Structure‐Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics

Structure‐based virtual screening using a D₂ receptor homology model was performed to identify dopamine D₂ receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D₂ ligands were identified (47.6 % success rate, among them D₂ receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5‐HT_2A receptors. The affinity (K_i values) of the compounds ranged from 58 nm to about 24 μm . Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D₂ receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D₂ pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20‐fold binding selectivity for the D₂ receptor over the D₃ receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction.     

Probing Ligand Structure–Activity Relationships in Pregnane X Receptor (PXR): Efavirenz and 8‐Hydroxyefavirenz Exhibit Divergence in Activation

Efavirenz (EFV), an antiretroviral that interacts clinically with co‐administered drugs via activation of the pregnane X receptor (PXR), is extensively metabolized by the cytochromes P450. We tested whether its primary metabolite, 8‐hydroxyEFV (8‐OHEFV) can activate PXR and potentially contribute to PXR‐mediated drug–drug interactions attributed to EFV. Luciferase reporter assays revealed that despite only differing from EFV by an oxygen atom, 8‐OHEFV does not activate PXR. Corroborating this, treatment with EFV for 72 h elevated the mRNA abundance of the PXR target gene, Cyp3a11, by approximately 28‐fold in primary hepatocytes isolated from PXR‐humanized mice, whereas treatment with 8‐OHEFV did not result in a change in Cyp3A11 mRNA levels. FRET‐based competitive binding assays and isothermal calorimetry demonstrated that even with the lack of ability to activate PXR, 8‐OHEFV displays an affinity for PXR (IC₅₀ 12.1 μm ; K_D 7.9 μm ) nearly identical to that of EFV (IC₅₀ 18.7 μm ; K_D 12.5 μm ). The use of 16 EFV analogues suggest that other discreet changes to the EFV structure beyond the 8‐position are well tolerated. Molecular docking simulations implicate an 8‐OHEFV binding mode that may underlie its divergence in PXR activation from EFV.     

Pramipexole Derivatives as Potent and Selective Dopamine D3 Receptor Agonists with Improved Human Microsomal Stability

Herein we report the synthesis and evaluation of a series of new pramipexole derivatives as highly potent and selective agonists of the dopamine‐3 (D₃) receptor. A number of these new compounds bind to the D₃ receptor with sub‐nanomolar affinity and show excellent selectivity (>10 000) for the D₃ receptor over the D₁ and D₂ receptors. For example, compound 23 (N‐(cis‐3‐(2‐(((S)‐2‐amino‐4,5,6,7‐tetrahydrobenzo[d]thiazol‐6‐yl)(propyl)amino)ethyl)‐3‐hydroxycyclobutyl)‐3‐(5‐methyl‐1,2,4‐oxadiazol‐3‐yl)benzamide) binds to the D₃ receptor with a K_i value of 0.53 nM and shows a selectivity of >20 000 over the D₂ and D₁ receptors in the binding assays using a rat brain preparation. It has excellent stability in human liver microsomes. Moreover, in vitro functional assays showed it to be a full agonist for the human D₃ receptor.     

Clozapine recognition via molecularly imprinted polymers; bulk polymerization versus precipitation method

Two clozapine (CLZ) imprinted polymers were prepared by bulk and precipitation methods. Methacrylic acid and ethylene glycol dimethacrylate (EDMA) were used as functional and crosslinker monomers, respectively. The mean diameter and particle size distribution of the imprinted (P‐MIP) and nonimprinted (P‐NIP) particles obtained in precipitation method were examined. A conventional batch‐adsorption test was applied for characterization of CLZ–polymer interaction. Dissociation constant (K_D) and maximum binding sites (B_max) were calculated using Scatchard analysis. To evaluate the recognition properties of polymers, phenytoin (PTN) binding to each polymer was also studied and compared to CLZ. The imprinting factor (IF) and selectivity factor (α) were also determined for each polymer. Average diameter and polydispersity of P‐MIP were 925 nm and 0.17, respectively. The data for P‐NIP were 1.05 μm and 0.18. The K_D, IF, and α values calculated for P‐MIP were 0.45 μM, 3.26, and 17.43, respectively. The data for imprinted polymer, prepared by bulk polymerization (B‐MIP), were 14.5 μM, 1.95, and 3.67. These results demonstrated that precipitation polymerization is a more convenient, more effective, and more reproducible method than bulk polymerization for the synthesis of uniformly sized micron and submicron‐imprinted polymer particles. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011     

The Discovery of Phenylbenzamide Derivatives as Grb7‐Based Antitumor Agents

Grb7 is a non‐catalytic protein, the overexpression of which has been associated with the proliferative and migratory potentials of cancer cells. Virtual screening strategies involving a shape‐based similarity search, molecular docking, and 2D‐similarity searches complemented by experimental binding studies (Thermofluor and isothermal titration calorimetry) resulted in the identification of nine novel phenylbenzamide‐based antagonists of the Grb7 SH2 domain. Moderate binding affinities were observed, ranging from K_d=32.3 μM for lead phenylbenzamide NSC 104999 ( 1 ) to K_d=1.1 μM for a structurally related compound, NSC 57148 ( 2 ). Deconvolution of the affinity data into its components revealed differences in lead binding, from being entropy based (lead 1 ) to enthalpically driven (NSC 100874 ( 3 ), NSC 55158 ( 4 ), and compound 2 ). Finally, the lead compound 1 was found to decrease the growth of MDA‐MB‐468 breast cancer cells, with an IC₅₀ value of 39.9 μM . It is expected that these structures will serve as novel leads in the development of Grb7‐based anticancer therapeutics.     

Molecular Recognition of Two 2,4‐syn‐Functionalized (S)‐Glutamate Analogues by the Kainate Receptor GluK3 Ligand Binding Domain

The kainate receptors are the least studied subfamily of ionotropic glutamate receptors. These receptors are thought to have a neuromodulatory role and have been associated with a variety of disorders in the central nervous system. This makes kainate receptors interesting potential drug targets. Today, structures of the ligand binding domain (LBD) of the kainate receptor GluK3 are only known in complex with the endogenous agonist glutamate, the natural product kainate, and two synthetic agonists. Herein we report structures of GluK3 LBD in complex with two 2,4‐syn‐functionalized (S)‐glutamate analogues to investigate their structural potential as chemical scaffolds. Similar binding affinities at GluK3 were determined for the 2‐(methylcarbamoyl)ethyl analogue (K_i=4.0 μM ) and the 2‐(methoxycarbonyl)ethyl analogue (K_i=1.7 μM ), in agreement with the similar positioning of the compounds within the binding pocket. As the binding affinity is similar to that of glutamate, this type of Cγ substituent could be used as a scaffold for introduction of even larger substituents reaching into unexplored binding site regions to achieve subtype selectivity.     

Distribution and diffusion coefficients of NaCl in polyamide (nylon‐6,6 and polyxylyleneadipamide) membranes

Thin membranes of an aliphatic polyamide (nylon‐6,6) and an aromatic polyamide (polyxylyleneadipamide) (PXAP) were prepared, and their distribution (K) and overall diffusion (D) coefficients of sodium chloride were measured with the unsteady‐state and steady‐state dialysis method. The overall diffusion coefficients at a zero concentration [D⁽⁰⁾] of sodium chloride for nylon‐6,6 and PXAP were 1.3–0.8 μm²/s (from 2 min of interfacial polymerization to 4 min) and 0.078, respectively. D⁽⁰⁾ for PXAP was about 3 times greater than that of a cellulose acetate (CA) membrane (0.024 μm²/s). The K values for nylon‐6,6 and PXAP were 0.7–0.5 from 2 to 4 min and 0.05, respectively. K for PXAP was almost the same as K for CA (0.06). A two‐part (dense and porous) model of the membrane structure was applied to obtain D_d (the diffusion coefficient in the dense part of the membrane) and D_p (the diffusion coefficient in the porous part of the membrane) for CA, PXAP, and nylon‐6,6 thin membranes. The values of D_d were almost the same for both nylon‐6,6 and PXAP (0.05–0.061 μm²/s) and about 10 times greater than the value for the CA membrane (5.6 × 10^?3 μm²/s). D_p for PXAP was almost the same as D_p for CA. However, D_p for the nylon‐6,6 membrane was 10–16 times greater than D_p for the PXAP membrane. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 2605–2612, 2002     

Exploring Non‐obvious Hydrophobic Binding Pockets on Protein Surfaces: Increasing Affinities in Peptide–Protein Interactions

A 42‐residue polypeptide conjugated to a small‐molecule organic ligand capable of targeting the phosphorylated side chain of Ser15 was shown to bind glycogen phosphorylase a (GPa) with a K_D value of 280 nm . The replacement of hydrophobic amino acids by Ala reduced affinities, whereas the incorporation of l ‐2‐aminooctanoic acid (Aoc) increased them. Replacing Nle5, Ile9 and Leu12 by Aoc reduced the K_D value from 280 to 27 nm . “Downsizing” the 42‐mer to an undecamer gave rise to an affinity for GPa an order of magnitude lower, but the undecamer in which Nle5, Ile9 and Leu12 were replaced by Aoc showed a K_D value of 550 nm , comparable with that of the parent 42‐mer. The use of Aoc residues offers a convenient route to increased affinity in protein recognition as well as a strategy for the “downsizing” of peptides essentially without loss of affinity. The results show that hydrophobic binding sites can be found on protein surfaces by comparing the affinities of polypeptide conjugates in which Aoc residues replace Nle, Ile, Leu or Phe with those of their unmodified counterparts. Polypeptide conjugates thus provide valuable opportunities for the optimization of peptides and small organic compounds in biotechnology and biomedicine.     

Synthesis and Structure–Activity Relationship Studies of 2‐(1,3,4‐Oxadiazole‐2(3H)‐thione)‐3‐amino‐5‐arylthieno[2,3‐b]pyridines as Inhibitors of DRAK2

In recent years, DAPK‐related apoptosis‐inducing protein kinase 2 (DRAK2) has emerged as a promising target for the treatment of a variety of autoimmune diseases and for the prevention of graft rejection after organ transplantation. However, medicinal chemistry optimization campaigns for the discovery of novel small‐molecule inhibitors of DRAK2 have not yet been published. Screening of a proprietary compound library led to the discovery of a benzothiophene analogue that displays an affinity constant (K_d) value of 0.25 μM . Variation of the core scaffold and of the substitution pattern afforded a series of 5‐arylthieno[2,3‐b]pyridines with strong binding affinity (K_d=0.008 μM for the most potent representative). These compounds also show promising activity in a functional biochemical DRAK2 enzyme assay, with an IC₅₀ value of 0.029 μM for the most potent congener. Selectivity profiling of the most potent compounds revealed that they lack selectivity within the DAPK family of kinases. However, one of the less potent analogues is a selective ligand for DRAK2 and can be used as starting point for the synthesis of selective and potent DRAK2 inhibitors.     

Prospective Validation of a Comprehensive In silico hERG Model and its Applications to Commercial Compound and Drug Databases

Ligand‐based in silico hERG models were generated for 2 644 compounds using linear discriminant analysis (LDA) and support vector machines (SVM). As a result, the dataset used for the model generation is the largest publicly available (see Supporting Information). Extended connectivity fingerprints (ECFPs) and functional class fingerprints (FCFPs) were used to describe chemical space. All models showed area under curve (AUC) values ranging from 0.89 to 0.94 in a fivefold cross‐validation, indicating high model consistency. Models correctly predicted 80 % of an additional, external test set; Y‐scrambling was also performed to rule out chance correlation. Additionally models based on patch clamp data and radioligand binding data were generated separately to analyze their predictive ability when compared to combined models. To experimentally validate the models, 50 of the predicted hERG blockers from the Chembridge database and ten of the predicted non‐hERG blockers from an in‐house compound library were selected for biological evaluation. Out of those 50 predicted hERG blockers, tested at a concentration of 10 μM , 18 compounds showed more than 50 % displacement of [³H]astemizole binding to cell membranes expressing the hERG channel. K_i values of four of the selected binders were determined to be in the micromolar and high nanomolar range (K_i (VH 01 )=2.0 μM , K_i (VH 06 )=0.15 μM , K_i (VH 19 )=1.1 μM and K_i (VH 47 )=18 μM ). Of these four compounds, VH 01 and VH 47 showed also a second, even higher affinity binding site with K_i values of 7.4 nM and 36 nM , respectively. In the case of non‐hERG blockers, all ten compounds tested were found to be inactive, showing less than 50 % displacement of [³H]astemizole binding at 10 μM . These experimentally validated models were then used to virtually screen commercial compound databases to evaluate whether they contain hERG blockers. 109 784 (23 %) of Chembridge, 133 175 (38 %) of Chemdiv, 111 737 (31 %) of Asinex and 11 116 (18 %) of the Maybridge database were predicted to be hERG blockers by at least two of the models, a prediction which could, for example, be used as a pre‐filtering tool for compounds with potential hERG liabilities.     

Discovery of a Small‐Molecule pBcl‐2 Inhibitor that Overcomes pBcl‐2‐Mediated Resistance to Apoptosis

Although the role of Bcl‐2 phosphorylation is still under debate, it has been identified in a resistance mechanism to BH3 mimetics, for example ABT‐737 and S1 . We identified an S1 analogue, S1‐16 , as a small‐molecule inhibitor of pBcl‐2. S1‐16 efficiently kills EEE‐Bcl‐2 (a T69E, S70E, and S87E mutant mimicking phosphorylation)‐expressing HL‐60 cells and high endogenously expressing pBcl‐2 cells, by disrupting EEE‐Bcl‐2 or native pBcl‐2 interactions with Bax and Bak, followed by apoptosis. In vitro binding assays showed that S1‐16 binds to the BH3 binding groove of EEE‐Bcl‐2 (K_d=0.38 μM by ITC; IC₅₀=0.16 μM by ELISA), as well as nonphosphorylated Bcl‐2 (npBcl‐2; K_d=0.38 μM ; IC₅₀=0.12 μM ). However, ABT‐737 and S1 had much weaker affinities to EEE‐Bcl‐2 (IC₅₀=1.43 and >10 μM , respectively), compared with npBcl‐2 (IC₅₀=0.011 and 0.74 μM , respectively). The allosteric effect on BH3 binding groove by Bcl‐2 phosphorylation in the loop region was illustrated for the first time.     

Artificial Metalloenzymes with the Neocarzinostatin Scaffold: Toward a Biocatalyst for the Diels–Alder Reaction

A copper(II) cofactor coupled to a testosterone anchor, copper(II)‐(5‐(Piperazin‐1‐yl)‐1,10‐phenanthroline)testosterone‐17‐hemisuccinamide ( 10 ) was synthesized and associated with a neocarzinostatin variant, NCS‐3.24 (K_D=3 μm ), thus generating a new artificial metalloenzyme by following a “Trojan horse” strategy. Interestingly, the artificial enzyme was able to efficiently catalyze the Diels–Alder cyclization reaction of cyclopentadiene ( 1 ) with 2‐azachalcone ( 2 ). In comparison with what was observed with cofactor 10 alone, the artificial enzymes favored formation of the exo products (endo/exo ratios of 84:16 and 62:38, respectively, after 12 h). Molecular modeling studies assigned the synergy between the copper complex and the testosterone (K_D=13 μm ) moieties in the binding of 10 to good van der Waals complementarity. Moreover, by pushing the modeling exercise to its limits, we hypothesize on the molecular grounds that are responsible for the observed selectivity.     

Inhibition Studies on Carbonic Anhydrase Isoforms I,II, IX,and XII with a Series of Sulfaguanidines

Two novel sulfaguanidine series, six N-(N,N′-dialkyl/dibenzyl-carbamimidoyl) benzenesulfonamide derivatives and nine N-(N-alkyl/benzyl-carbamimidoyl) benzenesulfonamide derivatives, were obtained by desulfidative amination of easily accessible dimethyl arylsulfonylcarbonimidodithioates under catalyst- and base-free conditions. The newly synthesized compounds were tested for the inhibition of four different isozymes of human carbonic anhydrase (hCA I, II, IX and XII, EC 4.2.1.1). Both series reported here were inactive against the off-target isozymes hCA I and II (K_i>100 μM). Interestingly, all investigated compounds inhibited both target isozymes hCA IX and XII in the submicromolar to micromolar ranges in which K_i values spanned from 0.168 to 0.921 μM against hCA IX and from 0.335 to 1.451 μM against hCA XII. The results indicated that N-(N-alkyl/benzyl-carbamimidoyl) benzenesulfonamides were slightly more potent inhibitors than N-(N,N′-dialkyl/dibenzyl-carbamimidoyl) benzenesulfonamides. Among the evaluated compounds, N-n-octyl-substituted N-carbamimidoylbenzenesulfonamide showed the most significant activity with a K_i value of 0.168 μM against hCA IX, which was four-fold more selective toward this isozyme versus hCA XII. Again, another derivative from N-(N-alkyl/benzyl-carbamimidoyl) benzenesulfonamide series, N-p-methylbenzyl-substituted N-carbamimidoylbenzenesulfonamide, demonstrated superior inhibitory activity against hCA XII with a K_i value of 0.335 μM.     

Synthesis and Evaluation of Novel Acyclic Nucleoside Phosphonates as Inhibitors of Plasmodium falciparum and Human 6‐Oxopurine Phosphoribosyltransferases

Acyclic nucleoside phosphonates (ANPs) are a promising class of antimalarial therapeutic drug leads that exhibit a wide variety of K_i values for Plasmodium falciparum (Pf) and human hypoxanthine‐guanine‐(xanthine) phosphoribosyltransferases [HG(X)PRTs]. A novel series of ANPs, analogues of previously reported 2‐(phosphonoethoxy)ethyl (PEE) and (R,S)‐3‐hydroxy‐2‐(phosphonomethoxy)propyl (HPMP) derivatives, were designed and synthesized to evaluate their ability to act as inhibitors of these enzymes and to extend our ongoing antimalarial structure–activity relationship studies. In this series, (S)‐3‐hydroxy‐2‐(phosphonoethoxy)propyl (HPEP), (S)‐2‐(phosphonomethoxy)propanoic acid (CPME), or (S)‐2‐(phosphonoethoxy)propanoic acid (CPEE) are the acyclic moieties. Of this group, (S)‐3‐hydroxy‐2‐(phosphonoethoxy)propylguanine (HPEPG) exhibits the highest potency for PfHGXPRT, with a K_i value of 0.1 μM and a K_i value for human HGPRT of 0.6 μM . The crystal structures of HPEPG and HPEPHx (where Hx=hypoxanthine) in complex with human HGPRT were obtained, showing specific interactions with active site residues. Prodrugs for the HPEP and CPEE analogues were synthesized and tested for in vitro antimalarial activity. The lowest IC₅₀ value (22 μM ) in a chloroquine‐resistant strain was observed for the bis‐amidate prodrug of HPEPG.     

Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (K_D=42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3–HSP90 binding was confirmed (K_D=13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.     

Carbohydrate–PNA and Aptamer–PNA Conjugates for the Spatial Screening of Lectins and Lectin Assemblies

Nucleic acid architectures offer intriguing opportunities for the interrogation of structural properties of protein receptors. In this study, we performed a DNA‐programmed spatial screening to characterize two functionally distinct receptor systems: 1) structurally well‐defined Ricinus communis agglutinin (RCA₁₂₀), and 2) rather ill‐defined assemblies of L‐selectin on nanoparticles and leukocytes. A robust synthesis route that allowed the attachment both of carbohydrate ligands—such as N‐acetyllactosamine (LacNAc), sialyl‐Lewis‐X (sLe^X), and mannose—and of a DNA aptamer to PNAs was developed. A systematically assembled series of different PNA–DNA complexes served as multivalent scaffolds to control the spatial alignments of appended lectin ligands. The spatial screening of the binding sites of RCA₁₂₀ was in agreement with the crystal structure analysis. The study revealed that two appropriately presented LacNAc ligands suffice to provide unprecedented RCA₁₂₀ affinity (K_D=4 μM ). In addition, a potential secondary binding site was identified. Less dramatic binding enhancements were obtained when the more flexible L‐selectin assemblies were probed. This study involved the bivalent display both of the weak‐affinity sLe^X ligand and of a high‐affinity DNA aptamer. Bivalent presentation led to rather modest (sixfold or less) enhancements of binding when the self‐assemblies were targeted against L‐selectin on gold nanoparticles. Spatial screening of L‐selectin on the surfaces of leukocytes showed higher affinity enhancements (25‐fold). This and the distance–activity relationships indicated that leukocytes permit dense clustering of L‐selectin.     

Exploring the Potent Inhibition of CTP Synthase by Gemcitabine‐5′‐Triphosphate

CTP synthase (CTPS) catalyzes the conversion of UTP to CTP and is a target for the development of antiviral, anticancer, antiprotozoal, and immunosuppressive agents. Exposure of cell lines to the antineoplastic cytidine analogue gemcitabine causes depletion of intracellular CTP levels, but the direct inhibition of CTPS by its metabolite gemcitabine‐5′‐triphosphate (dF‐dCTP) has not been demonstrated. We show that dF‐dCTP is a potent competitive inhibitor of Escherichia coli CTPS with respect to UTP [K_i=(3.0±0.1) μm ], and that its binding affinity exceeds that of CTP ≈75‐fold. Site‐directed mutagenesis studies indicated that Glu149 is an important binding determinant for both CTP and dF‐dCTP. Comparison of the binding affinities of the 5′‐triphosphates of 2′‐fluoro‐2′‐deoxycytidine and 2′‐fluoro‐2′‐deoxyarabinocytidine revealed that the 2′‐F‐arabino group contributes markedly to the strong binding of dF‐dCTP. Geminal 2′‐F substitution on UTP (dF‐dUTP) did not result in an increase in binding affinity with CTPS. Remarkably, CTPS catalyzed the conversion of dF‐dUTP into dF‐dCTP, thus suggesting that dF‐dCTP might be regenerated in vivo from its catabolite dF‐dUTP.     

Preparation and utilization of microporous molecularly imprinted polymer for sustained release of tetracycline

A polyacrylate tetracycline (TC) selective microporous molecularly imprinted polymer was prepared in three different porogenic solvents (chloroform, acetonitrile, and methanol) via precipitation polymerization, using methacrylic acid monomer, ethylene glycol dimethacrylate crosslinker, and TC as template. In all three solvents this method produced microporous particles in the scale range (200–400 nm), simply, quickly, cleanly, and in good yield. The effect of polarity of porogenic solvents on binding capacity was investigated. The imprinted polymer prepared in chloroform gave much higher binding capacity (K_D = 198.6) for TC than the polymers prepared in acetonitrile (K_D = 133.2) or methanol (K_D = 104.7). The selectivity of imprinted polymers was evaluated by rebinding other structurally similar compounds. The results clearly indicated that the imprinted acrylate polymer exhibits an excellent selectivity toward TC, and has better ability to control the release of TC than the non‐imprinted polymer.© 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

De Novo Design,Synthesis and Evaluation of Benzylpiperazine Derivatives as Highly Selective Binders of Mcl‐1

Considerable efforts have been made to the development of small‐molecule inhibitors of antiapoptotic B‐cell lymphoma 2 (Bcl‐2) family proteins (such as Bcl‐2, Bcl‐x_L, and Mcl‐1) as a new class of anticancer therapies. Unlike general inhibitors of the entire family, selective inhibitors of each member protein can hopefully reduce the adverse side effects in chemotherapy treatments of cancers overexpressing different Bcl‐2 family proteins. In this study, we designed four series of benzylpiperazine derivatives as plausible Bcl‐2 inhibitors based on the outcomes of a computational algorithm. A total of 81 compounds were synthesized, and their binding affinities to Bcl‐2, Bcl‐x_L, and Mcl‐1 measured. Encouragingly, 22 compounds exhibited binding affinities in the micromolar range (K_i<20 μM ) to at least one target protein. Moreover, some compounds were observed to be highly selective binders to Mcl‐1 with no detectable binding to Bcl‐2 or Bcl‐x_L, among which the most potent one has a K_i value of 0.18 μM for Mcl‐1. Binding modes of four selected compounds to Mcl‐1 and Bcl‐x_L were derived through molecular docking and molecular dynamics simulations. It seems that the binding affinity and selectivity of these compounds can be reasonably interpreted with these models. Our study demonstrated the possibility for obtaining selective Mcl‐1 inhibitors with relatively simple chemical scaffolds. The active compounds identified by us could be used as lead compounds for developing even more potent selective Mcl‐1 inhibitors with potential pharmaceutical applications.