Patents by Inventor Pranam Chatterjee

Pranam Chatterjee has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20230028069
    Abstract: A Streptococcus canis Cas9 (ScCas9) ortholog and its engineered variants, possessing novel PAM specificity, is an addition to the family of CRISPR-Cas9 systems. ScCas9 endonuclease is used in complex with guide RNA, consisting of identical non-target-specific sequence to that of the guide RNA SpCas9, for specific recognition and activity on a DNA target immediately upstream of either an “NNGT” or “NNNGT” PAM sequence. A novel DNA-interacting loop domain within ScCas9, and other Cas9 orthologs, such as those from Streptococcus gordonii and Streptococcus angionosis facilitates a divergent PAM sequence from the “NGG” PAM of SpCas9.
    Type: Application
    Filed: February 28, 2022
    Publication date: January 26, 2023
    Applicant: Massachusetts Institute of Technology
    Inventors: Joseph M. Jacobson, Noah Michael Jakimo, Pranam Chatterjee
  • Publication number: 20220392566
    Abstract: An attention-based graph architecture that exploits MSA Transformer embeddings to directly produce models of three-dimensional folded structures from protein sequences includes a method and system for augmenting the protein sequence to obtain multiple sequence alignments, producing enriched individual and pairwise embeddings from the multiple sequence alignments using an MSA-Transformer, extracting relevant features and structure latent states from the enriched individual and pairwise embeddings for use by a downstream graph transformer, assigning individual and pairwise embeddings to nodes and edges, respectively, using the downstream graph transformer to operate on node representations through an attention-based mechanism that considers pairwise edge attributes to obtain final node encodings, and projecting the final node encodings to form the computer-modeled folded protein structure. An induced distogram of the computer-modeled folded protein structure may be computed.
    Type: Application
    Filed: June 2, 2022
    Publication date: December 8, 2022
    Applicant: Massachusetts Institute of Technology
    Inventors: Pranam Chatterjee, Allan S Costa, Joseph M. Jacobson, Raghava Manvith Ponnapati
  • Patent number: 11453865
    Abstract: Engineered Streptococcus canis Cas9 (ScCas9) variants include an ScCas9 protein with its PID being the PID amino acid composition of Streptococcus pyogenes Cas9 (SpCas9)-NG, an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 in its amino acid sequence (Sc+), and an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 and a substitution of residues ADKKLRKRSGKLATE [SEQ ID No. 4] in position 365-379 in the ScCas9 open reading frame (Sc++). Also included are CRISPR-associated DNA endonucleases with a PAM specificity of 5?-NG-3? or 5?-NNG-3? and a method of altering expression of a gene product by utilizing the engineered ScCas9 variants.
    Type: Grant
    Filed: November 19, 2019
    Date of Patent: September 27, 2022
    Assignee: Massachusetts Institute of Technology
    Inventors: Pranam Chatterjee, Noah Michael Jakimo, Joseph M. Jacobson
  • Publication number: 20220162620
    Abstract: Applications of a Streptococcus Cas9 ortholog from Streptococcus macacae (Smac Cas9), possessing minimal adenine-rich PAM specificity, include an isolated Streptococcus macacae Cas9 protein or transgene expression thereof, a CRISPR-associated DNA endonuclease with PAM interacting domain amino acid sequences that are at least 80% identical to that of the isolated Streptococcus macacae Cas9 protein, and an isolated, engineered Streptococcus pyogenes Cas9 (Spy Cas9) protein with a PID as either the PID amino acid composition of the isolated Streptococcus macacae Cas9 (Smac Cas9) protein or of a CRISPR-associated DNA endonuclease with PID amino acid sequences that are at least 80% identical to that of the isolated Streptococcus macacae Cas9 protein. A method for altering expression of at least one gene product employs Streptococcus macacae Cas9 endonucleases in complex with guide RNA, for specific recognition and activity on a DNA target immediately upstream of either an “NAA” or “NA” or “NAAN” PAM sequence.
    Type: Application
    Filed: May 6, 2019
    Publication date: May 26, 2022
    Applicant: Massachusetts Institute of Technology
    Inventors: Pranam Chatterjee, Noah Michael Jakimo, Joseph M Jacobson
  • Publication number: 20220025341
    Abstract: Methods and compositions relating to an engineered peptide capable of binding to an infectious biological molecule for inhibition by mediated degradation using the ubiquitin proteasome pathway. The engineered peptide includes a targeting domain and an ubiquitin ligase recruiting domain. The engineered peptide includes a targeting domain and an ubiquitin ligase. The targeting domain is computationally-derived from a known receptor for the infectious biological molecule. The engineered peptide is optimized for minimal size and minimum off-target effects.
    Type: Application
    Filed: May 28, 2021
    Publication date: January 27, 2022
    Inventors: Pranam CHATTERJEE, Joseph M. JACOBSON
  • Publication number: 20220002700
    Abstract: Methods and compositions relating to an engineered peptide capable of binding to a biological molecule for viral inhibition. The engineered peptide is computationally-derived from soluble angiotensin-converting enzyme 2 (sACE2), a known receptor for viral spike proteins. The engineered peptide is optimized for minimal size and off-target effects. The engineered sACE2 peptide variants are a suitable targeting domain for fusion proteins of various effects.
    Type: Application
    Filed: April 5, 2021
    Publication date: January 6, 2022
    Inventors: Pranam CHATTERJEE, Raghava Manvitha PONNAPATI, Eyal PERRY, Joseph M. JACOBSON
  • Publication number: 20210324382
    Abstract: A chimeric DNA:RNA guide for very high accuracy Cas9 genome editing employs nucleotide-type substitutions in nucleic acid-guided endonucleases for enhanced specificity. The CRISPR-Cas9 gene editing system is manipulated to generate chimeric DNA:RNA guide strands to minimize the off-target cleavage events of the S. pyogenes Cas9 endonuclease. A DNA:RNA chimeric guide strand is sufficient to guide Cas9 to a specified target sequence for indel formation and minimize off-target cleavage events due to the specificity conferred by DNA-DNA interactions. Use of chimeric mismatch-evading lowered-thermostability guides (“melt-guides”) demonstrate that nucleotide-type substitutions in the spacer can reduce cleavage of sequences mismatched by as few as a single base pair. The chimeric mismatch-evading lowered-thermostability guides replace most gRNA spacer positions with DNA bases to suppress mismatched targets under Cas9's catalytic threshold.
    Type: Application
    Filed: January 22, 2021
    Publication date: October 21, 2021
    Applicant: Massachusetts Institute of Technology
    Inventors: Noah Jakimo, Pranam Chatterjee, Joseph M. Jacobson
  • Publication number: 20200332271
    Abstract: Engineered Streptococcus canis Cas9 (ScCas9) variants include an ScCas9 protein with its PID being the PID amino acid composition of Streptococcus pyogenes Cas9 (SpCas9)-NG, an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 in its amino acid sequence (Sc+), and an ScCas9 protein having a threonine-to-lysine substitution mutation at position 1227 and a substitution of residues ADKKLRKRSGKLATE in position 365-379 in the ScCas9 open reading frame (Sc++). Also included are CRISPR-associated DNA endonucleases with a PAM specificity of 5?-NG-3? or 5?-NNG-3? and a method of altering expression of a gene product by utilizing the engineered ScCas9 variants.
    Type: Application
    Filed: November 19, 2019
    Publication date: October 22, 2020
    Applicant: Massachusetts Institute of Technology
    Inventors: Pranam Chatterjee, Noah Michael Jakimo, Joseph M. Jacobson
  • Publication number: 20190218532
    Abstract: A Streptococcus canis Cas9 (ScCas9) ortholog and its engineered variants, possessing novel PAM specificity, is an addition to the family of CRISPR-Cas9 systems. ScCas9 endonuclease is used in complex with guide RNA, consisting of identical non-target-specific sequence to that of the guide RNA SpCas9, for specific recognition and activity on a DNA target immediately upstream of either an “NNGT” or “NNNGT” PAM sequence. A novel DNA-interacting loop domain within ScCas9, and other Cas9 orthologs, such as those from Streptococcus gordonii and Streptococcus angionosis facilitates a divergent PAM sequence from the “NGG” PAM of SpCas9.
    Type: Application
    Filed: September 19, 2018
    Publication date: July 18, 2019
    Applicant: Massachusetts Institute of Technology
    Inventors: Joseph M. Jacobson, Noah Michael Jakimo, Pranam Chatterjee
  • Publication number: 20180282722
    Abstract: A chimeric DNA:RNA guide for very high accuracy Cas9 genome editing employs nucleotide-type substitutions in nucleic acid-guided endonucleases for enhanced specificity. The CRISPR-Cas9 gene editing system is manipulated to generate chimeric DNA:RNA guide strands to minimize the off-target cleavage events of the S. pyogenes Cas9 endonuclease. A DNA:RNA chimeric guide strand is sufficient to guide Cas9 to a specified target sequence for indel formation and minimize off-target cleavage events due to the specificity conferred by DNA-DNA interactions. Use of chimeric mismatch-evading lowered-thermostability guides (“melt-guides”) demonstrate that nucleotide-type substitutions in the spacer can reduce cleavage of sequences mismatched by as few as a single base pair. The chimeric mismatch-evading lowered-thermostability guides replace most gRNA spacer positions with DNA bases to suppress mismatched targets under Cas9's catalytic threshold.
    Type: Application
    Filed: November 21, 2017
    Publication date: October 4, 2018
    Applicant: Massachusetts Institute of Technology
    Inventors: Noah Jakimo, Pranam Chatterjee, Joseph M. Jacobson