Falcipains (FPs) are hemoglobinases of Plasmodium falciparum that are validated targets for the development of antimalarial chemotherapy. A combined ligand- and structure-based virtual screening of commercial databases was performed to identify structural analogs of virtual screening hits previously discovered in our laboratory. A total of 28 low micromolar inhibitors of FP-2 and FP-3 were identified and the structure–activity relationship (SAR) in each series was elaborated. The SAR of the compounds was unusually steep in some cases and could not be explained by a traditional analysis of the ligand–protein interactions (van der Waals, electrostatics, and hydrogen bonds). To gain further insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domains of FP-2 and FP-3 was carried out to understand the roles played by water molecules in binding of these inhibitors. Indeed, the energetics associated with the displacement of water molecules upon ligand binding explained some of the complex trends in the SAR. Furthermore, low potency of a subset of FP-2 inhibitors that could not be understood by the water energetics was explained in the context of poor chemical reactivity of the reactive centers of these compounds. The present study highlights the importance of considering energetic contributors to binding beyond traditional ligand–protein interactions.

Malaria, in particular that caused by Plasmodium falciparum, is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum, falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure−activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.

Melanin concentrating hormone (MCH) is a cyclic 19-amino-acid peptide expressed mainly in the hypothalamus. It is involved in the control of feeding behavior, energy homeostasis, and body weight. Administration of MCH-R1 antagonists has been proved to reduce food intake and cause weight loss in animal models. In the present study, a homology model of the human MCH-R1 was constructed using the crystal structure of bovine rhodopsin (PDB: 1u19) as a template. Based on the observation that MCH-R1 can bind ligands of high chemical diversity, the initial model was subjected to an extensive ligand-supported refinement using antagonists of different chemotypes. The refinement process involved stepwise energy minimizations and molecular dynamics simulations. The refined model was inserted into a pre-equilibrated DPPC/TIP3P membrane system and then simulated for 20 ns in complex with structurally diverse antagonists. This protocol was able to explain the SAR of MCH-R1 antagonists with diverse chemical structures. Moreover, it reveals new insights into the critical recognition sites within the receptor. This work represents the first detailed study of molecular dynamics of MCH-R1 inserted into a membrane-aqueous environment.

SARS-CoV from the coronaviridae family has been identified as the etiological agent of Severe Acute Respiratory Syndrome (SARS), a highly contagious upper respiratory disease that reached epidemic status in 2002. SARS-3CLpro, a cysteine protease indispensible to the viral life cycle, has been identified as one of the key therapeutic targets against SARS. A combined ligand and structure-based virtual screening was carried out against the Asinex Platinum collection. Multiple low micromolar inhibitors of the enzyme were identified through this search, one of which also showed activity against SARS-CoV in a whole cell CPE assay. Furthermore, multinanosecond explicit solvent simulations were carried out using the docking poses of the identified hits to study the overall stability of the binding site interactions as well as identify important changes in the interaction profile that were not apparent from the docking study. Cumulative analysis of the evaluated compounds and the simulation studies led to the identification of certain protein–ligand interaction patterns which would be useful in further structure based design efforts.

We describe the design, combinatorial library synthesis and biological evaluation of compounds with benzothiazole and triazole cores as inhibitors of falcipain, cysteine proteases of the malaria parasite Plasmodium falciparum. These classes were originally discovered by structure-based virtual screening of a focused cysteine protease inhibitor library. Fifteen structural analogs of both series showed moderate inhibition of falcipain-2. Two compounds, 41 and 42, were predicted by docking studies to interact with polar residues buried in the S2 pockets of falcipain-2 and -3, and these compounds inhibited both enzymes. Compound 41 also demonstrated activity against chloroquine-resistant cultured P. falciparum parasites at the lower micromolar concentration. Evaluation of 41 and 42 against mammalian cysteine proteases of papain family suggest these polar residues of the S2 pocket may not be important for the design of selective inhibitors against falcipain.

Malaria is re-emerging in many tropical areas of the world and is often fatal due to drug resistance, leading to about a million deaths each year. Multiple drug resistance has required new efforts in drug discovery and development. Thus, the search for new drugs operating by novel mechanisms of action is receiving increased attention. Herein we report the synthesis and biological evaluation of a novel anti-malarial with micromolar activity against resistant strains of the parasite.

In addition to lowering blood pressure, telmisartan, an angiotensin (AT1) receptor blocker, has recently been shown to exert pleiotropic effects as a partial agonist of nuclear peroxisome proliferator-activated receptor γ (PPARγ). On the basis of these findings and docking pose similarity between telmisartan and rosiglitazone in PPARγ active site, two classes of benzimidazole derivatives were designed and synthesized as dual PPARγ agonist/angiotensin II antagonists for the possible treatment of metabolic syndrome. Compound 4, a bisbenzimidazole derivative showed the best affinity for the AT1 receptor with a Ki = 13.4 nM, but it was devoid of PPARγ activity. On the other hand 9, a monobenzimidazole derivative, showed the highest activity in PPARγ transactivation assay (69% activation) with no affinity for the AT1 receptor. Docking studies lead to the designing of a molecule with dual activity, 10, with moderate PPARγ activity (29%) and affinity for the AT1 receptor (Ki = 2.5 μM).

Design and synthesis of a guaianolide-endoperoxide (thaperoxide) 3 was pursued as a new antimalarial lead which was found to be noncytotoxic as compared to the natural product lead thapsigargin 2. Several analogues of 3 were successfully synthesized and found to be comparable to derivatives of artemisinin 1 in in vitro antimalarial assay. Among the synthesized compounds, 22 showed excellent in vitro potency against the cultured parasites (W2 IC50 = 13 nM) without apparent cytotoxicity. Furthermore, SAR trends in thaperoxide analogues are presented and explained with the help of docking studies in the homology model of PfSERCA(PfATP6).

Apoptosis, or programmed cell death, forms an important part of the cellular regulation machinery. The Bcl-2 protein family, comprising of proapoptotic and antiapoptotic members, forms an important part of the cells internal apoptotic pathway. Overexpression of the antiapoptotic members of the family in a number of cancer cell lines renders them immune to apoptosis and the ability to survive under conditions of cellular stress. Inhibition of the antiapoptotic members of the Bcl-2 family are, therefore, an interesting target for the development of anticancer therapy. An innovative structure-based virtual screening strategy was developed to identify inhibitors of Bcl-xL, an antiapoptotic member of the Bcl-2 family. Various innovative filters, such as receptor-based pharmacophore, cascade docking approach, cross-docking, and composite scoring with docking pose based descriptors were designed through exhaustive validation studies and implemented in the screening funnel. The 1.8 million ‘big-n-greasy’ subset from ZINC was screened using the protocol, and 45 compounds were finally selected for biological evaluation against Bcl-xL. The evaluation led to the identification of one low-micromolar and two weaker inhibitors belonging to novel scaffolds. Further evaluation of structure−activity relationships around these scaffolds could help in the development of anticancer leads against Bcl-xL.

The asymmetric total synthesis of (−)-berkeleyamide A (1), a naturally occurring caspase-1 inhibitor, has been achieved by employing Evans’ syn-aldol reaction of N-acyl-(4R)-benzyl oxazolidin-2-one 3 as the key step.

The purpose of the present investigation was to characterize the partitioning of artemisinin and its derivatives into both non-parasitized as well as Plasmodium falciparum parasitized red blood cells (RBCs). Artemisinin and selected derivatives at concentrations of 3.55 μM were incubated in RBCs with a hematocrit of 33% for 2 h at 37 °C, extracted from RBCs by solid phase extraction, and analyzed using liquid chromatography–mass spectrometry in positive electro-spray ionization mode with methanol as mobile phase. The uptake percent of artemisinin and selected derivatives into the non-parasitized RBCs ranged between 35% and 45%, while that into parasitized RBCs was between 51% and 72%. The results suggested that artemisinin and selected derivatives were preferentially distributed in parasitized RBCs. A Multiple Linear Regression model was built to gain insight about the essential structural properties required for the uptake of this class of compounds in parasitized RBCs and will provide instruction for designing of new derivatives of this class of compounds with improved uptake.Uptake studies of artemisinin and selected derivatives into normal and parasitized red blood cells (RBCs) and Multiple Regression Model for percent uptake of artemisinin and its derivates into the parasitized RBCs.

A novel hybrid class of telmisartan–rosiglitazone molecules was synthesized in an attempt to discover a dual peroxisome proliferator-activated receptor gamma (PPARγ) agonist/angiotensin II antagonist for treatment for metabolic syndrome. Almost all the synthesized molecules showed moderate PPARγ activity. However, none of the hybrid analogs showed binding affinity toward the AT1 receptor.

In our early studies, telmisartan was found to be a moderate peroxisome proliferator-activated receptor (PPAR) gamma activator in the human PPARγ-GAL-4 cell-based transactivation assay. Thus, novel analogs of telmisartan were designed, synthesized, and evaluated in the AT1 receptor binding assay and PPAR gamma transactivation assay. A total of 11 compounds were designed based on docking in both AT1 receptor model and PPAR gamma active pocket and synthesized. Introduction of an additional acidic group at the para position of the distal phenyl ring of telmisartan decreased affinity towards AT1 receptor and PPARγ activity. In the present study, the molecule with best results was MT003 with weak PPARγ activity (8% of maximum PPARγ activation achieved by full agonist rosiglitazone at 10 μM) and good binding affinity (Ki = 650 ± 139 nM) towards the AT1 receptor. Docking of MT003 into AT1 receptor model and PPAR gamma showed very similar interactions with the receptors as AT1 antagonist telmisartan and PPAR gamma agonist rosiglitazone.

Leishmania donovani and Leishmania major farnesyl pyrophosphate synthase (LdFPPS and LmFPPS) are potential targets for the development of antileishmanial therapy. The protein sequence for LdFPPS was recently elucidated in our laboratory. Highly refined homology models were generated using the protein sequences of LdFPPS and the closely related LmFPPS enzyme. A ligand-refined model of LmFPPS with a bound bisphosphonate ligand was generated using restraint-guided molecular mechanics followed by quantum mechanics/molecular mechanics refinement. The ligand-refined model of LmFPPS was further validated through extensive pose validation, enrichment, and other docking studies involving known bisphosphonate inhibitors. The model was able to explain the critical binding site interactions and site-directed mutagenesis data obtained from experimental studies on related FPPS enzymes. The ligand-refined model in conjunction with the validated docking protocol could be utilized in the future for structure-based virtual screening and rational drug design studies against these targets.

Severe acute respiratory syndrome is a highly infectious upper respiratory tract disease caused by SARS-CoV, a previously unidentified human coronavirus. SARS-3CLpro is a viral cysteine protease critical to the pathogen’s life cycle and hence a therapeutic target of importance. The recently elucidated crystal structures of this enzyme provide an opportunity for the discovery of inhibitors through rational drug design. In the current study, Gold docking program was utilized to conduct extensive docking studies against the target crystal structure to develop a robust and predictive docking protocol. The validated docking protocol was used to conduct a structure-based virtual screening of the Asinex Platinum collection. Biological evaluation of a screened selection of compounds was carried out to identify novel inhibitors of the viral protease.Novel inhibitors of the SARS-3CLpro were identified using a combination of structure-based virtual screening and biological evaluation.

The histone deacetylase (HDAC) enzyme from Plasmodium falciparum has been identified as a novel target for the development of antimalarial therapy. A ligand-refined homology model of PfHDAC-1 was generated from the crystal structures of human HDAC8 and HDLP using a restraint guided optimization procedure involving the OPLS/GBSA potential setup. The model was extensively validated using protein structure checking tools. A predictive docking study was carried out using a set of known human HDAC inhibitors, which were shown to have in vitro antimalarial activity against the chloroquine sensitive D6 and resistant W2 strains of P. falciparum. Pose validation and score-based active/inactive separation studies provided independent validation of the geometric accuracy and the predictive ability of the generated model. Comparative analysis was carried out with the human HDACs to identify differences in the binding site topology and interacting residues, which might be utilized to develop selective PfHDAC-1 inhibitors.A ligand-refined homology model of Plasmodium falciparum histone deacetylase 1 was generated and a predictive docking protocol was established for structure-based drug design applications.

The absolute stereo structure of the natural product laurenditerpenol (1S, 6R, 7S, 10R, 11R, 14S, 15R) has been accomplished from eight plausible stereoisomers by its first asymmetric total synthesis in a highly convergent and flexible synthetic pathway. Six stereoisomers of laurenditerpenol were synthesized and evaluated for their biological activity.

An efficient diastereoselective synthesis of cis- and trans-5-hydroxy-(2S)-N-benzyloxycarbonyl pipecolic acids, starting from trans-4-hydroxy-l-proline is described. The key synthetic strategies involve the regioisomeric ring expansion of keto ester 8 and diastereoselective reduction of ketone 11 in high selectivity and yield.N-Benzyloxycarbonyl-5-oxo-S-pipecolic acid tert-butyl esterC18H23NO5[α]D25=-4.8 (c 1.0, CHCl3)Source of chirality: asymmetric synthesisAbsolute configuration: (2S)N-Benzyloxycarbonyl-4-oxo-S-pipecolic acid tert-butyl esterC18H23NO5[α]D25=-15.4 (c 1.0, CHCl3)Source of chirality: asymmetric synthesisAbsolute configuration: (2S)N-Benzyloxycarbonyl-(2S,5S)-5-hydroxypipecolic acid tert-butyl esterC18H25NO5[α]D26=-27.9 (c 2.0, CHCl3)Source of chirality: asymmetric synthesisAbsolute configuration: (2S,5S)N-Benzyloxycarbonyl-(2S,5R)-5-hydroxypipecolic acid tert-butyl esterC18H25NO5[α]D26=-19.6 (c 2.0, CHCl3)Source of chirality: asymmetric synthesisAbsolute configuration: (2S,5R)N-Benzyloxycarbonyl-(2S,5S)-5-hydroxypipecolic acidC14H17NO5[α]D26=+76.5 (c 0.17, MeOH)Source of chirality: asymmetric synthesisAbsolute configuration: (2S,5S)N-Benzyloxycarbonyl-(2S,5R)-5-hydroxypipecolic acidC14H17NO5[α]D28=-7.2 (c 1.0, MeOH)Source of chirality: asymmetric synthesisAbsolute configuration: (2S,5R)

1,4,7-Trisubstituted isoquinolines were designed, synthesized and evaluated for their inhibition against Plasmodium falciparum cysteine protease falcipain-2. The 1-benzyloxyphenyl-dihydroisoquinoline and -isoquinoline derivatives were found to exhibit better activity against falcipain-2 than their corresponding 1-hydroxyphenyl or 1-methoxyphenyl analogues. The docking scores correlate with the IC50 values of compounds and give a high coefficient correlation of 0.94.Graphic

The novel chiral vinyl boronate (+)-1 was utilized as a dienophile in a series of [4+2] cycloadditions. The intermediate cyclized products obtained were oxidized directly (H2O2, NaOH). The resulting alcohols displayed enantiomeric excesses of 7–33%. A slight preference for the endo configuration was observed, in agreement with previous results.The novel chiral vinyl boronate (+)-1 was utilized as a dienophile in a series of [4+2] cycloadditions. After oxidation, the resulting alcohols displayed enantiomeric excesses of 7–33 %.