Conformational perturbation of SARS-CoV-2 spike protein using N-acetyl cysteine: an exploration of probable mechanism of action to combat COVID-19

The infection caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) resulted in a pandemic with huge death toll and economic consequences. The virus attaches itself to the human epithelial cells through noncovalent bonding of its spike protein with the angiotensin-converting enzyme-2 (ACE2) receptor on the host cell. Based on in silico studies we hypothesized that perturbing the functionally active conformation of spike protein through the reduction of its solvent accessible disulfide bonds, thereby disintegrating its structural architecture, may be a feasible strategy to prevent infection by reducing the binding affinity towards ACE2 enzyme. Proteomics data showed that N-acetyl cysteine (NAC), an antioxidant and mucolytic agent been widely in use in clinical medicine, forms covalent conjugates with solvent accessible cysteine residues of spike protein that were disulfide bonded in the native state. Further, in silico analysis indicated that the presence of the selective covalent conjugation of NAC with Cys525 perturbed the stereo specific orientations of the interacting key residues of spike protein that resulted in threefold weakening in the binding affinity of spike protein with ACE2 receptor. Interestingly, almost all SARS-CoV-2 variants conserved cystine residues in the spike protein. Our finding results possibly provides a molecular basis for identifying NAC and/or its analogues for targeting Cys-525 of the viral spike protein as fusion inhibitor and exploring in vivo pharmaco-preventive and its therapeutic potential activity for COVID-19 disease. However, in-vitro assay and animal model-based experiment are required to validate the probable mechanism of action.Communicated by Ramaswamy H. Sarma.

Molecular Dynamics Simulations of HDAC-ligand Complexes Towards the Design of New Anticancer Compounds

Quantitative Structure-activity Relationship (QSAR) studies gained a foothold in the mid-1960s to rationalise the biological activity of medicinally important compounds. Since then, the advancements in computer hardware and software added many new techniques and areas to this field of study. Molecular dynamics (MD) simulations are one such technique in direct drug design approaches. MD simulations have a special place in drug design studies because they decode the dynamics of intermolecular interactions between a biological target and its potential ligands/inhibitors. The trajectories from MD simulations provide different non-bonding interaction parameters to assess the compatibility of the protein-ligand complex and thereby facilitate the design of prospective compounds prior to their wet-lab exploration. Histone deacetylases (HDACs) play a key role in epigenetics and they are promising drug targets for cancer and various other diseases. This review attempts to shed some light on the modelling studies of HDAC inhibitors as anticancer agents. In view of the advantages of MD simulations in direct drug design, this review also discusses the fragment-based approach in designing new inhibitors of HDAC8 and HDAC2, starting from the interaction energies of ligand fragments obtained from the MD simulations of respective protein-ligand complexes. Here, the design of new anticancer compounds from largazole thiol, trichostatin A, vorinostat, and several other prototype compounds are reviewed. These studies may stimulate the interest of medicinal chemists in MD simulations as a direct drug design approach for new drug development.

Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation

Designing an inhibitor having strong affinity in the active site pocket is the cherished goal of structure based drug designing. To achieve this, it is considerably important to predict which structural scaffold is better suited for change to increase affinity. We have explored five HDAC2 co-crystals having PDB ligand code-SHH (vorinostat), LLX, 20Y, IWX (BRD4884) and 6EZ (BRD7232). For analyzing protein-ligand interaction at an atomistic level, we have employed the NAMD molecular dynamics (MD) package. The obtained 100 ns long MD trajectories were subjected to quantitative estimations of non-bonding energies (NBEs) for inferring their interactions with the whole protein or its composite active site (CAS). In addition, relative ΔG_bind was calculated to rank the inhibitors. These inhibitors' NBEs reveal that the phenyl moieties are the major structural scaffold where modifications should be attempted. We designed new compounds (NCs) via introducing hydroxyl groups at 4,5 position of the phenyl moiety of 6EZ, called NC1. Improvement in NC1 further encouraged us for CAP modification by isochromane and isoindoline moieties in place of oxabicyclooctane in NC1, resulting in NC2 and NC3. We also explored trifluoromethyl oxadiazole in 6EZ (NC4 and NC5) and SHH (NC6 and NC7). This moiety acts as a ZBG in NC4 while acting as a part of the foot-pocket in the rest. NC2 and NC6 have highest favorable NBEs among all studied ligands due increased favorable electrostatic contribution. We expect these NBEs data will provide atomistic level insights and benefit in designing new and improved HDAC2 inhibitors. Communicated by Ramaswamy H. Sarma.

N-(7-Chloroquinolinyl-4-aminoalkyl)arylsulfonamides as antimalarial agents: rationale for the activity with reference to inhibition of hemozoin formation

New chloroquinolinyl arylsulfonamides with potential antimalarial activity inhibited hemozoin formation exceedingly well.

Synthesis, biological evaluation and molecular modeling studies of new 2,3-diheteroaryl thiazolidin-4-ones as NNRTIs

In a focused exploration, thiazolidin-4-ones with different C-2 and N-3 substituent groups were synthesized and evaluated as non-nucleoside reverse transcriptase inhibitors against HIV-1. This has led to new active compounds sporting heteroaryls at both C-2 and N-3 positions prompting to view them in the backdrop of nevirapine. To assign the molecular attributes for the activity, the compounds are investigated by docking them into non-nucleoside inhibitor-binding pocket of HIV-1 reverse transcriptase (RT). The most active compounds of this series (7d and 7f) shared spatial features with nevirapine with added molecular flexibility. Furthermore, in molecular dynamics simulations carried out for up to 10 ns, the compounds 7d and 7f showed consistency in their interactions with non-nucleoside inhibitor-binding pocket of HIV-1 RT and suggested Tyr319 and Val106 as potential residues for H-bond interaction with these molecules. These results open new avenues for the exploration of 2,3-diheteroaryl thiazolidin-4-ones for prevention of HIV-1.

Topological and physicochemical characteristics of 1,2,3,4-Tetrahydroacridin- 9(10H)-ones and their antimalarial profiles: a composite insight to the structure-activity relation

The study reports the QSAR rationales from multilateral approaches for the antimalarial activities (against W2 and TM90-C2B strains of Plasmodium falciparum) and physical properties (aqueous solubility, permeability and logD) of 1,2,3,4-tetrahydroacridin-9(10H)-one (THA) derivatives. A modification to Free-Wilson matrix (parameter set) is introduced to improve the compound to parameter ratio of the analysis carried out in the study. The models from modified Free-Wilson and physicochemical parameters suggest that 5(th) (R1) and 8(th) (R4) positions of THA scaffold should be free from substitution for the antimalarial activity against both the strains. The THA' s 6(th) (R2) and 7(th) (R3) positions' substituents with a blend of hydrophobicity and polarity offer scope to modulate the activities of these compounds. The substituent group contributions derived here gives opportunity to examine various combinations possible from these analogues. The models from the topological and other structural indices has suggested that MLOGP, LP1 and JGI6 as three common important features for activity against W2 and TM90 strains. The topological indices participated in the models suggested a preference for longer path lengths in molecules for better activity against both strains. The PLS analysis of the descriptors identified in the feature selection approach, combinatorial protocol in multiple linear regression (CP-MLR), has suggested that MATS3e and nRORPh are best suited to modulate the W2 activity, and Me, T(S..F) and ARR are best suited to modulate the TM90 activity. In these derivatives the analysis of aqueous solubility, permeability and logD has suggested that most of the R1 and R4 substituents have contributed with same arithmetic sign to theses properties. For all other variations in these compounds, the permeability increased with increasing logD and decreased with increasing aqueous solubility. The results suggest ways for the activity-property modulation in these analogues.

Discovery of triazine mimetics as potent antileishmanial agents

The World Health Organization has classified the leishmaniasis as a major tropical disease. The discovery of new compounds for leishmaniasis is therefore a pressing concern for the anti-infective research program. We have synthesized 19 compounds of triazine dimers as novel antileishmanial agents. Most of the synthesized derivatives exhibited better activity against intracellular amastigotes (IC50 ranging from 0.77 to 10.32 μM) than the control, pentamidine (IC50 = 13.68 μM), and are not toxic to Vero cells. Compounds 14 and 15 showed significant in vivo inhibition of 74.41% and 62.64%, respectively, in L. donovani/hamster model. Moreover, expansion of Th1-type and suppression of Th2-type immune responses proved that compound 14 stimulates mouse macrophages to prevent the progression of leishmania parasite. The molecular docking studies involving PTR1 protein PDB further validated the concepts involved in the design of these compounds. Among the investigated analogues, compound 14 has emerged as the potential one to enlarge the scope of the study.

CoMFA and CoMSIA analysis of tetrahydroquinolines as potential antimalarial agents

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used on a dataset of compounds, some of them having been reported to inhibit Plasmodium falciparum protein, farnesyltransferase. The co-crystal structure of the lead molecule, BMS-214662 bound to Rat-PFT was used as a template. CoMFA yielded a good model, with r²(ncv) = 0.909, r²(cv) = 0.617 and was validated using an external set r²(pred) = 0.748). It compared favourably with CoMSIA. In the CoMFA model the steric and electrostatic fields exerted an almost equal influence on activity. The contour maps indicated the necessity for sterically large electropositive groups with electronegative tail to be present in these molecules for activity, and sterically large electronegative moieties on the sulfonamide linker. By incorporating these features some new compounds have been identified for further investigation.

QSAR of 2-(4-methylsulphonylphenyl)pyrimidine derivatives as cyclooxygenase-2 inhibitors: simple structural fragments as potential modulators of activity

The cyclooxygenase-2 (COX-2) inhibitory activity of 2-(4-methylsulphonylphenyl)pyrimidine derivatives has been quantitatively analyzed in terms of Dragon descriptors. The derived QSAR models have provided rationales to explain the activity of titled derivatives. The descriptors (Me, Mp, GATS1p and GATS5p) identified in CP-MLR analysis have highlighted the role of atomic properties, such as Sanderson electronegativity and polarizability, to explain the inhibitory activity. Additionally, prevalence of aromatic ether functionality (descriptor nRORPh) and certain structural fragments (number of Me groups, C-001; number of H attached to heteroatom, H-050 and number of H attached to α-C, H-051) in a molecular structure are helpful to rationalize the COX-2 inhibitory activity of pyrimidine derivatives. The partial least square (PLS) analysis has also confirmed the dominance of information content of CP-MLR-identified descriptors for modelling the activity.

Modelling of serotonin reuptake inhibitory and histamine H₃antagonistic activity of piperazine and diazepane amides: QSAR rationales for co-optimization of the activity profiles

Selective human serotonin reuptake transporter (hSERT) inhibition is the first line of treatment to deal with the depression. In clinical practice for managing depression, the stimulants are co-prescribed to overcome cognitive impairment and fatigue. Recently, histamine H(3) antagonists with serotonin reuptake inhibition activity have been proposed as alternative approach for the treatment of depression. In this context, a QSAR study of hSERT inhibitory and H(3) antagonistic activity of piperazine and diazepane amide derivatives has been carried out using the combinatorial protocol in multiple linear regression (CP-MLR) with 0D- to 2D-Dragon descriptors. The derived QSAR models have provided a rational approach for the development of new piperazine and diazepane amide derivatives as hSERT inhibitors and H(3) antagonists. In a concomitant partial least-squares (PLS) analysis of the hSERT and histamine H(3) activities, the fraction contributions of identified descriptors revealed their importance in modulating these activities. The PLS analysis of other biological endpoints, namely hNET, hDAT, and histamine H(3) activity in functional assay (H(3)pA(2)) of these analogues with the identified descriptors has further highlighted their scope in modulating these activities.

Specific targeting of insulin-like growth factor 1 receptor signaling in human estrogen dependent breast cancer cell by a novel tyrosine-based benzoxazepine derivative

The present study sought to investigate the in vitro and in vivo effects of a tyrosine-based benzoxazepine, 4-[4-(toluene-4-sulfonyl)-2,3,4,5-tetrahydro-benzo[f][1,4]oxazepin-3-ylmethyl]-phenol) [THBP] in human breast cancer cells, with a focus on determining its molecular target. THBP had growth inhibitory effect on MCF-7 and MDA-MD-231 cells. At IC(50) value (∼20 μM), THBP resulted in G1 arrest, decrease in cyclin D1 levels and induction of apoptosis of MCF-7 cells. Mechanistically, activation of caspase 8 contributes critically to the induction of apoptotic cell death as copresence of selective inhibition of caspase 8 effectively abrogates the cytotoxic effect of THBP in MCF-7 cells. Further, THBP increased pro-apoptotic protein, Bax; decreased anti-apoptotic protein, Bcl-2; and decreased mitochondrial membrane potential in MCF-7 cells, indicating involvement of an intrinsic pathway of apoptosis following caspase 8 activation. Out of the various growth factors/hormones, THBP selectively abrogated increased viability of MCF-7 cells by insulin-like growth factor 1 (IGF-1). Molecular docking studies revealed that THBP occupied the ATP binding pocket of IGF-1 receptor (IGF-1R). Accordingly THBP was found to inhibit IGF-1-induced phosphorylation of IGF-1R and insulin receptor substrate-1 (IRS-1) without inhibiting insulin signaling in MCF-7 cells. In athymic nude mice, compared with vehicle, THBP treatment significantly reduced the growth of MCF-7 xenograft tumors through inhibition of cancer cell proliferation as well as promotion of cell death that correlated with reduced phospho-IGF-1R levels. We suggest that interfering with the IGF-1R signaling by the benzoxazepine THBP offers a novel and selective therapeutic strategy for estrogen receptor-positive, postmenopausal breast cancer patients.

Consensus features of CP-MLR and GA in modeling HIV-1 RT inhibitory activity of 4-benzyl/benzoylpyridin-2-one analogues

The HIV-1 reverse transcriptase (RT) inhibitory activity of benzyl/benzoylpyridinones is modeled with molecular features identified in combinatorial protocol in multiple linear regression (CP-MLR) and genetic algorithm (GA). Among the features, nDB and LogP are found to be the most influential descriptors to modulate the activity. Although the coefficient of nDB suggested in favor of benzylpyridinones skeleton, the coefficient of LogP suggested the favorability of hydrophilic nature in compounds for better activity. The partial least squares analysis of the descriptors common to CP-MLR and GA has displayed their predictivity over the total descriptors identified in both the approaches. The back-propagation artificial neural networks model from the five most significant common descriptors (nDB, T(O..O), MATS8e, LogP, and BELp4) has explained 93.2% variance in the HIV-1 RT activity of the training set compounds and showed a test set r(2) of 0.89. The results suggest that the descriptors have the ability to identify the patterns in the compounds to predict potential analogues.

A quantitative structure-activity relationship study on serotonin 5-HT6) receptor ligands: indolyl and piperidinyl sulphonamides

The serotonin 5-HT(6) binding affinity of indolyl- and piperidinyl-sulphonamide derivatives has been analysed with topological and molecular features with DRAGON software. Analysis of the structural features in conjunction with the biological endpoints in combinatorial protocol in multiple linear regression (CP-MLR) led to the identification of 25 descriptors for modelling the activity. The study clearly suggested the role of an average Randic-type eigenvector-based index from adjacency matrix, VRA2, number of secondary aliphatic amines, nNHR, the sum of the topological distance between N and O, T(N...O), ring tertiary carbon atoms, nCrHR, and CH2RX type fragment, C-006, in a molecular structure to optimize the 5-HT(6) binding affinities of titled compounds. The PLS analysis confirmed the dominance of information content of CP-MLR identified descriptors for modelling the activity when compared with those of leftover ones.

Combinatorial protocol in multiple linear regression/partial least-squares directed rationale for the caspase-3 inhibition activity of isoquinoline-1,3,4-trione derivatives

The caspase-3 inhibition activity of isoquinoline-1,3,4-trione derivatives has been analysed with the topological and molecular features from Dragon software. Analysis of the structural features in conjunction with the biological endpoints in combinatorial protocol in multiple linear regression (CP-MLR) led to the identification of 45 descriptors for modelling the activity. The study clearly suggested the role of rotatable bonds, mean information on the distance degree equality, radial centricity, bond and structural information content of five-order neighbourhood symmetry, atomic van der Waals volumes and the presence or absence of certain structural fragments to optimise the caspase-3 inhibitory activity of titled compounds. The models developed and the participating descriptors advocate that the substituent groups of the isoquinoline moiety hold scope for further modification in the optimization of the caspase-3 inhibitory activity. Analysis of these descriptors in partial least squares (PLS) highlighted their relative significance in modulating the biological response. The selected descriptors are enriched with information corresponding to the activity when compared to the remaining ones.

Modeling of the growth hormone secretagogue receptor antagonistic activity using chemometric tools

A quantitative structure-activity relationship (QSAR) study has been carried out on growth hormone secretagogue receptor antagonistic activity of the derivatives of 2,4-diaminopyrimidine. To obtain significant QSARs, the approaches involving the non-parametric such as Fujita-Ban, and the parametric based on physicochemical and DRAGON descriptors in Hansch type of analysis have been employed. The Fujita-Ban approach, however, was constrained to 18 compounds only due to a limited number of substituents appeared at varying positions. The derived contributions of different substituents and the parent moiety were used to identify the potential congeners. The physicochemical model of Hansch was subsequently used to interpret the type of interactions involved between the receptor sites and varying positions of these compounds. The study, employing DRAGON descriptors in Hansch approach was also carried out on this data set to discuss the prevailing interactions in terms of topological descriptors. The derived highest significant model was discussed to delineate the type of interactions involved and suggestions have been made for different alterations to lead to further potential compounds of the series.

Topological descriptors in modeling malonyl coenzyme A decarboxylase inhibitory activity: N-Alkyl-N-(1,1,1,3,3,3-hexafluoro-2-hydroxypropylphenyl)amide derivatives

The malonyl-CoA decarboxylase (MCD) inhibition activity of derivatives of N-alkyl-N-(1,1,1,3,3,3-hexafluoro-2-hydroxypropylphenyl)amide has been analyzed through combinatorial protocol in multiple linear regression (CP-MLR) using different topological descriptors obtained from Dragon software for the energy minimized 3D-structures of these molecules. Among the topological descriptor classes considered in the study, the MCD inhibition activity is correlated with simple topological descriptors (TOPO) and 2D-autocorrelation descriptors (2DAUTO). The complementary information contents having neighborhood symmetry of 2-order, CIC2 from the TOPO class, the Geary autocorrelations-lag 8, weighted by atomic Sanderson electronegativities, GATS8e and the Moran autocorrelations-lag 6, weighted by atomic Sanderson electronegativities, MATS6e both from 2DAUTO class have contributed significantly in the development of a statistical significant model.

QSAR studies on benzoylaminobenzoic acid derivatives as inhibitors of β-ketoacyl-acyl carrier protein synthase III

Fatty acid biosynthesis is essential for most of the bacterial survival. Components of this biosynthetic pathway have been identified as attractive targets for the development of new antibacterial agents. FabH, beta-ketoacyl-ACP synthase III, is a attractive target since it is central to the initiation of fatty acid biosynthesis. Quantitative structure-activity relationship (QSAR) studies have been carried out on a series of benzoylaminobenzoic acid derivatives as potent inhibitors of FabH and antibacterial activity against Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus faecalis, Neisseria meningitidis and Escherichia coli, which demonstrate FabH inhibitory activity in cell free and whole cell system. The QSAR studies revealed that inhibitory activity increases with increase in hydrophobicity, molar refractivity, aromaticity, and presence of OH group (on x position of the nucleus). On the other side presence of hetero-atoms like N, O, or S at R(1) position of the nucleus decreases the inhibitory activity. The comparison of QSAR between the FabH inhibitory activity and antibacterial activity against S. aureus, S. pneumoniae, S. pyogenes, E. faecalis, N. meningitidis also demonstrates that the hydrophobicity, aromaticity and presence of OH group (on x position of the nucleus) are conducive for the inhibitory activity.

QSAR study on tetrahydroquinoline analogues as plasmodium protein farnesyltransferase inhibitors: a comparison of rationales of malarial and mammalian enzyme inhibitory activities for selectivity

The quantitative structure-activity relationships of Plasmodium falciparum and Rat protein farnesyltransferase (PFT) inhibitory activities of 6-cyano-1-(3-methyl-3H-imidazoly-4-ylmethyl)-3-substituted-1,2,3,4-tetrahydroquinoline (THQ) analogues are investigated in order to explore the similarities/deviations between the two enzymes for these analogues. The structure space of a ligand (BMS-214662) bound to Rat-PFT (PDB code 1SA5) has been used as the conformational space of the compounds under investigation. The study has been carried out using the combinatorial protocol in multiple linear regression with several 2D- and 3D-descriptors from molecular operating environment (MOE) representing the physicochemical and electronic features of the compounds. The molecular potential energy and partially charged van der Waals surface areas have taken part in the PFT models. They suggested in favor of molecular arrangement with minimum energy and low positively/negatively charged surfaces for optimum Pf-PFT inhibitory activity. Furthermore, less hydrophobic compounds are preferred for the activity. The Rat-PFT inhibitory activity models suggested in favor of more negatively as well as more positively charged surface area descriptors for the better activity. The PLS analysis carried out on the descriptors of the Pf-PFT and Rat-PFT models suggested that among the parameters, the partially charged surface areas in the range -0.20 to -0.15 (PEOE_VSA-3) and -0.30 to -0.25 (PEOE_VSA-5), hydrophobicity (a_hyd, logP(o/w) and SlogP_VSA4), and electronic energy (PM3_Eele) of the molecules hold promise for modulating the Pf-PFT/R-PFT inhibitory activities of the compounds. This suggested the possibility of modulating the Pf-PFT/R-PFT inhibitory activities and bringing about selectivity in the THQ analogues for the malarial parasite enzyme.

C-3 Alkyl/Arylalkyl-2,3-dideoxy Hex-2-enopyranosides as Antitubercular Agents: Synthesis, Biological Evaluation, and QSAR Study

A series of C-3 alkyl and arylalkyl 2,3-dideoxy hex-2-enopyranoside derivatives were synthesized by Morita-Baylis-Hillman reaction using enulosides 4, 5, and 6 and various aliphatic and aromatic aldehydes. The compounds were evaluated in vitro for the complete inhibition of growth of Mycobacterium tuberculosis H37Rv. They exhibited moderate to good activity in the range of 25-1.56 mug/mL. Among these, 4d, 4h, 5c, and 4hr showed activity at minimum inhibitory concentrations, 3.12, 6.25, 1.56, and 1.56 mug/mL, respectively. These compounds were safe against cytotoxicity in VERO cell line and mouse macrophage cell line J 744A.1. A QSAR analysis by CP-MLR with alignment-free 3D-descriptors indicated the relevance of structure space comparable to the minimum energy conformation (from conformational analysis) of 5c to the activity. The study indicates that the compounds attaining the conformational space of 5c and reflecting some symmetry, minimum eccentricity, and closely placed geometric and electronegativity centers therein are favorable for activity.

A high dimensional QSAR study on the aldose reductase inhibitory activity of some flavones: topological descriptors in modeling the activity

The quantitative structure-activity relationships (QSAR) of the Aldose Reductase (AR) inhibitory activity of 48 flavones were studied using Free-Wilson, Combinatorial Protocol in Multiple Linear Regression (CP-MLR), and Partial Least Squares (PLS) procedures. For the latter two procedures 152 Molconn-Z parameters and six indicators corresponding to the hydroxyls of flavones were used as molecular descriptors. Independently, all procedures suggested the significance of hydroxyls in modulating the activity of these compounds. The CP-MLR procedure identified 26 descriptors to model the activity. They suggested that structures rich in aromatic CH fragments, with a limited number of aliphatic fragments such as -CH2-, -CH<, and free hydroxyls at 7-, 3'-, and 4'-positions of the 2-arylbenzpyran-4-one core would be preferred for the activity. The PLS analysis agreed with the information content and the relative significance of the descriptors identified in the CP-MLR for modeling the activity. The study offers the scope to modulate the inhibitory activity of these compounds.

2-(Aryl)-3-furan-2-ylmethyl-thiazolidin-4-ones as selective HIV-RT Inhibitors

A series of 4-thiazolidinones were evaluated as selective inhibitors of the HIV-RT enzyme. Our attempt in correlating the derived physicochemical properties with the HIV-RT inhibitory activity resulted in some statistically significant QSAR models with good predictive ability. The QSAR studies indicated the role of lipophilicity, dipole moment and out-of-plane potential energy of the compounds in rationalizing the activity. One of the compounds, 1, inhibited the enzyme at 0.204 microM concentration with minimal toxicity to MT-4 cells.

Topological Descriptors in Modeling the HIV Inhibitory Activity of 2-Aryl-3- pyridyl-thiazolidin-4-ones

The HIV-1 RT inhibitory activity of 2-(2,6-dihalophenyl)-3-(substituted pyridin-2-yl)-thiazolidin-4-ones has been analyzed with different topological descriptors obtained from DRAGON software. Here, simple topological descriptors (TOPO), Galvez topological charge indices (GVZ) and 2D autocorrelation descriptors (2DAUTO) have been found to yield good predictive models for the activity of these compounds. The correlations obtained from the TOPO class descriptors suggest that less extended or compact saturated structural templates would be better for the activity. The participating GVZ class descriptors suggest that they have same degree of influence on the activity. In 2DAUTO class, the large participation of descriptors of lags seven and three indicate the association of activity information with the seven and three centered structural fragments of these compounds. The physicochemical weighting components of these descriptors suggest homogeneous influence of mass, volume, electronegativity and/ or polarizability on the activity.

Synthesis and QSAR Studies on Thiazolidinones as Anti-HIV Agents

Selected 4-thiazolidinone have been synthesized and tested as anti-HIV activity. The results of the in vitro tests showed that one of the compounds, 5, inhibited the enzyme at 0.204 microM concentration with minimal toxicity to MT-4 cell. Furthermore, the QSAR studies indicated the role of PMIZ, Ovality and Total energy content of the compounds in rationalizing the activity.

A Simple Algorithm for Unique Representation of Chemical StructuresCyclic/Acyclic Functionalized Achiral Molecules

An algorithm, based on "vertex priority values" has been proposed to uniquely sequence and represent connectivity matrices of chemical structures of cyclic/acyclic functionalized achiral hydrocarbons and their derivatives. In this method, "vertex priority values" have been assigned in terms of atomic weights, subgraph lengths, loops, and heteroatom contents. Subsequently, the terminal vertices have been considered upon completing the sequencing of the core vertices. This approach provides a multilayered connectivity graph, which can be put to use in comparing two or more structures or parts thereof for any given purpose. Furthermore, the basic vertex connection tables generated here are useful in the computation of characteristic matrices/topological indices and automorphism groups and in storing, sorting, and retrieving chemical structures from databases.

Topological Descriptors in Modeling the Antimalarial Activity of 4-(3‘,5‘-Disubstituted anilino)quinolines

Two series of closely related antimalarial agents, 7-chloro-4-(3',5'-disubstituted anilino)quinolines, have been analyzed using Combinatorial Protocol in Multiple Linear Regression (CP-MLR) for the structure-activity relations with more than 450 topological descriptors for each set. The study clearly suggested that 3'- and 5'-substituents of the anilino moiety map different domains in the activity space. While one domain favors the compact structural frames having aromatic, heterocyclic ring(s) substituted with closely spaced F, NO(2), and O functional groups, the other prefers structural frames enriched with unsaturation, loops, branches, electronic content, and devoid of carbonyl function. Also, this study gives an indication in favor of the electron rich centers in the aniline substituent groups for better antimalarial activity, an observation in line with several of the previous reports too. The models developed, and the participating descriptors suggest that the substituent groups of the 4-anilino moiety of the 4-(3',5'-disubstituted anilino)quinolines hold scope for further modification in the optimization of the antimalarial activity.

CP-MLR directed QSAR studies on the antimycobacterial activity of functionalized alkenols—topological descriptors in modeling the activity

The antimycobacterial activity of nitro/acetamido alkenol derivatives and chloro/amino alkenol derivatives has been analyzed through combinatorial protocol in multiple linear regression (CP-MLR) using different topological descriptors obtained from Dragon software. Among the topological descriptor classes considered in the study, the activity is correlated with simple topological descriptors (TOPO) and more complex 2D autocorrelation descriptors (2DAUTO). In model building the descriptors from other classes, that is, empirical, constitutional, molecular walk counts, modified Burden eigenvalues, and Galvez topological charge indices have made secondary contribution in association with TOPO and/or 2DAUTO classes. The structure-activity correlations obtained with the TOPO descriptors suggest that less branched and saturated structural templates would be better for the activity. For both the series of compounds, in 2DAUTO the activity has been correlated to the descriptors having mass, volume and/or polarizability as weighting component. In these two series of compounds, however, the regression coefficients of the descriptors have opposite arithmetic signs with respect to one another. Outwardly these two series of compounds appear very similar. But in terms of activity they belong to different segments of descriptor-activity profiles. This difference in the activity of these two series of compounds may be mainly due to the spacing difference between the C1 (also C6) substituents and rest of the functional groups in them.

A theoretical study of hydrophobic fragment and factor constants of Hansch and Leo: estimation of a few non-available fragments and factors

Hydrophobic fragment constants (f) of benzotriazol-2-yl and Ar-N[CO-]2 systems, and aliphatic H/S polar interaction factors F(H/S) in Cl2CHCONH-Ar and Cl3CCONH-Ar, of Hansch and Leo's constructionist approach, were estimated as 0.69 (standard deviation = 0.17), -1.98, 0.95 and 0.98 respectively. The validity of the first constant has been tested by calculating the log P of compounds not included in the regression.

QSAR study of phosphodiesterase inhibitory activity of imidazo[2,1-b]-quinazolines: active site analysis

Published c-AMP phosphodiesterase inhibitory activities of 7-substituted-1,2,3,5-tetrahydro-2-oxoimidazo[2,1-b]quinazolines are used in a QSAR study to analyse a proposed model of the c-AMP PDE (type IV) active site. Based on the regression equations involving hydrophobic parameters and activities, additional subsites G1 and G2 are identified in the secondary binding region G, and steric hydrophobic tolerance at these subsites is discussed.

QSAR study of the role of hydrophobicity in the activity of HMGR inhibitors

The 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) inhibitory activity of 7-(aryl/biphenyl)-6-heptenoic acids was quantitatively analysed using hydrophobicity, van der Waals volume and electronic parameters. The activity was primarily a function of hydrophobicity, and was well correlated with the hydrophobicity of ortho and meta substituents on the aryl/biphenyl moiety. The electronic properties of para substituents on the aryl/biphenyl ring influenced the inhibition. Our equations predict that substituents with positive polar and sigma and negative resonance constants might lead to better inhibition.

Quantitative structure-activity relationship study on amsacrine derivatives

Various biological activities of amsacrine derivatives were analyzed in relation to various physico-chemical parameters. The in vitro activity parameters like DNA-binding and cell inhibition constants were found to have significant correlations but with varying physico-chemical parameters. DNA-binding constants were found to be the function of van der Waals volume and the cell inhibition constant to be the function of the hydrophobic parameter. But the in vivo antitumor activity parameters like optimal dose administered intraperitoneally in mice injected with P388 leukemia cells and the percentage increase in life span of treated animals over that of control animals were not found to be related with any property of the molecules.

Effect of molecular size on the activity of adriamycin analogues: a quantitative structure-activity relationship study

The in vitro anti-tumor activity (inhibition of human lymphoblastic leukemia cells) of some adriamycin analogues is found to be significantly correlated with the van Waals volume (VW) of the substituents. Activity is also found to be well correlated with first-order valence molecular connectivity index (1 chi V) but no correlation is found to exist between it and the hydrophobic parameter, log P (P: octanol-water partition coefficient). On the basis of these findings, it is suggested that the activity would be affected by the steric influence and to some extent by the electronic character of the substituents. From the correlating equations, it is observed that the size of C-7 glycoside ring and that of NHR2 group at its third position would greatly affect the activity. The size of C-14-R1 however, is not found to have much effect on the activity.