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Mutation breeding has a long track record in the development of crop cultivars with improved tolerance to abiotic stresses such as heat, salinity and drought. Oryza sativa L. cv IR64 is a very popular high yielding rice, but susceptible to major abiotic stresses, such as low and high temperatures, salinity and drought. We subjected IR64 to gamma irradiation and generated a mutant population (M3) with ~2,000 families. These were screened at the seedling stage for tolerance to high-temperature stress using hydroponics and controlled-environment chambers, resulting in the identification of three mutant lines showing a robust seedling phenotype. Under heat stress, higher CO2 assimilation (10-30%), higher spikelet fertility (40-45%) and higher antioxidant activity (15-20% catalase activity) confirmed superiority of the selected mutant lines over wild type plants at seedling and flowering stages. Upon exposure to salinity and drought stress, the three selected lines also exhibited better tolerance than wild type in terms of higher CO2 assimilation, stomatal conductance, transpiration and chlorophyll fluorescence. Transcript and protein abundance analyses confirmed higher constitutive levels of heat shock proteins and antioxidant enzymes in the mutant lines relative to wild type. Tolerance to multiple abiotic stresses was reflected in higher (25-30%) grain yield than wild type. It is anticipated that the mutant lines identified will be useful for developing new improved cultivars for dry and saline areas and may be exploited to dissect the molecular basis of multiple stress tolerance in crop plants

The lithiation of 2,4-lutidine (1) with non-nucleophilic bases, such as lithium diisopropylamide (LDA) and lithium diethylamide (LDEA) affords different regioisomers under similar reaction conditions. The mechanism of these reactions and the factors determining selectivity have not been well understood. The present endeavor explores experimental and quantum chemical approaches to investigate factors that determine regioselectivity of the reaction. It has been found that transition states of LDA/LDEA determine regioselectivity and the presence of acatalyst (LiCl) plays a vital role. The LDA mediated lithiation of 1 proceeds through a disolvated open dimer of LDA, leading to a 2-methyl lithiated product. LDEA mediated lithiation is dominated by a route involving interception of 1 with a trisolvated monomer-based transition state of LDEA resulting in a 4-methyl lithiated product. The mechanism is supported by LiCl catalyzed reactions. LiCl has also been found to effect a change in selectivity of the lithiation of BF3-complexed 2,4-lutidine.

P218 is one of the very important and recent lead compounds for antimalarial research. The 3D structural and electronic details of P218 are not available. In this article, quantum chemical studies to understand the possible 3D structures of P218 are reported and compared with 3D structures from the active site cavities of hDHFR and PfDHFR. The neutral P218, can adopt open chain as well as cyclic arrangements. Under implicit solvent condition a zwitterionic-cyclic conformer is found to be quite possible. Microsolvation studies using explicit water molecules indicate that one water molecule may bridge the two ends of zwitterionic-cyclic P218. It was observed that the protonation occurs preferentially at N1 position of the 2,4-diaminopyrimidine ring, with a proton affinity of 274.49 kcal/mol (implicit solvent phase) and 236.35 kcal/mol (gas phase). A dimer of P218 may be zwitterionic dimer, the dimer formation can release upto ∼28.60 kcal/mol (implicit solvent phase).

The design and microwave-assisted synthesis of four series (IIIa–IIIo, Va–Vg, VIIa–VIIg and IXa–IXe) of mono and bis-amide derivatives of ferulic acid have been achieved under solvent-free conditions and, subsequently characterized by spectroscopic techniques. During thermal analysis, all the compounds were found stable up to 100 °C and decomposed through single step at higher temperature. The derivatives were screened for their in vitro cytotoxicity and antioxidant activity, respectively and observed that compound Vb was most active against breast (MCF-7; IC50 = 07.49 µM and MDA-MB-231; IC50 = 07.28 µM), Vd against lung (A549; IC50 = 07.11 µM) and liver (HepG2; IC50 = 08.32 µM), and Ve against cervical (HeLa; IC50 = 07.14 µM) cancer cell lines, while compounds IIIf, IIIl, IIIo, VIIe and IXa–IXe were found to exhibit the strong antioxidant activity with respect to their parent molecule. Previous reports for the biological applications of ferulic acid amides also confirmed the importance of work presented here. The 3D-QSAR studies for anticancer and antioxidant activities were also performed by using CoMFA, and the corresponding contour maps of electrostatic and steric fields have been computed. Statistical analysis between experimental and CoMFA-predicted data for pIC50 have been accomplished by curve fitting analysis which showed the significant correlation.

The substrate to the enzyme PfDHFR (Plasmodium falciparum Dihydrofolate Reductase) is a small molecule dihydrofolate (DHF), it gets converted to tetrahydrofolate (THF) in the active site of the enzyme. The PfDHFR reaction surface involves the protonation of DHF to DHFP as an initial step before the catalytic conversion. The binding affinities of all these species (DHF, DHFP and THF) contribute to the mechanism of DHFR catalytic action. Molecular dynamics (MD) simulations and Quantum Mechanics/Molecular Mechanics (QM/MM) analysis were performed to evaluate the binding affinity and molecular recognition interactions of the substrate DHF/DHFP and the product THF, in the active site of wild-type PfDHFR (wtPfDHFR). The binding affinities of the cofactor NADPH/NADP+ were also estimated in all the three complexes. The molecular dynamics (MD) simulations of the substrate, product and cofactor in the cavities of wtPfDHFR revealed the variation of the atomic level interactions during the course of the catalytic conversion. It was found that the DHFP binds very strongly to the PfDHFR active site and pulls the cofactor NADPH closer to itself. The QM/MM analysis revealed that the binding energy of DHFP (−59.82 kcal/mol) and NADPH (−100.24 kcal/mol) in DHFP-wtPfDHFR complex, is higher in comparison to the binding energy of DHF (−38.67 kcal/mol) and NADPH (−77.53 kcal/mol) in DHF-wtPfDHFR complex and the binding energy of THF (−30.72 kcal/mol) and NADP+ (−73.72 kcal/mol) in THF-wtPfDHFR complex. The hydride ion donor-acceptor distance (DAD) analysis was also carried out. This combined MD and QM/MM analysis revealed that the protonation of DHF increases the proximity between the substrate and the cofactor, thus facilitates the reaction profile of PfDHFR.

6-Endo-dig-cyclization is an efficient method for the synthesis of 1,2-dihydroisoquinolines. We have synthesized few 1,2-dihydroisoquinolines having different functionality at the C-1, C-3, C-7, and N-2 positions for evaluation against HIV-1 integrase (HIV1-IN) inhibitory activity. A direct nitro-Mannich condensation of o-alkynylaldimines and dual activation of o-alkynyl aldehydes by inexpensive cobalt chloride yielded desired compounds. Out of 24 compounds, 4m and 6c came out as potent integrase inhibitors in in vitro strand transfer (ST) assay, with IC50 value of 0.7 and 0.8 μM, respectively. Molecular docking of these compounds in integrase revealed strong interaction between metal and ligands, which stabilizes the enzyme-inhibitor complex. The ten most active compounds were subjected to antiviral assay. Out of those, 6c reduced the level of p24 viral antigen by 91%, which is comparable to RAL in antiviral assay. Interestingly, these compounds showed similar ST inhibitory activity in G140S mutant, suggesting they can act against resistant strains.

The Paal–Knorr synthesis of furan, pyrrole and thiophene rings is one of the most important methods of generating these very important heterocycles, but the mechanism of this reaction is not well understood. Though several mechanistic paths are suggested, the exact energy requirements of this reaction, the structural features of transition states associated with the cyclization step, have not been established, especially for furan and thiophene synthesis. In this work, we explore the mechanism of the Paal–Knorr method and establish the energy requirements, using quantum chemical methods. The Paal–Knorr reaction to give furans is endergonic by 3.7 kcal mol−1 whereas the same reaction is exergonic for pyrrole and thiophene generation by 16.4 and 15.9 kcal mol−1, using G2MP2 method. The cyclization step is associated with high energy barrier, however, explicit water participation reduces the barrier significantly. For example, under the neutral condition two water mediated pathways – (i) monoenol and (ii) hemiketal, are possible on the reaction leading to furan. The cyclization step in these two pathways require 28.9 and 27.1 kcal mol−1, respectively. The ring formation step becomes highly favorable in the presence of H3O+ with a barrier of only 11.5 kcal mol−1 (solvent phase) from the monoenol to dihydrofuran derivative and 5.5 kcal mol−1 (solvent phase) from hemiketal to dihydroxy dihydrofuran derivative. Similarly, a water mediated pathway involving the intermediacy of hemialcohols has been found to be energetically preferred mechanism for pyrrole and thiophene also.

A simple and efficient trifluoroacetic acid mediated protocol for ortho-amidomethylation of phenols in aqueous medium has been described. Developed protocol has a good substrate scope, involves mild reaction conditions, and products are obtained in good yields. The quantum chemical calculations were performed in implicit solvent (water) conditions, which helped in tracing the reaction mechanism and getting insights on the possible reaction pathway, which involves the N C bond formation and simultaneous hydrogen transfer to give final product. The applicability of this protocol for one-pot synthesis of flavans from phenols, formaldehyde and styrene has also been demonstrated.

Copper bromide catalyzed aerobic oxidative coupling of 2-aminopyridines with cinnamaldehydes directly led to the formation of 3-formyl-2-phenyl-imidazo[1,2-a]pyridines. The quantum chemical calculations were performed to trace the reaction mechanism and get insights into the possible reaction pathway. 2-Aminopyridines on coupling with cinnamaldehyde generate (E)-3-phenyl-3-(pyridin-2-ylamino)acrylaldehyde IV as a key intermediate, which undergoes C–N bond formation reaction to produce 3-formyl-2-phenyl-imidazo[1,2-a]pyridines.

A simple and efficient trifluoroacetic acid mediated protocol for ortho-amidomethylation of phenols in aqueous medium has been described. Developed protocol has a good substrate scope, involves mild reaction conditions, and products are obtained in good yields. The quantum chemical calculations were performed in implicit solvent (water) conditions, which helped in tracing the reaction mechanism and getting insights on the possible reaction pathway, which involves the N C bond formation and simultaneous hydrogen transfer to give final product. The applicability of this protocol for one-pot synthesis of flavans from phenols, formaldehyde and styrene has also been demonstrated.

The formation of 1,2-diketones succeeds upon the reaction between aryl hydrazines and aryl alkynes, but fails using aliphatic alkynes.

Copper bromide catalyzed aerobic oxidative coupling of 2-aminopyridines with cinnamaldehydes directly led to the formation of 3-formyl-2-phenyl-imidazo[1,2-a]pyridines. The quantum chemical calculations were performed to trace the reaction mechanism and get insights into the possible reaction pathway. 2-Aminopyridines on coupling with cinnamaldehyde generate (E)-3-phenyl-3-(pyridin-2-ylamino)acrylaldehyde IV as a key intermediate, which undergoes C–N bond formation reaction to produce 3-formyl-2-phenyl-imidazo[1,2-a]pyridines.

A cobalt acetylacetonate catalyzed oxidative diketonation of alkynes via C(sp)–H bond functionalization has been described. The reaction involves a free-radical mechanism, wherein the phenyl radical formed from phenyl hydrazine couples with Co(II) activated alkyne to produce 1,2-diketones. The reaction proceeds at room temperature in DMF with the use of Ag2O/air as the oxidizing system. The utility of the protocol for the synthesis of a series of imidazoles including a potent platelet aggregation inhibitor trifenagrel has been demonstrated.

[via TFA-catalyzed C—C bond cleavage followed by intermolecular [4 + 2] cycloaddition of in situ formed styrenyl trifluoroacetate intermediates; 27 examples].

Molecular dynamics simulations were performed to evaluate the origin of the antimalarial effect of the lead compound P218. The simulations of the ligand in the cavities of wild-type, mutant Plasmodium falciparum Dihydrofolate Reductase (PfDHFR) and the human DHFR revealed the differences in the atomic-level interactions and also provided explanation for the specificity of this ligand toward PfDHFR. The binding free energy estimation using Molecular Mechanics Poisson-Boltzmann Surface Area method revealed that P218 has higher binding affinity (~ −30 to −35 kcal/mol) toward PfDHFR (both in wild-type and mutant forms) than human DHFR (~ −22 kcal/mol), corroborating the experimental observations. Intermolecular hydrogen bonding analysis of the trajectories showed that P218 formed two stable hydrogen bonds with human DHFR (Ile7 and Glu30), wild-type and double-mutant PfDHFR’s (Asp54 and Arg122), while it formed three stable hydrogen bonds with quadruple-mutant PfDHFR (Asp54, Arg59, and Arg122). Additionally, P218 binding in PfDHFR is stabilized by hydrogen bonds with residues Ile14 and Ile164. It was found that mutant residues do not reduce the binding affinity of P218 to PfDHFR, in contrast, Cys59Arg mutation strongly favors inhibitor binding to quadruple-mutant PfDHFR. The atomistic-level details explored in this work will be highly useful for the design of non-resistant novel PfDHFR inhibitors as antimalarial agents.

A new simple and efficient method for the synthesis of 2-phenylnaphthalenes from electron-rich 1-styryl-2-methoxybenzenes has been described. The reaction proceeds via TFA catalyzed C–C bond cleavage followed by intermolecular [4+2]-Diels–Alder cycloaddition of an in situ formed styrenyl trifluoroacetate intermediate. The quantum chemical calculations identified the transition state for the cycloaddition reaction and helped in tracing the reaction mechanism. The method has been efficiently utilized for synthesis of the phenanthrene skeleton and a naphthalene-based potent and selective ER-β agonist.

Proguanil, an anti-malarial prodrug, undergoes cytochrome P450 catalyzed biotransformation to the pharmacologically active triazine metabolite (cycloguanil), which inhibits plasmodial dihydrofolate reductase. This cyclization is catalyzed by CYP2C19 and many anti-malarial lead compounds are being designed and synthesized to exploit this pathway. Quantum chemical calculations were performed using the model species (Cpd I for active species of cytochrome and N4-isopropyl-N6-methylbiguanide for proguanil) to elucidate the mechanism of the cyclization pathway. The overall reaction involves the loss of a water molecule, and is exothermic by approximately 55 kcal/mol, and involves a barrier of approximately 17 kcal/mol. The plausible reaction pathway involves the initial H-radical abstraction from the isopropyl group by Cpd I, followed by two alternative paths- (i) oxygen rebound to provide hydroxyl derivative and (ii) loss of additional H-radical to yield 1,3,5-triazatriene, which undergoes cyclization. This study helped in understanding the role of the active species of cytochromes in this important cyclization reaction.