Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0.

The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.

ChatGPT in the Material Design: Selected Case Studies to Assess the Potential of ChatGPT.

The pursuit of designing smart and functional materials is of paramount importance across various domains, such as material science, engineering, chemical technology, electronics, biomedicine, energy, and numerous others. Consequently, researchers are actively involved in the development of innovative models and strategies for material design. Recent advancements in analytical tools, experimentation, and computer technology additionally enhance the material design possibilities. Notably, data-driven techniques like artificial intelligence and machine learning have achieved substantial progress in exploring various applications within material science. One such approach, ChatGPT, a large language model, holds transformative potential for addressing complex queries. In this article, we explore ChatGPT's understanding of material science by assigning some simple tasks across various subareas of computational material science. The findings indicate that while ChatGPT may make some minor errors in accomplishing general tasks, it demonstrates the capability to learn and adapt through human interactions. However, issues like output consistency, probable hidden errors, and ethical consequences should be addressed.

Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study.

Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.

Controlled Ni doping on a g-C3N4/CuWO4 photocatalyst for improved hydrogen evolution.

The development of a low-cost, environment-friendly and suitable semiconductor-based heterogeneous photocatalyst poses a great challenge towards extremely competent and substantial hydrogen evolution. A series of environment-friendly and proficient S-scheme Ni-doped CuWO4 nanocrystals supported on g-C3N4 nanocomposites (Ni-CuWO4/g-C3N4) were constructed to ameliorate the photocatalytic efficacy of pure g-C3N4 and Ni-CuWO4 and their activity in H2 generation through photocatalytic water splitting was evaluated. The Ni-CuWO4 nanoparticles were synthesized through doping of Ni2+ on wolframite CuWO4 crystals via the chemical precipitation method. An elevated hydrogen generation rate of 1980 µmol h-1 g-1 was accomplished over the 0.2Ni-CuWO4/g-C3N4 (0.2NCWCN) nanocomposite with an apparent quantum yield (AQY) of 6.49% upon visible light illumination (λ ≥ 420 nm), which is evidently 7.1 and 17.2 fold higher than those produced from pristine g-C3N4 and Ni-CuWO4. The substantial enhancement in the photocatalytic behaviour is primarily because of the large surface area, limited band gap energy of the semiconductor composite and magnified light harvesting capability towards visible light through the inclusion of g-C3N4, thus diminishing the reassembly rate of photoinduced excitons. Further, density functional theory (DFT) calculations were performed to investigate the structural, electronic and optical properties of the composite. Theoretical results confirmed that the Ni-CuWO4/g-C3N4 composite is a potential candidate for visible-light-driven photocatalysts and corroborated with the experimental findings. This research provides a meaningful and appealing perspective on developing cost-effective and very proficient two-dimensional (2D) g-C3N4-based materials for photocatalytic H2 production to accelerate the separation and transmission process of radiative charge carriers.

Towards systematic exploration of chemical space: building the fragment library module in molecular property diagnostic suite.

A fragment-based drug discovery (FBDD) approach has traditionally been of utmost significance in drug design studies. It allows the exploration of large chemical space to find novel scaffolds and chemotypes which can be improved into selective inhibitors with good affinity. In the current work, several public domain chemical libraries (ChEMBL, DrugCentral, PDB ligands, COCONUT, and SAVI) comprising bioactive and virtual molecules were retrieved to develop a fragment library. A systematic fragmentation method that breaks a given molecule into rings, linkers, and substituents was used to cleave the molecules and the fragments were analyzed. Further, only the ring framework was taken into the consideration to develop a fragment library that consists of a total number of 107,614 unique fragments. This set represents a rich diverse structure framework that covers a wide variety of yet-to-be-explored fragments for a wide range of small molecule-based applications. This fragment library is an integral part of the molecular property diagnostic suite (MPDS) suite that can be used with other modeling and informatics methods for FBDD approaches. The fragment library module of MPDS can be accessed at http://mpds.neist.res.in:8085 .

Molecular Property Diagnostic Suite Compound Library (MPDS-CL): a structure-based classification of the chemical space.

Molecular Property Diagnostic Suite Compound Library (MPDS-CL) is an open-source Galaxy-based cheminformatics web portal which presents a structure-based classification of the molecules. A structure-based classification of nearly 150 million unique compounds, obtained from 42 publicly available databases and curated for redundancy removal through 97 hierarchically well-defined atom composition-based portions, has been done. These are further subjected to 56-bit fingerprint-based classification algorithm which led to the formation of 56 structurally well-defined classes. The classes thus obtained were further divided into clusters based on their molecular weight. Thus, the entire set of molecules was put into 56 different classes and 625 clusters. This led to the assignment of a unique ID, named as MPDS-AadharID, for each of these 149,169,443 molecules. MPDS-AadharID is akin to the unique number given to citizens in India (similar to SSN in the US and NINO in the UK). The unique features of MPDS-CL are (a) several search options, such as exact structure search, substructure search, property-based search, fingerprint-based search, using SMILES, InChIKey and key-in; (b) automatic generation of information for the processing for MPDS and other galaxy tools; (c) providing the class and cluster of a molecule which makes it easier and fast to search for similar molecules and (d) information related to the presence of the molecules in multiple databases. The MPDS-CL can be accessed at https://mpds.neist.res.in:8086/ .

Drug repositioning for anti-tuberculosis drugs: an in silico polypharmacology approach.

Development of potential antitubercular molecules is a challenging task due to the rapidly emerging drug-resistant strains of Mycobacterium tuberculosis (M.tb). Structure-based approaches hold greater benefit in identifying compounds/drugs with desired polypharmacological profiles. These methods can be employed based on the knowledge of protein binding sites to identify the complementary ligands. In this study, polypharmacology guided computational drug repurposing approach was applied to identify potential antitubercular drugs. 20 important druggable protein targets in M.tb were considered from the target library of Molecular Property Diagnostic Suite-Tuberculosis (MPDSTB- http://mpds.neist.res.in:8084 ) for virtual screening. FDA approved drugs were collected, preprocessed and docked in the active sites of the 20 M.tb targets. The top 300 drug molecules from each target (20 × 300) were filtered-in and subsequently screened for possible antitubercular and antimycobacterial activity using PASS tool. Using this approach, 34 drugs with predicted antitubercular and anti-mycobacterial activity were identified along with good binding affinity against multiple M.tb targets. Interestingly, 21 out of the 34 identified drugs are antibiotics while 4 drug molecules (nitrofural, stavudine, quinine and quinidine) are non-antibiotics showing promising predicted antitubercular activity. Most of these molecules have the similar privileged antimycobacterial drugs scaffold. Further drug likeness properties were calculated to get deeper insights to M.tb lead molecules. Interestingly, it was also observed that the drugs identified from the study are under different stages of drug discovery (i.e., in vitro, clinical trials) for the effective treatment of various diseases including cancer, degenerative diseases, dengue virus infection, tuberculosis, etc. Krasavin et al., 2017 synthesized nitrofuran analogues with appreciable MICs (22-23 µM) against M.tb H37Rv. These experiments further add to the credibility of the drugs identified in this study (TB).

Protein-protein interaction of RdRp with its co-factor NSP8 and NSP7 to decipher the interface hotspot residues for drug targeting: A comparison between SARS-CoV-2 and SARS-CoV.

In this study we explored the molecular mechanism of RdRp (Non-Structural Protein, NSP12) interaction with its co-factors NSP7 and NSP8 which is the main toolbox for RNA replication and transcription of SARS-CoV-2 and SARS-CoV. The replication complex is a heterotetramer consists of one NSP12, one NSP7 and two NSP8. Extensive molecular dynamics (MD) simulations were applied on both the heterotetramer complexes to generate the conformations and were used to estimate the MMPBSA binding free energy (BFE) and per-residue energy decomposition of NSP12-NSP8 and NSP12-NSP7 and NSP7-NSP8 complexes. The BFE of SARS-CoV-2 heterotetramer complex with its corresponding partner protein was significantly higher as compared to SARS-CoV. Interface hotspot residues were predicted using different methods implemented in KFC (Knowledge-based FADA and Contracts), HotRegion and Robetta web servers. Per-residue energy decomposition analysis showed that the predicted interface hotspot residues contribute more energy towards the formation of complexes and most of the predicted hotspot residues are clustered together. However, there is a slight difference in the residue-wise energy contribution in the interface NSPs on heterotetramer viral replication complex of both coronaviruses. While the overall replication complex of SARS-CoV-2 was found to be slightly flexible as compared to SARS-CoV. This difference in terms of structural flexibility/stability and energetic characteristics of interface residues including hotspots at PPI interface in the viral replication complexes may be the reason of higher rate of RNA replication of SARS-CoV-2 as compared to SARS-CoV. Overall, the interaction profile at PPI interface such as, interface area, hotspot residues, nature of bonds and energies between NSPs, may provide valuable insights in designing of small molecules or peptide/peptidomimetic ligands which can fit into the PPI interface to disrupt the interaction.

Uncovering Structural and Molecular Dynamics of ESAT-6:ß2M Interaction: Asp53 of Human ß2-Microglobulin Is Critical for the ESAT-6:ß2M Complexation.

ESAT-6 is a small secreted protein of Mycobacterium tuberculosis involved in the ESAT-6 secretion system (ESX-1)-mediated virulence and pathogenesis. The protein interacts with ß2M, causing downregulation of MHC class I Ag presentation, which could be one of the mechanisms by which it favors increased survival of the bacilli inside the host. In an earlier study, we have shown that the C-terminal region of ESAT-6 is crucial for its interaction with ß2M. However, the interface of ß2M involved in interaction with ESAT-6 and detailed physicochemical changes associated with ESAT-6:ß2M complexation are not fully defined. In this study, using computational and site-directed mutagenesis studies, we demonstrate the presence of strong noncovalent hydrophobic interactions between ESAT-6 and ß2M in addition to the vital hydrogen bonding between the aspartate residue (Asp53) of ß2M and methionine (Met93) of ESAT-6. Docking-based high-throughput virtual screening followed by 16-point screening on microscale thermophoresis resulted in the identification of two potent inhibitors (SM09 and SM15) that mask the critical Met93 residue of ESAT-6 that is required for ESAT-6:ß2M interaction and could rescue cell surface expression of ß2M and HLA in human macrophages as well as MHC class I Ag presentation suppressed by ESAT-6 in peritoneal macrophages isolated from C57BL/6 mice. Both SM09 and SM15 significantly inhibited intracellular survival of M. tuberculosis in human macrophages. Further, we characterized the physicochemical properties involved in the ESAT-6:ß2M complexation, which may help in understanding host-pathogen interactions.

Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study.

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously. Therefore, in this study, we have attempted to characterize the non-covalent bonds by considering a total of 85 model systems depicting different chemical bonds comprising 43 non-covalent and 42 other bonds such as covalent, ionic, and coordinate bonds. The characterization has been done based on interaction energy, energy decomposition analysis (EDA), the NCI plot, and the analysis of topological properties of electron density. The interaction energy values, energy decomposition analysis, and NCI plot give insights into the full understanding of bond strength and its nature, but they fail to distinctively characterize the interaction as a non-covalent bond. Herein, a special criterion has been developed based on the topological parameters to characterize an interaction as a non-covalent bond. Topological parameters illustrate that the values of both ∇2ρ and H(r) are positive with a value of ρ < 0.03 a.u. and [-G(r)/V(r)] ≥ 1.00 for the non-covalent bonds. The value of ρ increases up to 0.06 a.u. with a positive value of ∇2ρ and a negative value of H(r) if the non-covalent bond is partially covalent in nature. The analysis of G(r) suggests that it dominates the H(r) of non-covalent bonds with greater than 50% contribution, whereas the contribution of G(r) varies between 35 and 50% in the case of bonds which are partially covalent in nature. The criterion based on topological parameters is likely to be very helpful to comprehend and ascertain the non-covalent bonds in the chemical as well as complex biological systems.

Targeting progesterone metabolism in breast cancer with l-proline derived new 14-azasteroids.

Breast cancer cell proliferation is promoted by a variety of mitogenic signals. Classically estrogen is considered as most predominant mitogenic signal in hormone-dependent breast cancer and progesterone is primarily considered to have protective effect. However, it is suggested that some progesterone metabolite may promote breast cancer and progesterone metabolites like 5α-pregnane and 4-pregnene could serve as regulators of estrogen-responsiveness of breast cancer cells. Here, we estimated the potential of alternate targeting of breast cancer via progesterone signalling. l-Proline derived novel 14-azasteroid compounds were screened against MCF-7 and MDA-MB-231 cell lines using MTT assay. In silico studies, cell cycle, Annexin-V-FITC/PI, JC-1 mitochondrial assay, ROS analysis were performed to analyse the impact of hit compound 3b on breast cancer cells. Further, we analysed the impact of hit 3b on the progesterone, its metabolites and enzymes responsible for the conversion of progesterone and its metabolites using ELISA. Data suggests that compound 3b binds and down regulates of 5α-reductase by specifically inhibiting production of progesterone metabolites that are capable of promoting breast cancer proliferation, epithelial mesenchymal transition and migration. This study establishes the proof of concept and generation of new leads for additional targeting of breast cancer.

Buckybowls as adsorbents for CO2, CH4, and C2H2: Binding and structural insights from computational study.

Noncovalent functionalization of buckybowls sumanene (S), corannulene (R), and coronene (C) with greenhouse gases (GGs) such as CO2 , CH4 (M), and C2 H2 (A) has been studied using hybrid density functional theory. The propensity and preferences of these small molecules to interact with the concave and convex surfaces of the buckybowls has been quantitatively estimated. The results indicate that curvature plays a significant role in the adsorption of these small molecules on the π surface and it is observed that buckybowls have higher binding energies (BEs) compared with their planar counterpart coronene. The concave surface of the buckybowl is found to be more feasible for adsorption of small molecules. BEs of small molecules towards π systems is CO2 > A > M and the BEs of π systems toward small molecules is S > R > C. Obviously, the binding preference is dictated by the way in which various noncovalent interactions, such as π···π, lone pair···π, and CH···π manifest themselves on carbaneous surfaces. To delineate the intricate details of the interactions, we have employed Bader's quantum theory of atoms in molecule and localized molecular orbital energy decomposition analysis (LMO-EDA). LMO-EDA, which measures the contribution of various components and traces the physical origin of the interactions, indicates that the complexes are stabilized largely by dispersion interactions.

Dynamics based pharmacophore models for screening potential inhibitors of mycobacterial cyclopropane synthase.

The therapeutic challenges in the treatment of tuberculosis demand multidisciplinary approaches for the identification of potential drug targets as well as fast and accurate techniques to screen huge chemical libraries. Mycobacterial cyclopropane synthase (CmaA1) has been shown to be essential for the survival of the bacteria due to its critical role in the synthesis of mycolic acids. The present study proposes pharmacophore models based on the structure of CmaA1 taking into account its various states in the cyclopropanation process, and their dynamic nature as assessed using molecular dynamics (MD) simulations. The qualities of these pharmacophore models were validated by mapping 23 molecules that have been previously reported to exhibit inhibitory activities on CmaA1. Additionally, 1398 compounds that have been shown to be inactive for tuberculosis were collected from the ChEMBL database and were screened against the models for validation. The models were further validated by comparing the results from pharmacophore mapping with the results obtained from docking these molecules with the respective protein structures. The best models are suggested by validating all the models based on their screening abilities and by comparing with docking results. The models generated from the MD trajectories were found to perform better than the one generated based on the crystal structure demonstrating the importance of incorporating receptor flexibility in drug design.

Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation.

Density functional theory (DFT) calculations have been employed on 165 complexes of onium ions (NH4(+), PH4(+), OH3(+), SH3(+)) and methylated onium ions with CO2, aromatic (C6H6) and heteroaromatic (C5H5X, X = N, P; C4H5Y, Y = N, P; C4H4Z, Z = O, S) systems. The stability of CO2···onium, CO2···π and onium···π complexes was shown to be mediated through various noncovalent interactions such as hydrogen bonding, NH-π, PH-π, OH-π, SH-π, CH-π and π-π. We have discussed 17 complexes wherein the proton transfer occurs between the onium ion and the heteroaromatic system. The binding energy is found to decrease with increasing methyl substitution of the complexes containing onium ions. Binding energy components of all the noncovalent complexes were explored using localized molecular orbital energy decomposition analysis (LMO-EDA). The CO2···π complexes were primarily stabilized by the dispersion term followed by contributions from electrostatic and polarization components. In general, for onium ion complexes with CO2 or π systems, the electrostatic and polarization terms primarily contribute to stabilize the complex. As the number of methyl groups increases on the onium ion, the dispersion term is seen to have a key role in the stabilization of the complex. Quantum theory of atoms in molecules (QTAIM) analysis and charges based on natural population analysis (NPA) in various complexes have also been reported in order to determine the nature of noncovalent interactions in different complexes.

Molecular dynamics investigation of the active site dynamics of mycobacterial cyclopropane synthase during various stages of the cyclopropanation process.

Mycobacterial cyclopropane synthase 1 (CmaA1) is one of the most important drug targets in anti tuberculosis drug discovery as it is responsible for cis-cyclopropanation at the distal position of unsaturated mycolates, which is an essential step for the pathogenicity, persistence and drug resistance. Five representative models of CmaA1 which correspond to different stages in the cyclopropanation process have been studied using molecular dynamics (MD) simulations. The MD simulations and structural analyses provide a detailed account of the structural changes in the active sites of CmaA1. CmaA1 has two distinct binding sites, i.e., cofactor binding site (CBS) and acyl substrate binding site (ASBS). The apo state of CmaA1 corresponds to a closed conformation where the CBS is inaccessible due to the existence of H-bond between Pro202 of loop10 (L10) and Asn11 of N-terminal α1 helix. However, cofactor binding leads to the breaking of this H-bond and thus the H-bond is absent in the holo form. The hydrophobic side chains orient towards the inner side of the ASBS upon cofactor binding to create a hydrophobic environment for the substrate. The cofactor and substrate tend to come close to each other facilitated by opening of L10 to exchange the methyl group from the cofactor to the substrate. The MD study also revealed that the system tends to regain the apo conformation within 40ns after releasing the product.

A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms.

Tryptophan is an essential amino acid, and understanding the conformational preferences of monomer and dimer is a subject of outstanding relevance in biological systems. An exhaustive first principles investigation of tryptophan (W) and its ionized counterparts cations (WC), anions (WA), and zwitterions (WZ) has been carried out. A comprehensive and systematic study of tryptophan dimer (WD) conformations resulted in about 62 distinct minima on the potential energy surface. The hydrogen bonds and a variety of noncovalent interactions such as OH-π, NH-π, CH-π, CH-O, and π-π interactions stabilized different forms of tryptophan and its dimers. Over all in monomeric conformers which have NH-O, hydrogen bonds showed higher stability than other conformers. A cursory analysis reveal that the most stable dimers stabilized by hydrogen bonding interactions while the less stable dimers showed aromatic side chain interactions. Protein Data Bank analysis of tryptophan dimers reveals that at a larger distance greater than 5 Å, T-shaped orientations (CH-π interactions) are more prevalent, while stacked orientations (π-π interactions) are predominant at a smaller distance.

Pyrazole derivatives as potent inhibitors of c-Jun N-terminal kinase: synthesis and SAR studies.

Mitogen activated protein kinases including c-Jun N-terminal kinase play an indispensable role in inflammatory diseases. Investigation of reported JNK-1 inhibitors indicated that diverse heterocyclic compounds bearing an amide group rendered potent JNK-1 inhibitory activity which prompted us to synthesize new JNK-1 inhibitors containing a pyrazole heterocyclic group. A DABCO mediated 1,3-dipolar cycloaddition reaction in neat resulted in pyrazole carboxylic acid which was converted to desired amides. Upon confirmation of the structures, all the compounds were screened for JNK-1 inhibitory activity and in vivo anti-inflammatory activity. Several synthesized analogues have exhibited JNK-1 inhibitory activity less than 10 µM, in particular compounds 9 c, 10 a and 10 d were found to be potent among all the compounds.

Cation-alkane interaction.

Ab initio computations, up to CCSD(T)/CBS on model systems, and MP2/cc-pVTZ and DFT calculations are performed on cation-alkane and cation-alkene complexes, cation = Li(+), Na(+), Be(2+), Mg(2+), Ca(2+), Cu(+) and Zn(2+); alkane = C(n)H2(n+2) (n = 1-10) and C6H12; and alkene = C2H4 and C6H6. Density functional theory-symmetry adapted perturbation theory (DFT-SAPT) calculations reveal that the cation-alkane interactions are predominantly constituted of induction component. The dramatic modulation of the strength of their interaction and the topological features obtained from atoms in molecules (AIM) analysis are consistent with the characteristics of a typical noncovalent interaction. In contrast to many of the conventional noncovalent interactions, cation-alkane interactions are substantially strong and are comparable in strength to the well studied cation-π interactions.

Green synthesis of nanocellulose supported cu-bionanocomposites and their profound applicability in the synthesis of amide derivatives and controlling of food-borne pathogens.

Copper bionanocomposites (CBNCS) were synthesized using Ipomoea carnea- sourced nanocellulose as support via an eco-friendly and cost-effective method. X-ray Diffractometer (XRD) pattern of CBNCS confirmed the octahedral structure of Cu2O, the face-centered cubic (FCC) crystal structure of Cu(0). XRD also revealed the crystal lattice of cellulose II. Surface Electron Microscope (SEM) and Transmission Electron Microscope (TEM) revealed the uniform distribution of copper nanoparticles (Cu NPs) with an average size of 10 nm due to the presence of nanocellulose. X-ray photoelectron spectroscopy (XPS) provided information about the electronic, chemical state and elemental composition of CBNCS. Thermogravimetric Analysis (TGA) showed the thermal stability of CBNCS. CBNCS catalyzed the rearrangement of oximes to primary amides in a very mild condition with a high yield of up to 92 %. CBNCS effectively inhibited the growth of Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with lower minimum inhibitory concentration MIC values. Antioxidant activity and electrical conductivity of CBNCS were also determined.

CRISPR/Cas9-based genome editing and functional analysis of SlHyPRP1 and SlDEA1 genes of Solanum lycopersicum L. in imparting genetic tolerance to multiple stress factors.

CRISPR/Cas is a breakthrough genome editing system because of its precision, target specificity, and efficiency. As a speed breeding system, it is more robust than the conventional breeding and biotechnological approaches for qualitative and quantitative trait improvement. Tomato (Solanum lycopersicum L.) is an economically important crop, but its yield and productivity have been severely impacted due to different abiotic and biotic stresses. The recently identified SlHyPRP1 and SlDEA1 are two potential negative regulatory genes in response to different abiotic (drought and salinity) and biotic stress (bacterial leaf spot and bacterial wilt) conditions in S. lycopersicum L. The present study aimed to evaluate the drought, salinity, bacterial leaf spot, and bacterial wilt tolerance response in S. lycopersicum L. crop through CRISPR/Cas9 genome editing of SlHyPRP1 and SlDEA1 and their functional analysis. The transient single- and dual-gene SlHyPRP1 and SlDEA1 CRISPR-edited plants were phenotypically better responsive to multiple stress factors taken under the study. The CRISPR-edited SlHyPRP1 and SlDEA1 plants showed a higher level of chlorophyll and proline content compared to wild-type (WT) plants under abiotic stress conditions. Reactive oxygen species accumulation and the cell death count per total area of leaves and roots under biotic stress were less in CRISPR-edited SlHyPRP1 and SlDEA1 plants compared to WT plants. The study reveals that the combined loss-of-function of SlHyPRP1 along with SlDEA1 is essential for imparting significant multi-stress tolerance (drought, salinity, bacterial leaf spot, and bacterial wilt) in S. lycopersicum L. The main feature of the study is the detailed genetic characterization of SlDEA1, a poorly studied 8CM family gene in multi-stress tolerance, through the CRISPR/Cas9 gene editing system. The study revealed the key negative regulatory role of SlDEA1 that function together as an anchor gene with SlHyPRP1 in imparting multi-stress tolerance in S. lycopersicum L. It was interesting that the present study also showed that transient CRISPR/Cas9 editing events of SlHyPRP1 and SlDEA1 genes were successfully replicated in stably generated parent-genome-edited line (GEd0) and genome-edited first-generation lines (GEd1) of S. lycopersicum L. With these upshots, the study's key findings demonstrate outstanding value in developing sustainable multi-stress tolerance in S. lycopersicum L. and other crops to cope with climate change.