In silico exploration and in vitro validation of the filarial thioredoxin reductase inhibitory activity of Scytonemin and its derivatives.

Lymphatic filariasis (LF) caused by the vector borne parasitic nematode Wuchereria bancrofti is of major concern of the World Health Organization (WHO). Lack of potential drug candidates worsens the situation. Presently available drugs are promising in killing the microfilaria (mf) but are not effective as adulticidal therapeutics. Previous studies have revealed that routine administration of the available drugs (albendazole, ivermectin and albendazole) sometime is associated with severe adverse effects (SAEs) in co-infection state. Therefore, potential and safe therapeutics are still required. Earlier studies on filarial thioredoxin reductase (TrxR) have shown that successful inhibition of it can lead to apoptotic death of the parasites. TrxR in filarial parasites plays a significant role in disease progression and pathogenesis, hence efficient non-reversible inhibition of TrxR can be a good strategy to treat LF. In this research, inhibitory potential of Scytonemin, a cyanobacterial metabolite on filarial TrxR was evaluated via different in silico methods and validated through in vitro experiments. Parasite death upon exposure to Scytonemin can be correlated with the TrxR inhibiting capacity of the compound. Therefore, this cyanobacterial-derived compound may possibly be used further as novel and safe therapeutic candidate against filarial infection.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.

Insights from molecular dynamics simulations of TRPV1 channel modulators in pain.

TRPV1 is a nonselective cation channel vital for detecting noxious stimuli (heat, acid, capsaicin). Its role in pain makes it a potential drug target for chronic pain management, migraines, and related disorders. This review updates molecular dynamics (MD) simulation studies on the TRPV1 channel, focusing on its gating mechanism, ligand-binding sites, and implications for drug design. The article also explores challenges in developing modulators, SAR optimization, and clinical trial studies. Efforts have been undertaken to concisely present MD simulation findings, with a focus on their relevance to drug discovery.

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.

Discovery of 2,3-dihydro-1H-pyrrolo[3,4-b]quinolin-1-one derivatives as possible antileishmanial agents.

A series of uniquely functionalized 2,3,-dihydro-1H-pyyrolo[3,4-b]quinolin-1-one derivatives were synthesized in one to two steps by utilizing a post-Ugi modification strategy and were evaluated for antileishmanial efficacy against visceral leishmaniasis (VL). Among the library compounds, compound 5m exhibited potential in vitro antileishmanial activity (CC50 = 65.11 µM, SI = 7.79, anti-amastigote IC50 = 8.36 µM). In vivo antileishmanial evaluation of 5m demonstrated 56.2% inhibition in liver and 61.1% inhibition in spleen parasite burden in infected Balb/c mice (12.5 mg kg-1, i.p.). In vitro pharmacokinetic study ascertained the stability of 5m in both simulated gastric fluid and simulated intestinal fluid. All the active compounds passed the PAINS filter and showed no toxicity in in silico predictions.

C-Mannosyltransferase Is Essential for Malaria Transmission in Plasmodium berghei.

C-Mannosylation of the thrombospondin type I repeat (TSR) domains is one of the most important factors involved in their function. It occurs on the first tryptophan of the WXXWXXC conserved motif where the tryptophan is usually surrounded by arginine or lysine forming the ligand-binding stretch of this sticky domain. It is found in its canonical or modified forms in many Plasmodium proteins. TSR containing proteins such as thrombospondin-like anonymous protein (TRAP), circumsporozoite protein (CSP), CSP and TRAP related protein (CTRP), and secreted protein with altered thrombospondin repeat (SPATR) have all been shown to be important for various parasite processes and life cycle stages. Here, we show that C-mannosylation catalyzing enzyme C-mannosyltransferase (CmanT) plays an essential role in malaria transmission in Plasmodium berghei. Disruption of the CmanT does not affect asexual blood stage propagation or gametocyte development but abolishes the formation of oocysts in mosquitoes. CmanT knockout (CmanT-) parasites showed normal ookinete formation; however, these ookinetes failed in their ability to glide. CmanT- was complemented by reintroducing the gene, restoring mosquito transmission to wild-type level. We also investigated the effect of C-mannosylation on the folding and heparin-binding capacity of the Plasmodium falciparum TRAP TSR domain in silico, which suggested that this phenotype should be due to its involvement in the global stabilization of TSR residue side chain interactions.

Copper-Catalyzed Oxidative [3 + 2]-Annulation of Quinoxalin-2(1H)-one with Oxime Esters toward Functionalized Pyrazolo[1,5-a]quinoxalin-4(5H)-ones as Opioid Receptor Modulators.

Pyrazolo[1,5-a]quinoxalin-4(5H)-one derivatives as novel opioid receptor modulators have been synthesized via copper-catalyzed oxidative [3 + 2]-annulation of quinoxalin-2(1H)-one and oxime-O-acetates. This hydrazine-free C-C and N-N bond formation strategy starts with the generation of C2N1 synthon using oxime acetate, which reacts in a [3 + 2] manner with quinoxalin-2(1H)-one, followed by oxidative aromatization. The synthesized compounds were tested against opioid receptors, of which eight compounds exhibited an antagonistic effect with EC50 < 5 µM at various opioid receptors. Molecular docking studies were performed to identify the binding of active pyrazolo[1,5-a]quinoxalin-4(5H)-one ligands with hKOR protein. Docking results indicated that compounds 3d and 3g participate in hydrogen bonding with the hydroxyl group of T111 of the active site pocket residue.

Instigating the In Vitro Anticancer Activity of New Pyridine-Thiazole-Based Co(III), Mn(II), and Ni(II) Complexes: Synthesis, Structure, DFT, Docking, and MD Simulation Studies.

The perchlorate salt of (4-(4-methoxy phenyl)-2-(2-(1-pyridine-2-yl)ethylidene)hydrazinyl)thiazole (PytH·ClO4) and its metal perchlorate derivatives, namely, [Co(Pyt)2]ClO4 (1), [Mn(PytH)2](ClO4)2 (2), and [Ni(PytH)2](ClO4)2 (3), have been synthesized and characterized through single X-ray crystallography and spectroscopic methods. The ligand crystallizes in a space group P21/n in a nearly planar structure. The overall geometry of the complex salts is described as a distorted octahedron with a MN6 chromophore. The ligand (PytH·ClO4) behaves as a neutral N,N,N-tridentate donor toward the "soft" Mn(II) and Ni(II) centers, whereas the deprotonated ligand stabilizes the "hard" Co(III) center. The DNA binding constant (Kb) values of PytH·ClO4, 1, 2, and 3 are determined using the UV-vis spectroscopic method, and the Kb values are 9.29 × 105, 7.11 × 105, 8.71 × 105, and 7.82 × 105 mol-1, respectively, indicating the intercalative mode of interactions with CT-DNA. All the derivatives show effective antiproliferative activity against U-937 human monocytic tumor cells with IC50 values 4.374 ± 0.02, 5.583 ± 0.12, 0.3976 ± 0.05, and 11.63 ± 0.01 µM for PytH·ClO4, 1, 2, and 3, respectively. The best apoptosis mode of cell death is shown by 2 followed by PytH·ClO4 and 1 at an equivalent concentration of IC50 values. The combined molecular docking and dynamics simulation study evaluates the binding energies of anticancer agents, providing groove binding property with DNA. The 20 ns molecular dynamics simulation study reveals the maximum DNA binding stability of 2 corroborating the experimental results. The new class of metal derivatives of pyridine-thiazole can be used for advanced cancer therapeutics.

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 ΔGbind 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.

Investigation of HDAC8-ligands' intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents.

Histone deacetylases are zinc-dependent isoform enzymes and play important role in cellular homeostasis. Among these, HDAC8 is a potential anticancer drug target. To design new inhibitors using protein-ligand energy profiles, an all atom molecular dynamics (MD) simulations were carried out on nine HDAC8-ligand co-crystals (PDBs: 1T64, 1T69, 1T67, 3F07, 1W22, 1VKG, 5FCW, 3SFF and 3SFH). TSN, SHH, B3N, AGE, NHB, CRI, 5YA, 0DI and 1DI are ligands of PDBs, respectively. For these HDAC8-ligands, relative Gibbs binding free energy (ΔGbind) from MM/PBSA method and non-bonding energies (NBE) are in agreement with each other (r2=0.678). Therefore, the NBEs are used to analyze ligands' sub-structures, namely zinc-binding, linker and CAP groups. For linker/CAP regions, this identified carbonyl, amide, and sulfonamide moieties as desirable and alkyl/aryl moieties as electrostatically unfavourable. Using this information, systematically new compounds were designed and subjected to MD simulations. This resulted in seven compounds (NC-I to NC-VII) with encouraging energy profiles (NBE: -76.25 to -127.09 kcal/mol; ΔGbind: -17.21 to -57.42 kcal/mol) in comparison to that of the HDAC8 ligands (NBE: -46.25 to -106.29 kcal/mol; ΔGbind: -14.74 to -49.52 kcal/mol). From these, NC-VI showed best energy profile (NBE = -126.15 kcal/mol; ΔGbind = -57.42 kcal/mol) suggesting its binding affinity and thermodynamic stability. In addition to this, NC-II and NC-III have shown promising NBE and ΔGbind profiles. These may serve as lead molecules for exploration against HDAC8 in cancer therapy. This has provided a basis for designing new compounds with improved NBE and ΔGbind profiles by modifying the unfavourable or not so favourable regions of ligands. [Formula: see text] Communicated by Ramaswamy H. Sarma.

Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds.

The X-ray crystal structures of HDAC8 complexed with largazole thiol (LAR, PubChem CID: 56663191) and its synthetic variants (Ligand ID in PDB, PubChem CID: L6G, 91667418; L7G, 91667421; L8G, 91667420) (PDB codes: 3RQD, 4RN0, 4RN2 and 4RN1) were analyzed using molecular dynamics simulations to comprehend protein-ligand nonbonding energies (NBEs). The NBEs of ligands' substructures vis-à-vis active site indicated that pyridyl fragment (F2B4) in L7G and L8G, and amide fragment (F2B5) in LAR and L6G are in high energy states. Based on ligands' substructures and active site residues properties new compounds were designed by introducing phenolic and amidine moieties, respectively, for F2B4 and F2B5. This improved NBEs of new compounds (NC2, -60.93 kcal/mol; NC3, -42.42 kcal/mol). Also, Zn2+ group (substructure F1) of largazoles was modified with that of SAHA and Trapoxin A. Here, the results indicated in favor of Zn2+ group of Trapoxin A. New compound NC6 incorporating aforesaid modifications i.e. phenolic moiety for F2B4, amidine moiety for F2B5 and Zn2+ group of Trapoxin A in F1, offered best interactions with HDAC8 (-89.75 kcal/mol). Thus, the study revealed new depsipeptides as potential HDAC8 inhibitors. AbbreviationsCAScomposite active siteCHARMMchemistry at Harvard Macromolecular MechanicsCUDAcompute unified device architectureHAThistone acetyletransferaseHDAChistone deacetylaseLARlargazole thiol (or) (2R,5R,8R,11R)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-10-oxa-3,17-dithia-7,14,19,20-tetraazatricyclo[14.2.1.1 ∼ 2,5∼]icosa-1(18),16(19)-diene-6,9,13-trioneL6G(5R, 8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3,17-dithia-7,10,14,19,20-pentaazatricyclo[14.2.1.1 ∼ 2,5∼]icosa-1(18),2(20),16(19)-triene-6,9,13-trione)L7G(5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,17,21-pentaazatricyclo[14.3.1.1 ∼ 2,5∼]henicosa-1(20),2 (21),16,18-tetraene-6,9,13-trioneL8G(5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,20,21-pentaazatricyclo[14.3.1.1 ∼ 2,5∼]henicosa-1(20),2(21),16,18-tetraene-6,9,13-trioneMDmolecular dynamicsMOEmolecular operating environmentNAMDnanoscale molecular dynamicsNBEnonbonding energyNBEEelectrostatic nonbonding energyNBEVVan der Waals nonbonding energyNBEFnonbonding energy of fragmentNBEFEelectrostatic nonbonding energy of fragmentNBEFVVan der Waals nonbonding energy of fragmentNCnew compound; Rg: radius of gyration;RMSDroot mean square deviationRMSFroot mean square fluctuationVMDvisual molecular dynamics.Communicated by Ramaswamy H. Sarma.

In silico study and validation of phosphotransacetylase (PTA) as a putative drug target for Staphylococcus aureus by homology-based modelling and virtual screening.

Staphylococcus aureus, a Gram-positive bacterium, can cause a range of illnesses from minor skin infections to life-threatening diseases, such as bacteraemia, endocarditis, meningitis, osteomyelitis, pneumonia, toxic shock syndrome and sepsis. Due to the emergence of antibiotic resistance strains, there is a need to develop of new class of antibiotics or drug for this pathogen. The phosphotransacetylase enzyme plays an important role in the acetate metabolism and found to be essential for the survival of the S. aureus. This enzyme was evaluated as a putative drug target for S. aureus by in silico analysis. The 3D structure of the phosphotransacetylase from S. aureus was modelled, using the 1TD9 chain 'A' from Bacillus subtilis as a template at the resolution of 2.75 Å. The generated model has been validated by PROCHECK, WHAT IF and SuperPose. The docking was performed by the Molegro virtual docker using the ZINC database generated ligand library. The ligand library was generated within the limitation of the Lipinski rule of five. Based on the dock-score, five molecules have been subjected to ADME/TOX analysis and subjected for pharmacophore model generation. The zinc IDs of the potential inhibitors are ZINC08442078, ZINC8442200, ZINC 8442087 and ZINC 8442184 and found to be pharmacologically active antagonist of phosphotransacetylase. The molecules were evaluated as no-carcinogenic and persistent molecule by START programme.