Molecular Dynamic Simulations of Bromodomain and Extra-Terminal Protein 4 Bonded to Potent Inhibitors

Bromodomain and extra-terminal domain (BET) subfamily is the most studied subfamily of bromodomain-containing proteins (BCPs) family which can modulate acetylation signal transduction and produce diverse physiological functions. Thus, the BET family can be treated as an alternative strategy for targeting androgen-receptor (AR)-driven cancers. In order to explore the effect of inhibitors binding to BRD4 (the most studied member of BET family), four 150 ns molecular dynamic simulations were performed (free BRD4, Cpd4-BRD4, Cpd9-BRD4 and Cpd19-BRD4). Docking studies showed that Cpd9 and Cpd19 were located at the active pocket, as well as Cpd4. Molecular dynamics (MD) simulations indicated that only Cpd19 binding to BRD4 can induce residue Trp81-Ala89 partly become α-helix during MD simulations. MM-GBSA calculations suggested that Cpd19 had the best binding effect with BRD4 followed by Cpd4 and Cpd9. Computational alanine scanning results indicated that mutations in Phe83 made the greatest effects in Cpd9-BRD4 and Cpd19-BRD4 complexes, showing that Phe83 may play crucial roles in Cpd9 and Cpd19 binding to BRD4. Our results can provide some useful clues for further BCPs family search.     

Studies on New Steroidal Saponins from Allii macrostemonis Bulbus and Their Antitumor Activities Design and Synthesis of Novel Bispecific Molecules for InducingBRD4 Protein Degradation

Proteolysis targeting chimeras(PROTACs) are bispecific molecules containing a target protein binder and a ubiquitin ligase binder connected by a linker. Recently, some heterobifunctional small molecule bromodomain-containing protein 4(BRD4) degraders based on the concept of PROTACs were designed to induce the degradation of BRD4 protein. Herein, we synthesized a new class of PROTAC BRD4 degraders. One of the most promising compound 22f exhibited robust potency of BRD4 inhibition with IC₅₀ value of (9.4±0.6) nmol/L. Furthermore, compound 22f potently inhibited cell proliferation in BRD4-sensitive cell lines RS4;11 with IC₅₀ value of (27.6±1.6) nmol/L and capable of inducing degradation of BRD4 protein at 0.5―1.0 μmol/L in the RS4;11 cells. These data establish that compound 22f is a potent and efficacious BRD4 degrader.     

Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis

ABSTRACT

It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were integrated together to uncover binding modes of inhibitors 8P9, 8PU, and 8PX to BRD4(1). The results obtained from binding free energy calculations show that van der Waals interactions act as the main regulator in bindings of inhibitors to BRD4(1). The information stemming from PCA reveals that inhibitor associations extremely affect conformational changes, internal dynamics, and movement patterns of BRD4(1). Residue-based free energy decomposition method was wielded to unveil contributions of independent residues to inhibitor bindings and the data signify that hydrogen bonding interactions and hydrophobic interactions are decisive factors affecting bindings of inhibitors to BRD4(1). Meanwhile, eight residues Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asn140, and Ile146 are recognized as the common hot interaction spots of three inhibitors with BRD4(1). The results from this work are expected to provide a meaningfully theoretical guidance for design and development of effective inhibitors inhibiting of the activity of BRD4.     

Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses

ABSTRACT

Emerging evidences indicate bromodomain-containing proteins 2 and 4 (BRD2 and BRD4) play critical roles in cancers, inflammations, cardiovascular diseases and other pathologies. Multiple short molecular dynamics (MSMD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were applied to investigate the binding selectivity of three inhibitors 87D, 88M and 89G towards BRD2 over BRD4. The root-mean-square fluctuation (RMSF) analysis indicates that the structural flexibility of BRD4 is stronger than that of BRD2. Moreover the calculated distances between the C_α atoms in the centres of the ZA_loop and BC_loop of BRD4 are also bigger than that of BRD2. The rank of binding free energies calculated using MM-GBSA method agrees well with that determined by experimental data. The results show that 87D can bind more favourably to BRD2 than BRD4, while 88M has better selectivity on BRD4 over BRD2. Residue-based free-energy decomposition method was utilized to estimate the inhibitor-residue interaction spectrum and the results not only identify the hot interaction spots of inhibitors with BRD2 and BRD4, but also demonstrate that several common residues, including (W370, W374), (P371, P375), (V376, V380) and (L381, L385) belonging to (BRD2, BRD4), generate significant binding difference of inhibitors to BRD2 and BRD4.     

Discovery of [1,2,4]triazolo[1,5-a]pyrimidine derivatives as new bromodomain-containing protein 4 (BRD4) inhibitors

Targeting bromodomain-containing protein 4(BRD4) has been proved to be an effective strategy for cancer therapy.To date,numerous BRD4 inhibitors and degraders have been identified,some of which have advanced into clinical trials.In this work,a focused library of new [1,2,4]triazolo [1,5-a]pyrimidine derivatives were discovered to be able to inhibit BRD4.WS-722 inactivated BRD4(BD1/BD2),BRD2(BD1/BD2) and BRD3(BD1/BD2) broadly with the IC₅₀ values less than 5 μmol/L.Besides,WS-722 inhibited growth of THP-1 cells with an IC₅₀ value of 3.86 μmol/L.Like(+)-JQ1,WS-722 inhibited BRD4 in a reversible manner and enhanced protein stability.Docking studies showed that WS-722 occupied the central acetyl-lysine(Kac) binding cavity and formed a hydrogen bond with Asn140.In THP-1 cells,WS-722 showed target engagement to BRD4.Cellular effects of WS-722 on THP-1 cells were also examined,showing that WS-722 could block c-MYC expression,induce G0/G1 phase arrest and p21 up-regulation,and promote differentiation of THP-1 cells.BRD4 inhibition by WS-722 resulted in cell apoptosis and upregulated expression of cleaved caspased-3/7 and PARP in THP-1 cell lines.The [1,2,4]triazolo[1,5-a]pyrimidine is a new template for the development of new BRD4 inhibitors.     

Investigating the hydrogen-bond acceptor site of the nicotinic pharmacophore model: a computational and experimental study using epibatidine-related molecular probes

The binding mode of nicotinic agonists has been thoroughly investigated in the last decades. It is now accepted that the charged amino group is bound by a cation-π interaction to a conserved tryptophan residue, and that the aromatic moiety is projected into a hydrophobic pocket deeply located inside the binding cleft. A hydrogen bond donor/acceptor, maybe a water molecule solvating this receptor subsite, contributes to further stabilize the nicotinic ligands. The position of this water molecule has been established by several X-ray structures of the acetylcholine-binding protein. In this study, we computationally analyzed the role of this water molecule as a putative hydrogen bond donor/acceptor moiety in the agonist binding site of the three most relevant heteromeric (α4β2, α3β4) and homomeric (α7) neuronal nicotinic acetylcholine receptor (nAChR) subtypes. Our theoretical investigation made use of epibatidine 1 and deschloroepibatidine 2 as molecular probes, and was then extended to their analogues 3 and 4, which were subsequently synthesized and tested at the three target receptor subtypes. Although the pharmacological data for the new ligands 3 and 4 indicated a reduction of the affinity at the studied nAChRs with respect to reference agonists, a variation of the selectivity profile was clearly evidenced.     

Hydrogen-bonded liquid-crystalline complexes of polyester containing a pyridyl moiety with 4-(alkoxy)benzoic acid

Novel hydrogen-bonded polyester complexes from mesogenic 4-(butyloxy)benzoic acid (2a), 4-(octyloxy)benzoic acid (2b), 4-(dodecyloxy)benzoic acid (2c) and 4-(tetradecyloxy)benzoic acid (2d) as the hydrogen bond donors and a polyester (3) based on 2,6-pyridine dicarboxylic acid as the hydrogen bond acceptor were prepared by the melt method. The association by hydrogen bonding was confirmed by means of FTIR. The components were miscible up to 0.1 mole ratio of 2d and 2c versus the polyester repeat unit. The limiting mole ratio for 2b and 2a to 3 were 0.2 and 0.4, respectively. Phase separation in the supramolecular complexes occurred above these limiting values and a two phase system consisting of a polyester supramolecular complex and 4-(alkyloxy)benzoic acid was formed. This was due to weak hydrogen bonding between the low molecular acid (especially the acid with longer terminal alkoxy group) and pyridyl unit of polyester in comparison with thermodynamically more favorable dimerization of acid molecules. The liquid crystalline behavior of these supramolecular polymeric complexes was confirmed by differential scanning calorimetry (DSC) and polarizing optical microscopy (POM). It was found that 2a exhibits no mesomorphism when mixed with polyester. However, among the other acid derivatives, 2b exhibited stable mesogenic complexes.     

Synthesis,crystal structure and infrared spectroscopy of a novel copper strontium formate: CuSr(HCOO)4(H2O)2

The title compound CuSr(HCOO)₄(H₂O)₂ (1) forms a 3D polymeric structure, which basic structural units are SrO₉ polyhedra in the form of monocapped square antiprisms and distorted CuO₆ octahedra. The former groups organize as strips running parallel to the unique b axis, while interconnected by the latter into a strongly linked 3D covalent network.The infrared spectra of (1) confirm the existence of four nonequivalent formate groups with large deviations from C_2v molecular symmetry. The frequencies of the OD modes (isotopically dilute samples) are assigned on the basis of the respective intermolecular O_w⋯O bond lengths, the metal−water interactions (synergetic effect) and the different hydrogen bond acceptor capability of the oxygen atoms. The hydrogen bond acceptor strengths of the formate oxygen atoms are discussed within the framework of the Brown’s bond–valence theory. Intramolecular OH distances are derived from the novel ν_OD versus r_OH correlation curves [J. Mol. Struct. 351 (1995) 205; J. Mol. Struct. 404 (1997) 63)]. The librations of the water molecules are also discussed.     

Direct functionalization of the cyclometalated 2-(2′-pyridyl)phenyl ligand bound to iridium(III)

Treatment of [Ir(ppy)₂(μ-Cl)]₂ and [Ir(ppy)₂(dtbpy)][OTf] (ppy = 2-(2′-pyridyl)phenyl; dtbpy = 4,4′-di-tert-butyl-2,2′-bipyridine; OTf = triflate) with pyridinium tribromide in the presence of Fe powder led to isolation of [Ir(4-Br-ppy)(μ-Br)]₂ (1) and [Ir(4-Br-ppy)₂(dtbpy)][OTf] (2), respectively. Pd-catalyzed cross-coupling of 2 with RB(OH)₂ afforded [Ir(4-R-ppy)₂(dtbpy)][OTf] (R = 4′-FC₆H₄ (3)), 4′-PhC₆H₄ (4), 2′-thienyl (5), 4′-C₆H₄CH₂OH (6). Treatment of 4 with B₂(pin)₂ (pin = pinacolate) afforded [Ir{4-(pin)B-ppy}₂(dtbpy)][OTf] (7). The alkynyl complexes [Ir(4-PhCC-ppy)₂(dtbpy)][OTf] (8) and [Ir{4-Me₂(OH)CC-ppy}(4-Br-ppy)(dtbpy)][OTf] (9) were prepared by cross-coupling of 2 with PhCCSnMe₃ and Me₂C(OH)CCH, respectively. Ethynylation of [Ir(fppy)₂(dtbpy)][OTf] (fppy = 5-formyl-2-(2′-pyridyl)phenyl) with Ohira’s reagent MeCOC(N₂)P(O)(OEt)₂ afforded [Ir{5-HCC-ppy}₂(dtbpy)][OTf] (10). The solid-state structures of 2, 5, 7, and 10 have been determined.     

UV/Vis Spectroscopic Properties of N -(2′-Hydroxy-4′- N , N -dimethyl-aminobenzylidene)-4-nitroaniline in Various Solvents and Solid Environments

 N-(2′-Hydroxy-4′-N,N-dimethylaminobenzylidene)-4-nitroaniline [HDBN] has been used as a model for investigating intra- and intermolecular D–A (donor–acceptor) interactions in various environments by means of UV/Vis spectroscopy. UV/Vis spectra of HDBN have been measured in various solvents, ethanolic solutions of different pH, adsorbed on silica, and in the solid state. A bathochromic shift of ν_max is observed with increasing the dipolarity/polarizability and HBD (hydrogen bond donor) capacity of the solvent, which is described by means of a multiple LSE (linear solvation energy) relationship in terms of the empirical Kamlet-Taft solvent polarity parameters. The adsorption of HDBN on Aerosil^? 300-silica particles in non-HBA (hydrogen bond acceptor) solvents is explained in the same sense. Mobile protons and sol–gel entrapping cause a hypsochromic shift due to protonation of the lone electron pair of the 4′-N,N-dimethylamino group. Hydroxide ions attack the 2′-hydroxy group which causes a bathochromic shift. A strong intramolecular hydrogen bond between the 2′-hydroxyl hydrogen and the imine nitrogen atom is present in the solid-state structure causing an unprecedented bathochromic shift.     

Molecular dynamics and pharmacophore modelling studies of different subtype (ALK and EGFR (T790M)) inhibitors in NSCLC

Extensively validated 3D pharmacophore models for ALK (anaplastic lymphoma kinase) and EGFR (T790M) (epithelial growth factor receptor with acquired secondary mutation) were developed. The pharmacophore model for ALK (r² = 0.96, q² = 0.692) suggested that two hydrogen bond acceptors and three hydrophobic groups arranged in 3-D space are essential for the binding affinity of ALK inhibitors. Similarly, the pharmacophore model for EGFR (T790M) (r² = 0.92, q² = 0.72) suggested that the presence of a hydrogen bond acceptor, two hydrogen bond donors and a hydrophobic group plays vital role in binding of an inhibitor of EGFR (T790M). These pharmacophore models allowed searches for novel ALK and EGFR (T790M) dual inhibitors from multiconformer 3D databases (Asinex, Chembridge and Maybridge). Finally, the eight best hits were selected for molecular dynamics simulation, to study the stability of their complexes with both proteins and final binding orientations of these molecules. After molecular dynamics simulations, one hit has been predicted to possess good binding affinity for both ALK and EGFR (T790M), which can be further investigated for its experimental in-vitro/in-vivo activities.     

Structural and spectral studies of 3-(2-hydroxyphenylimino)-1-phenylbutan-1-one and its diorganotin(IV) complexes

Two diorganotin(IV) complexes of the general formula R₂Sn[Ph(O)CCH-C(Me)N-C₆H₄(O)] (R = Ph, 1a; R = Me, 1b) have been synthesized from the corresponding diorganotin(IV) dichlorides and the ligand, 3-(2-hydroxyphenylimino)-1-phenylbutan-1-one (1) in methanol at room temperature in presence of triethylamine. Both compounds have been characterized by elemental analyses, IR and ¹H, ¹³C, ¹⁵N, ¹¹⁹Sn NMR spectra. The structures of the free ligand and the complexes have been confirmed by single crystal X-ray diffraction. There are three independent molecules in the crystal structure of the ligand 1 and in all three the O-bound proton is transferred to the imine nitrogen and makes an intramolecular N-H?O hydrogen bond with the carbonyl oxygen. In turn this makes an intermolecular hydrogen bond with the phenolic H atom. The crystal structure of 1 is trigonal and a new polymorph; triclinic and monoclinic forms have already been published. In 1a, the central tin atom adopts distorted trigonal-bipyramidal coordination geometry whereas in dimeric 1b it is distorted octahedral when including the intermolecular Sn-O(phenolic) bond [2.7998(20) Å]. The δ (¹¹⁹Sn) values for the complexes 1a and 1b are −306.6 and −127.9 ppm, respectively, thus indicating penta-coordinated Sn centres in solution.     

聚乙烯基吡啶共聚物与取代苯基偶氮苯酚复合物的制备及其液晶性质

通过分子间弱相互作用力组装形成的液晶高分子与一般侧链液晶高分子相比，其介晶基元与聚合物主链搭配选择范围宽，且易于组装制备．因此，将氢键［１，２］，离子键［３，４］等引入液晶高分子制备领域，越来越引起人们的兴趣．目前以吡啶 羧基氢键组装成的侧链液晶高分...     

Nickel(II) and zinc(II) complexes of N-substituted di(2-picolyl)amine derivatives: Synthetic and structural studies

The interaction of di(2-picolyl)amine (1) and its secondary N-substituted derivatives, N-(4-pyridylmethyl)-di(2-picolyl)amine (2), N-(4-carboxymethyl-benzyl)-di(2-picolyl)amine (3), N-(4-carboxybenzyl)-di(2-picolyl)amine (4), N-(1-naphthylmethyl)-di(2-picolyl)amine (5), N-(9-anthracenylmethyl)-di(2-picolyl)amine (6), 1,4-bis[di(2-picolyl)aminomethyl]benzene (7), 1,3-bis[di(2-picolyl)aminomethyl]benzene (8) and 2,4,6-tris[di(2-picolyl)amino]triazine (9) with Ni(II) and/or Zn(II) nitrate has resulted in the isolation of [Ni(1)(NO₃)₂], [Ni(2)(NO₃)₂], [Ni(3)(NO₃)₂], [Ni(4)(NO₃)₂]·CH₃CN, [Ni(5)(NO₃)₂], [Ni(6)(NO₃)₂], [Ni₂(7)(NO₃)₄], [Ni₂(8)(NO₃)₄], [Ni₃(9)(NO₃)₆]·3H₂O, [Zn(3)(NO₃)₂]·0.5CH₃OH, [Zn(5)(NO₃)₂], [Zn(6)(NO₃)₂], [Zn(8)(NO₃)₂] and [Zn₂(9)(NO₃)₄]·0.5H₂O. X-ray structures of [Ni(4)(NO₃)₂]·CH₃CN, [Ni(6)(NO₃)₂] and [Zn(5)(NO₃)₂] have been obtained. Both nickel complexes exhibit related distorted octahedral coordination geometries in which 4 and 6 are tridentate and bound meridionally via their respective N₃-donor sets, with the remaining coordination positions in each complex occupied by a monodentate and a bidentate nitrato ligand. For [Ni(4)(NO₃)₂]·CH₃CN, intramolecular hydrogen bond interactions are present between the carboxylic OH group on one complex and the oxygen of a monodentate nitrate on an adjacent complex such that the complexes are linked in chains which are in turn crosslinked by intermolecular offset π-π stacking between pyridyl rings in adjacent chains. In the case of [Ni(6)(NO₃)₂], two weak CH?O hydrogen bonds are present between the axial methylene hydrogen atoms on one complex and the oxygen of a monodentate nitrate ligand on a second unit such that four hydrogen bonds link pairs of complexes; in addition, an extensive series of π-π stacking interactions link individual complex units throughout the crystal lattice. The X-ray structure of [Zn(5)(NO₃)₂] shows that the metal centre once again has a distorted six-coordinated geometry, with the N₃-donor set of N-(1-naphthylmethyl)-di(2-picolyl)amine (5) coordinating in a meridional fashion and the remaining coordination positions occupied by a monodentate and a bidentate nitrato ligand. The crystal lattice is stabilized by weak intermolecular interactions between oxygens on the bound nitrato ligands and aromatic CH hydrogens on adjacent complexes; intermolecular π-π stacking between aromatic rings is also present.     

Temperature-dependent polymorphism of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide: experimental and theoretical studies on intermolecular interactions in the crystal state

X-ray analysis of N-(4-fluorophenyl)-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide reveals the temperature-dependent polymorphism associated with the crystallographic symmetry conversion. The observed crystal structure transformation corresponds to a symmetry reduction from I4₁ /a (I) to P4₃ (II) space groups. The phase transition mainly concerns the subtle but clearly noticeable reorganization of molecules in the crystal space, with the structure of individual molecules left almost unchanged. The Hirshfeld surface analysis shows that various intermolecular contacts play an important role in the crystal packing, revealing graphically the differences in spatial arrangements of the molecules in both polymorphs. The N-oxide oxygen atom acts as a formally negatively charged hydrogen bonding acceptor in intramolecular hydrogen bond of N–H…O^? type. The combined crystallographic and theoretical DFT methods demonstrate that the observed intramolecular N-oxide N–H…O hydrogen bond should be classified as a very strong charge-assisted and closed-shell non-covalent interaction.     

Synthesis, structure and magnetic properties of cobalt(II) and copper(II) coordination polymers assembled by phthalate and 4-methylimidazole

New coordination polymers [M(Pht)(4-MeIm)₂(H₂O)]_n (M=Co (1), Cu (2); Pht²⁻=dianion of o-phthalic acid; 4-MeIm=4-methylimidazole) have been synthesized and characterized by IR spectroscopy, X-ray crystallography, thermogravimetric analysis and magnetic measurements. The crystal structures of 1 and 2 are isostructural and consist of [M(4-MeIm)₂(H₂O)] building units linked in infinite 1D helical chains by 1,6-bridging phthalate ions which also act as chelating ligands through two O atoms from one carboxylate group in the case of 1. In complex 1, each Co(II) atom adopts a distorted octahedral N₂O₄ geometry being coordinated by two N atoms from two 4-MeIm, three O atoms of two phthalate residues and one O atom of a water molecule, whereas the square-pyramidal N₂O₃ coordination of the Cu(II) atom in 2 includes two N atoms of N-containing ligands, two O atoms of two carboxylate groups from different Pht, and a water molecule. An additional strong O-H?O hydrogen bond between a carboxylate group of the phthalate ligand and a coordinated water molecule join the 1D helical chains to form a 2D network in both compounds. The thermal dependences of the magnetic susceptibilities of the polymeric helical Co(II) chain compound 1 were simulated within the temperature range 20-300 K as a single ion case, whereas for the Cu(II) compound 2, the simulations between 25 and 300 K, were made for a linear chain using the Bonner-Fisher approximation. Modelling the experimental data of compound 1 with MAGPACK resulted in: g=2.6, |D|=62 cm⁻¹. Calculations using the Bonner-Fisher approximation gave the following result for compound 2: g=2.18, J=-0.4 cm⁻¹.     

New rhodium(I) supramolecular structures containing pyridyl and bipyridyl ligands

The use of dimeric [RhCl(CO)₂]₂ as acceptor unit in the construction of mono-, bi- and three-dimensional metallosupramolecular structures is reported.The reaction of the dimer with the alkynylgold complex [Au(CCC₅H₄N)(CNC₆H₄O(O)CC₆H₄OC₁₀H₂₁)] resulted in the mononuclear rhodium complex 1, through an unexpected transfer of the isonitrile ligand from the gold to the rhodium centres.The reaction of the linear unit [RhCl(CO)₂]₂(μ-4,4′-bipy) (3) with the diphosphine 1,4-bis(diphenylphosphino)butane (dppb) yielded the simultaneous formation of both metallomacrocycles [RhCl(CO)(dppb)]₂ (4) and {[RhCl(CO)]₂(μ-4,4′-bipy)}₂(μ-dppb)₂ (5). The use of a diphosphine with smaller bite angle, 1,1′-bis-(diphenylphosphino)methane, (dppm) formed the three-dimensional {[RhCl(CO)]₂(μ-4,4′-bipy)}₂(μ-dppm)₄ complex (6) that incorporates four diphosphine units connecting two [RhCl(CO)₂]₂(μ-bipy) linear edges. PM3 semi-empirical method has been used to calculate the optimised geometry of compound 6.     

A possible potential COVID-19 drug candidate: Diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate: Docking of disordered independent molecules of a novel crystal structure,HSA/DFT/XRD and cytotoxicity

This study reports the synthesis, characterization and importance of a novel diethyl 2-(2-(2-(3-methyl-2-oxoquinoxalin-1(2H)-yl)acetyl)hydrazono)malonate (MQOAHM). Two independent molecular structures of the disordered MQOAHM have been established by XRD?single?crystal analysis in a ratio of 0.596(3)/0.404(3), MQOAHM (a) and MQOAHM (b), respectively. MQOAHM was characterized by means of various spectroscopic tools ESI-MS, IR, ¹H &¹³C NMR analyses. Density Functional Theory (DFT) method, B3LYP, 6–311++G(d,p) basis set was used to optimize MQOAHM molecule. The obtained theoretical structure and experimental structure were superimposed on each other, and the correlation between them was calculated. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) were created, and the energy gap between these orbitals was calculated. For analyzing intermolecular interactions, Molecular Electrostatic Potential (MEP) and Hirshfeld Surface Analysis were studied. For a fair comparative study, the two forms of the title compound were docked together with 18 approved drugs and N3 under precisely the same conditions. The disordered molecule structure's binding scores against 7BQY were ?7.0 and ?6.9 kcal/mol^?1 for MQOAHM (a) and MQOAHM (b), respectively. Both the forms show almost identical superimposed structures and scores indicating that the disorder of the molecule, in this study, has no obvious effect. The high binding score of the molecule was attributed to the multi-hydrogen bond and hydrophobic interactions between the ligand and the receptor's active amino acid residues. Worth pointing out here that the aim of using the free energy in Silico molecular docking approach is to rank the title molecule compared to the wide range of approved drugs and a well-established ligand N3. The binding scores of all the molecules used in this study are ranged from ?9.9 to ?4.5 kcal/mol^?1. These results and the supporting statistical analyses suggest that this malonate-based ligand merits further research in the context of possible therapeutic agents for COVID-19. Cheap computational techniques, PASS, Way2drug and ADMET, online software tools, were used in this study to uncover the title compound's potential biological activities and cytotoxicity.