strategies for designing antagonists to anti-apoptotic proteins have been concisely discussed.Cancer cells evade apoptosis, which is regulated by proteins of Bcl-2 family in the intrinsic pathways. Numerous experimental three-dimensional (3D) structures of the apoptotic proteins and the proteins bound with small chemical molecules/peptides/proteins have been reported in the literature. In this review article, the 3D structures of the Bcl-2 family proteins from Homo sapiens and as well complex structures of the anti-apoptotic proteins bound with small molecular inhibitors reported in the literature to date have been comprehensively listed out and described in detail. Moreover, the molecular mechanisms by which the Bcl-2 family proteins modulate the apoptotic processes and strategies for designing antagonists to anti-apoptotic proteins have been concisely discussed. عرض أقل

Cancerous cells develop resistance to cell death by over expression of anti-apoptotic proteins, which are specific to interact with pro-apoptotic and BH3-only proteins of Bcl-2 family. Delineating crucial residues mediating the heterodimer complexes (anti-apoptotic proteins - pro-apoptotic/BH3-only proteins) is indispensable to develop specific antagonists to anti-apoptotic proteins. In these backgrounds, we have herein reported crucial residues of hBaxBH3 and hBcl-B (an anti-apoptotic protein… عرض المزيد

Cancerous cells develop resistance to cell death by over expression of anti-apoptotic proteins, which are specific to interact with pro-apoptotic and BH3-only proteins of Bcl-2 family. Delineating crucial residues mediating the heterodimer complexes (anti-apoptotic proteins - pro-apoptotic/BH3-only proteins) is indispensable to develop specific antagonists to anti-apoptotic proteins. In these backgrounds, we have herein reported crucial residues of hBaxBH3 and hBcl-B (an anti-apoptotic protein specifically interacts with human Bax but does not interact with human Bak) for hetero dimerization of the polypeptides and as well validated the structural determinants of the polypeptides through variety of virtual 'alanine mutants' and 'switch mutants' by using an array of computational methods. Residues such as D53, S60, E61, K64, E69 and D71 of hBaxBH3 and R45, H50, F53, F54, Y57, M71, S74, V75, R86, V88, T89, F93 and F159 of hBcl-B were found to be crucial residues of the polypeptides for intermolecular interaction leading hetero dimerization. Moreover, 'pharmacophoric residues' for the hBaxBH3 and hBcl-B have also been figured out and rationalized. عرض أقل

Designing small molecular prototypes having potential to disrupt binding interfaces of pro-apoptotic–anti-apoptotic/BH3-only proteins is a promising strategy in cancer chemotherapy. Several natural and synthetic chemical compounds have been reported as inhibitors or BH3-mimetics to anti-apoptotic proteins of the Bcl-2 family playing essential roles in apoptosis. In the present study, chemical synthesis, structural characterizations and anti-cancer effect of 2-hydroxy-3,5-dinitrobenzamide… عرض المزيد

Designing small molecular prototypes having potential to disrupt binding interfaces of pro-apoptotic–anti-apoptotic/BH3-only proteins is a promising strategy in cancer chemotherapy. Several natural and synthetic chemical compounds have been reported as inhibitors or BH3-mimetics to anti-apoptotic proteins of the Bcl-2 family playing essential roles in apoptosis. In the present study, chemical synthesis, structural characterizations and anti-cancer effect of 2-hydroxy-3,5-dinitrobenzamide (HDNB), a chemical compound identified on the basis of pharmacophoric features of hBaxBH3 peptide have been systematically reported. The chemopreventive effect of the HDNB was assessed on N-nitroso-N-methylurea-induced Wistar female rats of mammary gland carcinogenesis for the study period of 18 weeks. The carcinogenesis Wistar rats were subjected to oral administration of a low-dose (8 mg kg−1 b.w.), medium-dose (40 mg kg−1 b.w.) and high-dose (200 mg kg−1 b.w.) of the HDNB in three different experimental setups. Strikingly, a medium-dose (40 mg kg−1 b.w.) of the HDNB showed appreciable potential to reverse the abnormalities of various biochemical parameters in blood samples and as well in breast tissues to the values close to that of healthy control or to that of the standard (tamoxifen) control. The chemopreventive potential of the HDNB could be chiefly attributed to its ability to restore antioxidants and as well apoptosis inducing properties in Wistar animal models. عرض أقل

The present study was aimed at randomly mutating the microalga, Chlorella vulgaris, in order to alter its cellular behaviour towards increased lipid production for efficient biodiesel production from algal biomass. Individual mutants from ultraviolet light (UV-1 (30 s exposure), UV-2 (60 s exposure) and UV-3 (90 s exposure)) and 5′fluorodeoxyuridine (5′FDU-1 (0.25 mM) and 5′FDU-2 (0.50 mM)) exposed cells were identified to explore an alternative method for lipid enhancement. A marginally… عرض المزيد

The present study was aimed at randomly mutating the microalga, Chlorella vulgaris, in order to alter its cellular behaviour towards increased lipid production for efficient biodiesel production from algal biomass. Individual mutants from ultraviolet light (UV-1 (30 s exposure), UV-2 (60 s exposure) and UV-3 (90 s exposure)) and 5′fluorodeoxyuridine (5′FDU-1 (0.25 mM) and 5′FDU-2 (0.50 mM)) exposed cells were identified to explore an alternative method for lipid enhancement. A marginally significant decrease in biomass in the UV mutants; marked increase in the lipid content in UV-2 and 5′FDU-1 mutants; significant increase in saturated fatty acids level, especially in UV-2 mutant; insignificant increase in lipid production when these mutants were subjected to an additional stress of nitrogen starvation and predominantly enhanced level of unsaturated fatty acids in all the strains except UV-2 were noted. Chloroplast ultrastructural alterations and defective biosynthesis of chloroplast specific lipid constituents were observed in the mutants. Modelling of three-dimensional structures of acetyl coA carboxylase (ACCase), omega-6, plastid delta-12 and microsomal delta-12 fatty acid desaturases for the first time and ligand-interaction studies greatly substantiated our findings. A replacement of leucine by a serine residue in the acetyl coA carboxylase gene of UV-2 mutant suggests the reason behind lipid enhancement in UV-2 mutant. Higher activity of ACCase in UV-2 and 5′FDU-1 strongly proves the functional consequences of gene mutation to lipid production. In conclusion, algal mutants exhibited significant impact on biodiesel production through structural alterations in the lipid-metabolizing genes, thereby enhancing lipid production and saturated fatty acid levels. عرض أقل

We have herein computationally examined binding affinities and specificity of 2-hydroxy-3,5-dinitrobenzamide (HDNB), a small chemical molecular BH3-mimetic identified by means of ‘peptidodynmimetic method’, on the BH3-binding grooves of six anti-apoptotic proteins (Bcl-2, Bcl-B, Bcl-W, Bcl-XL, Bfl-1 and Mcl-1) from human beings. The HDNB ligand was found to interact on the BH3-binding grooves of Bcl-2, Bcl-B, Bcl-XL, Bfl-1 and Mcl-1, whereas it did not act as BH3-mimetic to Bcl-W. Moreover… عرض المزيد

We have herein computationally examined binding affinities and specificity of 2-hydroxy-3,5-dinitrobenzamide (HDNB), a small chemical molecular BH3-mimetic identified by means of ‘peptidodynmimetic method’, on the BH3-binding grooves of six anti-apoptotic proteins (Bcl-2, Bcl-B, Bcl-W, Bcl-XL, Bfl-1 and Mcl-1) from human beings. The HDNB ligand was found to interact on the BH3-binding grooves of Bcl-2, Bcl-B, Bcl-XL, Bfl-1 and Mcl-1, whereas it did not act as BH3-mimetic to Bcl-W. Moreover, binding affinities of the HDNB towards the anti-apoptotic proteins were significantly different from each other. The differential binding affinities and specificity of the HDNB towards the anti-apoptotic proteins have been chiefly attributed to the differences in the chemical properties of BH3-binding grooves of the proteins. Implications of the study to design efficient de novo antagonists to the anti-apoptotic proteins using the HDNB as seed molecule have been discussed. عرض أقل

Multidrug-resistant Salmonella serovars have been a recent concern in curing infectious diseases like typhoid. Salmonella BaeS and BaeR are the two-component system (TCS) that signal transduction proteins found to play an important role in its multidrug resistance. A canonical TCS comprises a histidine kinase (HK) and its cognate partner response regulator (RR). The general approaches for therapeutic targeting are either the catalytic ATP-binding domain or the dimerization domain HisKA (DHp) of… عرض المزيد

Multidrug-resistant Salmonella serovars have been a recent concern in curing infectious diseases like typhoid. Salmonella BaeS and BaeR are the two-component system (TCS) that signal transduction proteins found to play an important role in its multidrug resistance. A canonical TCS comprises a histidine kinase (HK) and its cognate partner response regulator (RR). The general approaches for therapeutic targeting are either the catalytic ATP-binding domain or the dimerization domain HisKA (DHp) of the HK, and in some cases, the receiver or the regulatory domain of the RR proteins. Earlier efforts of identifying novel drugs targeting the signal transduction protein have not been quite successful, as it shares similar ATP-binding domain with the key house keeping gene products of the mammalian GHL family. However, targeting the dimerization domain of HisKA through which the signals are received from the RR can be a better approach. In this article, we show stepwise procedure to specifically identify the key interacting residues involved in the dimerization with the RR along with effective targeting by ligands screened from the public database. We have found a few inhibitors which target effectively the important residues for the dimerization activity. Our results suggest a plausible de novo design of better DHp domain inhibitors. عرض أقل

The crucial residues of hBaxBH3 peptide for interaction with hBcl-B, an anti-apoptotic protein, were identified using molecular docking studies on the polypeptides and temperature-specific molecular dynamic simulations performed for the protein–peptide complex at near-physiological conditions (pH 7.0, 1 atmospheric pressure and 0.1 M NaCl). The data from the methods were examined by a ‘strong residue contacts’ filter strategy and the data analyses of the former and latter methods identified 10… عرض المزيد

The crucial residues of hBaxBH3 peptide for interaction with hBcl-B, an anti-apoptotic protein, were identified using molecular docking studies on the polypeptides and temperature-specific molecular dynamic simulations performed for the protein–peptide complex at near-physiological conditions (pH 7.0, 1 atmospheric pressure and 0.1 M NaCl). The data from the methods were examined by a ‘strong residue contacts’ filter strategy and the data analyses of the former and latter methods identified 10 (Q52, K57, S60, L63, K64, R65, G67, D68, D71 & S72) and 3 (S60, E61 & K64) crucial residues of the hBaxBH3 peptide for interacting with the protein, respectively. We have herein demonstrated that BH3-chemical mimetics screened using the pharmacophoric residues of hBaxBH3 obtained from the ‘peptidodynmimetic method’ were superior in terms of ligand efficiencies, bioavailability and pharmacokinetic properties vis-à-vis that of small molecule BH3-mimetics retrieved using the conventional ‘peptidomimetic method’. The unique advantages of the ‘peptidodynmimetic method’ to identify efficient BH3-mimetics for modulating interfaces (composed of a large number of amino acids) of other anti-apoptotic proteins–BH3-only peptides have also been discussed in detail. عرض أقل

Anti-apoptotic proteins such as Bcl-XL and Mcl-1 have been reported to be over expressed in most cancer forms and consequently, designing dual inhibitors to the proteins is becoming an important strategy in cancer chemotherapy. Interestingly, the Bcl-XL and Mcl-1 show differential binding affinities with BH3-only peptides of Bim and NOXA, notwithstanding their similar three-dimensional folds. The structural determinants for the differential interactions of the proteins with the BH3-only… عرض المزيد

Anti-apoptotic proteins such as Bcl-XL and Mcl-1 have been reported to be over expressed in most cancer forms and consequently, designing dual inhibitors to the proteins is becoming an important strategy in cancer chemotherapy. Interestingly, the Bcl-XL and Mcl-1 show differential binding affinities with BH3-only peptides of Bim and NOXA, notwithstanding their similar three-dimensional folds. The structural determinants for the differential interactions of the proteins with the BH3-only peptides have been scrutinized using molecular docking and temperature-dependent dynamic studies. The comprehensive analysis of the data from the studies paved a way of designing dual inhibitors to the proteins, on the basis of the chemical structures of ABT-737, which is a highly potent inhibitor to the Bcl-XL. The unique feature of this approach on designing the dual inhibitors to the anti-apoptotic proteins have also been brought into detail through a comparative analysis with a few existing strategies reported on the same line in the literature. عرض أقل

Designing antagonists to anti-apoptotic proteins of Bcl-2 family has become an important strategy in cancer chemotherapy. Using experimental techniques and computational methods, a few numbers of lead inhibitors to the antiapoptotic proteins have been reported in the literature and a few of them are under clinical trials. In this review, the lead inhibitors designed using in silico methodologies are exclusively covered, systematically organized and critically evaluated. An orchestrated in… عرض المزيد

Designing antagonists to anti-apoptotic proteins of Bcl-2 family has become an important strategy in cancer chemotherapy. Using experimental techniques and computational methods, a few numbers of lead inhibitors to the antiapoptotic proteins have been reported in the literature and a few of them are under clinical trials. In this review, the lead inhibitors designed using in silico methodologies are exclusively covered, systematically organized and critically evaluated. An orchestrated in silico strategy for screening and identifying efficient antagonists to the anti-apoptotic proteins has also been brought into fore. عرض أقل

A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be associated with gene LIG1 in dbSNP. Different web server namely SIFT, PolyPhen, CUPSAT, FASTSNP, MAPPER and dbSMR were used to identify potentially functional SNPs in gene LIG1. SIFT, PolyPhen and… عرض المزيد

A computational approach for identifying functionally relevant SNPs in gene LIG1 has been proposed. LIG1 is a crucial gene which is involved in excision repair pathways and mutations in this gene may lead to increase sensitivity towards DNA damaging agents. A total of 792 SNPs were reported to be associated with gene LIG1 in dbSNP. Different web server namely SIFT, PolyPhen, CUPSAT, FASTSNP, MAPPER and dbSMR were used to identify potentially functional SNPs in gene LIG1. SIFT, PolyPhen and CUPSAT servers predicted eleven nsSNPs to be intolerant, thirteen nsSNP to be damaging and two nsSNPs have the potential to destabilize protein structure. The nsSNP rs11666150 was predicted to be damaging by all three servers and its mutant structure showed significant increase in overall energy. FASTSNP predicted twenty SNPs to be present in splicing modifier binding sites while rSNP module from MAPPER server predicted nine SNPs to influence the binding of transcription factors. The results from the study may provide vital clues in establishing affect of polymorphism on phenotype and in elucidating drug response عرض أقل

Ribavirin and its 553 analogues have been docked with NS5-methyltransferase of Dengue viruses using Glide- HTVS and Glide-XP computational tools and the compounds have been screened based on their Glide-Gscores to identify lead ribavirin analogues that may act as inhibitors to the enzyme. Upon studying the interactions of ribavirin triphosphate (RTP) and triphosphate of lead ribavirin analogues with NS5-methyltransferase and Janus tyrosine Kinase-2 (JAK2) enzymes using molecular docking and… عرض المزيد

Ribavirin and its 553 analogues have been docked with NS5-methyltransferase of Dengue viruses using Glide- HTVS and Glide-XP computational tools and the compounds have been screened based on their Glide-Gscores to identify lead ribavirin analogues that may act as inhibitors to the enzyme. Upon studying the interactions of ribavirin triphosphate (RTP) and triphosphate of lead ribavirin analogues with NS5-methyltransferase and Janus tyrosine Kinase-2 (JAK2) enzymes using molecular docking and dynamic methods, the possible mechanism by which the ribavirin causes haemolytic anaemia has been proposed. De novo RTP-analogues showing stronger affinities with NS5-methyltransferase and weaker affinities with JAK2 have been designed. The essential structural features of the de novo RTP-analogues for developing them as specific antiviral drugs against the infections due to dengue viruses have been discussed in detail. عرض أقل

Designing BH3-mimitics, that are capable of displacing BH3-peptides from BH3-binding groove of anti-apoptotic proteins, is a promising strategy to develop therapeutics of cancer chemotherapy. ABT-737, a BH3-mimitic shown to act as potent inhibitor of anti-apoptotic proteins, failed to clear the clinical trials due to its poor bioavailability. ABT-263, an analog of ABT-737, is shown as potent inhibitor with appreciable bioavailability. We have herein shown that ABT-737 docks on CYP3A4, a… عرض المزيد

Designing BH3-mimitics, that are capable of displacing BH3-peptides from BH3-binding groove of anti-apoptotic proteins, is a promising strategy to develop therapeutics of cancer chemotherapy. ABT-737, a BH3-mimitic shown to act as potent inhibitor of anti-apoptotic proteins, failed to clear the clinical trials due to its poor bioavailability. ABT-263, an analog of ABT-737, is shown as potent inhibitor with appreciable bioavailability. We have herein shown that ABT-737 docks on CYP3A4, a metabolic enzyme present in intestine of human beings, with stronger binding affinity than the binding affinity of ABT-263 with the enzyme. Based on the binding affinities and mode of interactions between the ligands and the enzymes, the differential bioavailability of the ABT-737 and ABT-263 is attributed to their pre-systemic metabolic reactions that are presumably different from each other. عرض أقل