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Article: Screening of caspase-3 inhibitors from natural molecule database using e-pharmacophore and docking studies.

Eda, Sasidhar Reddy / Veeramachaneni, Ganesh Kumar / Bondili, Jayakumar Singh / Jinka, Rajeswari

2019 Volume 15, Issue 4, Page(s) 240–245

Abstract: Caspase a protease family member, have a vital role in cell death and inflammation process. Caspase-3, an effector caspase controls the regulation of apoptosis and has an anti apoptotic function. The mechanical significance of restoring apoptosis ... ...

Abstract	Caspase a protease family member, have a vital role in cell death and inflammation process. Caspase-3, an effector caspase controls the regulation of apoptosis and has an anti apoptotic function. The mechanical significance of restoring apoptosis signaling to selectively target malignant cells is utilized to develop strong therapeutic strategies by the caspase family of mortality - induction molecules. Caspase-3 has currently no clear role in treatment for tumor progression and tumor sensitivity. The present study was aimed to screen caspase for potential inhibitors using computer aided docking methodologies. For this, zinc natural molecule database molecules were screened using e-pharmacophore and ADME protocols along with docking studies. Docking analysis selected two molecules, namely ZINC13341044 and ZINC13507846 with G-scores -5.27 and -6.19 respectively. These two potential hits are predicted as caspase inhibitors based on the results and can be further processed for in vitro validation.
Language	English
Publishing date	2019-03-31
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630015240
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Article ; Online: Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor.

Veeramachaneni, Ganesh Kumar / Thunuguntla, V B S C / Bobbillapati, Janakiram / Bondili, Jayakumar Singh

Journal of biomolecular structure & dynamics

2020 Volume 39, Issue 11, Page(s) 4015–4025

Abstract: The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE2) receptor initiates the entry of corona virus ... ...

Abstract	The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE2) receptor initiates the entry of corona virus into the host cells leading to the infection. However, considering the mutations reported in the SARS-CoV 2 (nCoV), the structural changes and the binding interactions of the S-protein RBD of nCoV were not clear. The present study was designed to elucidate the structural changes, hot spot binding residues and their interactions between the nCoV S-protein RBD and ACE2 receptor through computational approaches. Based on the sequence alignment, a total of 58 residues were found mutated in nCoV S-protein RBD. These mutations led to the structural changes in the nCoV S-protein RBD 3d structure with 4 helices, 10 sheets and intermittent loops. The nCoV RBD was found binding to ACE2 receptor with 11 hydrogen bonds and 1 salt bridge. The major hot spot amino acids involved in the binding identified by interaction analysis after simulations includes Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 34 amino acid residues of ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 417 residues in nCoV S-protein RBD. Based on the hydrogen bonding, RMSD and RMSF, total and potential energies, the nCoV was found binding to ACE2 receptor with higher stability and rigidity. Concluding, the hotspots information will be useful in designing blockers for the nCoV spike protein RBD. [Formula: see text]Communicated by Ramaswamy H. Sarma.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; COVID-19 ; Humans ; Protein Binding ; SARS-CoV-2 ; Severe Acute Respiratory Syndrome ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Keywords	covid19
Language	English
Publishing date	2020-06-04
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1773318
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Article ; Online: Specific panallergen peptide of Sorghum Polcalcin showing IgE response identified based on in silico and in vivo peptide mapping.

Bokka, Chandra Sekhar / Veeramachaneni, Ganesh Kumar / Thunuguntla, V B S C / Manda, Naresh Kumar / Bondili, Jayakumar Singh

Bioscience reports

2019 Volume 39, Issue 11

Abstract: In India, Sorghum plant allergenicity was reported to be approximately 54.9%. Sorghum bicolor Polcalcin (Sorb PC) was identified as the panallergen but the specificity of this allergen is yet to be characterized. The present study was aimed to ... ...

Abstract	In India, Sorghum plant allergenicity was reported to be approximately 54.9%. Sorghum bicolor Polcalcin (Sorb PC) was identified as the panallergen but the specificity of this allergen is yet to be characterized. The present study was aimed to characterize the antigenic determinants of Sorb PC that are responsible for eliciting the IgE response. In silico modeling, simulation studies and docking of Sorb PC peptides (PC1-11) against IgG and IgE followed by in vivo evaluation was adopted. Peptide docking studies revealed PC 6 with highest G-score -12.85 against IgE followed by PC-11, 5, 1 and 7 (-10.91) peptides. The mice sensitized with PC7 peptide showed interleukin (IL) 4 (IL-4), IL-5, IL-12, TNF-α and GMCSF levels increased when compared with other peptides and controls, signifying a strong T helper type 2 (Th2)-based response. In tandem, the T helper type 1 (Th1) pathway was inhibited by low levels of cytokine IL-2, interferon γ (IFN-γ) and increased IL-10 levels justifying the role of PC7 in allergic IgE response. Considering the above data of overlapping peptides of PC6 and PC7, N-terminal part of the PC7 peptide (DEVQRMM) is found to play a crucial role in Sorghum Polcalcin allergenic response.
MeSH term(s)	Allergens/immunology ; Animals ; Cytokines/immunology ; Epitopes/immunology ; Female ; Hypersensitivity/immunology ; Immunoglobulin E/immunology ; Immunoglobulin G/immunology ; India ; Interferon-gamma/immunology ; Interleukin-12/immunology ; Interleukin-4/immunology ; Mice ; Mice, Inbred BALB C ; Peptide Mapping/methods ; Peptides/immunology ; Sorghum/immunology ; Th1 Cells/immunology ; Th2 Cells/immunology
Chemical Substances	Allergens ; Cytokines ; Epitopes ; Immunoglobulin G ; Peptides ; Interleukin-12 (187348-17-0) ; Interleukin-4 (207137-56-2) ; Immunoglobulin E (37341-29-0) ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2019-11-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	764946-0
ISSN	1573-4935 ; 0144-8463
ISSN (online)	1573-4935
ISSN	0144-8463
DOI	10.1042/BSR20191835
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Article ; Online: Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT

Veeramachaneni, Ganesh Kumar / Thunuguntla, V B S C / Bhaswant, Maharshi / Mathai, Michael L / Bondili, Jayakumar Singh

Biomolecules

2019 Volume 9, Issue 10

Abstract: Obesity prevalence continues to be a foremost health concern across the globe leading to the development of major health risk conditions like type II diabetes, hyperlipidemia, hypertension and even cancers. Because of the deprived drug-based management ... ...

Abstract	Obesity prevalence continues to be a foremost health concern across the globe leading to the development of major health risk conditions like type II diabetes, hyperlipidemia, hypertension and even cancers. Because of the deprived drug-based management system, there is an urgent need for the development of new drugs aiming at satiety and appetite control targets. Among the reported satiety signaling targets, 5HT
MeSH term(s)	Asparagine/metabolism ; Binding Sites ; Biological Products/chemistry ; Biological Products/pharmacology ; Computer Simulation ; Drug Design ; Humans ; Models, Molecular ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Molecular Structure ; Receptor, Serotonin, 5-HT2C/chemistry ; Receptor, Serotonin, 5-HT2C/metabolism ; Serotonin 5-HT2 Receptor Agonists/chemistry ; Serotonin 5-HT2 Receptor Agonists/pharmacology ; Zinc/chemistry
Chemical Substances	Biological Products ; HTR2C protein, human ; Receptor, Serotonin, 5-HT2C ; Serotonin 5-HT2 Receptor Agonists ; Asparagine (7006-34-0) ; Zinc (J41CSQ7QDS)
Language	English
Publishing date	2019-10-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom9100556
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Article ; Online: Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor

Veeramachaneni, Ganesh Kumar / Thunuguntla, V. B. S. C. / Bobbillapati, Janakiram / Bondili, Jayakumar Singh

Journal of Biomolecular Structure and Dynamics

2020 , Page(s) 1–11

Keywords	Molecular Biology ; Structural Biology ; General Medicine ; covid19
Language	English
Publisher	Informa UK Limited
Publishing country	uk
Document type	Article ; Online
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2020.1773318
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Peptide Mapping, In Silico and In Vivo Analysis of Allergenic Sorghum Profilin Peptides.

Bokka, Chandra Sekhar / Veeramachaneni, Ganesh Kumar / Thunuguntla, V B S C / Bobbillapati, Janakiram / Bondili, Jayakumar Singh

Medicina (Kaunas, Lithuania)

2019 Volume 55, Issue 5

Abstract: Background and objectives: Nearly 20-30% of the world's population suffers from allergic rhinitis, among them 15% are progressing to asthma conditions. : Materials and methods: To map the antigenic determinants responsible for IgE binding, the ... ...

Abstract	Background and objectives: Nearly 20-30% of the world's population suffers from allergic rhinitis, among them 15% are progressing to asthma conditions. Materials and methods: To map the antigenic determinants responsible for IgE binding, the present study is focused on in silico modeling, simulation of Sorb PF and docking of the Sorb PF peptides (PF1-6) against IgG and IgE, followed by in vivo evaluation of the peptides for its allergenicity in mice. Results: Peptide PF3 and PF4 displayed high docking G-scores (-9.05) against IgE only. The mice sensitized with PF3 peptide showed increased levels of IL5, IL12, TNF-alpha, and GMCSF when compared to other peptides and controls, signifying a strong, Th2-based response. Concurrently, the Th1 pathway was inhibited by low levels of cytokine IL2, IFN-γ, and IL-10 justifying the role of PF3 in allergenic IgE response. Conclusions: Based on the results of overlapping peptides PF3 and PF4, the N-terminal part of the PF3 peptide (TGQALVI) plays a crucial role in allergenic response of Sorghum profilin.
MeSH term(s)	Animals ; Computer Simulation ; Disease Models, Animal ; Epitopes/analysis ; Mice ; Peptide Mapping/methods ; Profilins/analysis ; Profilins/blood ; Sorghum/adverse effects ; Sorghum/cytology
Chemical Substances	Epitopes ; Profilins
Language	English
Publishing date	2019-05-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2188113-3
ISSN	1648-9144 ; 1010-660X
ISSN (online)	1648-9144
ISSN	1010-660X
DOI	10.3390/medicina55050178
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Article: Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor

Veeramachaneni, Ganesh Kumar / Thunuguntla, V B S C / Bobbillapati, Janakiram / Bondili, Jayakumar Singh

J Biomol Struct Dyn

Abstract	The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE2) receptor initiates the entry of corona virus into the host cells leading to the infection. However, considering the mutations reported in the SARS-CoV 2 (nCoV), the structural changes and the binding interactions of the S-protein RBD of nCoV were not clear. The present study was designed to elucidate the structural changes, hot spot binding residues and their interactions between the nCoV S-protein RBD and ACE2 receptor through computational approaches. Based on the sequence alignment, a total of 58 residues were found mutated in nCoV S-protein RBD. These mutations led to the structural changes in the nCoV S-protein RBD 3d structure with 4 helices, 10 sheets and intermittent loops. The nCoV RBD was found binding to ACE2 receptor with 11 hydrogen bonds and 1 salt bridge. The major hot spot amino acids involved in the binding identified by interaction analysis after simulations includes Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 34 amino acid residues of ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 417 residues in nCoV S-protein RBD. Based on the hydrogen bonding, RMSD and RMSF, total and potential energies, the nCoV was found binding to ACE2 receptor with higher stability and rigidity. Concluding, the hotspots information will be useful in designing blockers for the nCoV spike protein RBD. [Formula: see text]Communicated by Ramaswamy H. Sarma.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #637972
Database	COVID19

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Article ; Online: Palmitoylethanolamide (PEA) Inhibits SARS-CoV-2 Entry by Interacting with S Protein and ACE-2 Receptor.

Fonnesu, Rossella / Thunuguntla, Venkata Bala Sai Chaitanya / Veeramachaneni, Ganesh Kumar / Bondili, Jayakumar Singh / La Rocca, Veronica / Filipponi, Carolina / Spezia, Pietro Giorgio / Sidoti, Maria / Plicanti, Erika / Quaranta, Paola / Freer, Giulia / Pistello, Mauro / Mathai, Michael Lee / Lai, Michele

Viruses

2022 Volume 14, Issue 5

Abstract: Lipids play a crucial role in the entry and egress of viruses, regardless of whether they are naked or enveloped. Recent evidence shows that lipid involvement in viral infection goes much further. During replication, many viruses rearrange internal lipid ...

Abstract	Lipids play a crucial role in the entry and egress of viruses, regardless of whether they are naked or enveloped. Recent evidence shows that lipid involvement in viral infection goes much further. During replication, many viruses rearrange internal lipid membranes to create niches where they replicate and assemble. Because of the close connection between lipids and inflammation, the derangement of lipid metabolism also results in the production of inflammatory stimuli. Due to its pivotal function in the viral life cycle, lipid metabolism has become an area of intense research to understand how viruses seize lipids and to design antiviral drugs targeting lipid pathways. Palmitoylethanolamide (PEA) is a lipid-derived peroxisome proliferator-activated receptor-α (PPAR-α) agonist that also counteracts SARS-CoV-2 entry and its replication. Our work highlights for the first time the antiviral potency of PEA against SARS-CoV-2, exerting its activity by two different mechanisms. First, its binding to the SARS-CoV-2 S protein causes a drop in viral infection of ~70%. We show that this activity is specific for SARS-CoV-2, as it does not prevent infection by VSV or HSV-2, other enveloped viruses that use different glycoproteins and entry receptors to mediate their entry. Second, we show that in infected Huh-7 cells, treatment with PEA dismantles lipid droplets, preventing the usage of these vesicular bodies by SARS-CoV-2 as a source of energy and protection against innate cellular defenses. This is not surprising since PEA activates PPAR-α, a transcription factor that, once activated, generates a cascade of events that leads to the disruption of fatty acid droplets, thereby bringing about lipid droplet degradation through β-oxidation. In conclusion, the present work demonstrates a novel mechanism of action for PEA as a direct and indirect antiviral agent against SARS-CoV-2. This evidence reinforces the notion that treatment with this compound might significantly impact the course of COVID-19. Indeed, considering that the protective effects of PEA in COVID-19 are the current objectives of two clinical trials (NCT04619706 and NCT04568876) and given the relative lack of toxicity of PEA in humans, further preclinical and clinical tests will be needed to fully consider PEA as a promising adjuvant therapy in the current COVID-19 pandemic or against emerging RNA viruses that share the same route of replication as coronaviruses.
MeSH term(s)	Amides ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Ethanolamines ; Humans ; Palmitic Acids/pharmacology ; Pandemics ; Pisum sativum ; Peroxisome Proliferator-Activated Receptors ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; COVID-19 Drug Treatment
Chemical Substances	Amides ; Antiviral Agents ; Ethanolamines ; Palmitic Acids ; Peroxisome Proliferator-Activated Receptors ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; palmidrol (6R8T1UDM3V)
Language	English
Publishing date	2022-05-17
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14051080
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Article ; Online: In vitro and in silico characterization of angiogenic inhibitors from Sophora interrupta.

Mathi, Pardhasaradhi / Veeramachaneni, Ganesh Kumar / Raj, K Kranthi / Talluri, Venkateswara Rao / Bokka, Venkata Raman / Botlagunta, Mahendran

Journal of molecular modeling

2016 Volume 22, Issue 10, Page(s) 247

Abstract: Sophora interrupta Bedd, (Fabaceae) is used in Indian folk medicine to treat cancer. Angiogenesis is one of the crucial characteristics of cancer metastasis and is regulated by vascular endothelial growth factor (VEGF). In this study, we examined the ... ...

Abstract	Sophora interrupta Bedd, (Fabaceae) is used in Indian folk medicine to treat cancer. Angiogenesis is one of the crucial characteristics of cancer metastasis and is regulated by vascular endothelial growth factor (VEGF). In this study, we examined the antiangiogenic properties of the root ethyl acetate extract of Sophora interrupta by various methods. In vitro antioxidant activity (100-600 μg/ml) of S. interrupta ethyl acetate (SEA) extract was evaluated by DPPH and ABTS, anti-inflammatory activity (50, 100 and 150 μg/ml) by estimating nitric oxide (NO) levels, anti-angiogenic activity (200 and 500 μg/ml) was validated by chorio allantoic membrane (CAM) assay and in silico molecular dynamic (MD) simulations analyses (25 ns) were performed to identify the anti-angiogenic compounds extracted from root extract. The antioxidative activity of SEA extract at IC
Language	English
Publishing date	2016-10
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1284729-x
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-016-3102-1
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Article ; Online: Peptide Mapping, In Silico and In Vivo Analysis of Allergenic Sorghum Profilin Peptides

Chandra Sekhar Bokka / Ganesh Kumar Veeramachaneni / V. B. S. C. Thunuguntla / Janakiram Bobbillapati / Jayakumar Singh Bondili

Medicina, Vol 55, Iss 5, p

2019 Volume 178

Abstract: Background and objectives : Nearly 20−30% of the world’s population suffers from allergic rhinitis, among them 15% are progressing to asthma conditions. Sorghum bicolor profilin (Sorb PF), one of the panallergens, was identified, but the allergen ... ...

Abstract	Background and objectives : Nearly 20−30% of the world’s population suffers from allergic rhinitis, among them 15% are progressing to asthma conditions. Sorghum bicolor profilin (Sorb PF), one of the panallergens, was identified, but the allergen specificity is not yet characterized. Materials and Methods : To map the antigenic determinants responsible for IgE binding, the present study is focused on in silico modeling, simulation of Sorb PF and docking of the Sorb PF peptides (PF1-6) against IgG and IgE, followed by in vivo evaluation of the peptides for its allergenicity in mice. Results : Peptide PF3 and PF4 displayed high docking G-scores (−9.05) against IgE only. The mice sensitized with PF3 peptide showed increased levels of IL5, IL12, TNF-alpha, and GMCSF when compared to other peptides and controls, signifying a strong, Th2-based response. Concurrently, the Th1 pathway was inhibited by low levels of cytokine IL2, IFN-γ, and IL-10 justifying the role of PF3 in allergenic IgE response. Conclusions : Based on the results of overlapping peptides PF3 and PF4, the N-terminal part of the PF3 peptide (TGQALVI) plays a crucial role in allergenic response of Sorghum profilin.
Keywords	Sorghum ; pollen allergen ; profilin ; peptide mapping ; modeling ; Th1 and Th2 cytokine ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2019-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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